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Ghahremani S, Kanwal A, Pettinato A, Ladha F, Legere N, Thakar K, Zhu Y, Tjong H, Wilderman A, Stump WT, Greenberg L, Greenberg MJ, Cotney J, Wei CL, Hinson JT. CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants. Circulation 2024; 149:1285-1297. [PMID: 38235591 PMCID: PMC11031707 DOI: 10.1161/circulationaha.123.063972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND TTN truncation variants (TTNtvs) are the most common genetic lesion identified in individuals with dilated cardiomyopathy, a disease with high morbidity and mortality rates. TTNtvs reduce normal TTN (titin) protein levels, produce truncated proteins, and impair sarcomere content and function. Therapeutics targeting TTNtvs have been elusive because of the immense size of TTN, the rarity of specific TTNtvs, and incomplete knowledge of TTNtv pathogenicity. METHODS We adapted CRISPR activation using dCas9-VPR to functionally interrogate TTNtv pathogenicity and develop a therapeutic in human cardiomyocytes and 3-dimensional cardiac microtissues engineered from induced pluripotent stem cell models harboring a dilated cardiomyopathy-associated TTNtv. We performed guide RNA screening with custom TTN reporter assays, agarose gel electrophoresis to quantify TTN protein levels and isoforms, and RNA sequencing to identify molecular consequences of TTN activation. Cardiomyocyte epigenetic assays were also used to nominate DNA regulatory elements to enable cardiomyocyte-specific TTN activation. RESULTS CRISPR activation of TTN using single guide RNAs targeting either the TTN promoter or regulatory elements in spatial proximity to the TTN promoter through 3-dimensional chromatin interactions rescued TTN protein deficits disturbed by TTNtvs. Increasing TTN protein levels normalized sarcomere content and contractile function despite increasing truncated TTN protein. In addition to TTN transcripts, CRISPR activation also increased levels of myofibril assembly-related and sarcomere-related transcripts. CONCLUSIONS TTN CRISPR activation rescued TTNtv-related functional deficits despite increasing truncated TTN levels, which provides evidence to support haploinsufficiency as a relevant genetic mechanism underlying heterozygous TTNtvs. CRISPR activation could be developed as a therapeutic to treat a large proportion of TTNtvs.
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Affiliation(s)
| | - Aditya Kanwal
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Anthony Pettinato
- Cardiology Center, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Feria Ladha
- Cardiology Center, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Nicholas Legere
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ketan Thakar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Andrea Wilderman
- Cardiology Center, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - W. Tom Stump
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lina Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Justin Cotney
- Cardiology Center, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - J. Travis Hinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Cardiology Center, University of Connecticut Health Center, Farmington, CT 06030, USA
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2
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Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. bioRxiv 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Present address: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Equal contributions
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Equal contributions
| | - Patricia A. Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Equal contributions
| | - I (Eli) Chien
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai, China
| | - Jianhao Peng
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, P.R. China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Rafael Casellas
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Albert W. Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
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3
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Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y. ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. Nat Commun 2023; 14:213. [PMID: 36639381 PMCID: PMC9839710 DOI: 10.1038/s41467-023-35879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Connecting genes to their cis-regulatory elements has been enabled by genome-wide mapping of chromatin interactions using proximity ligation in ChIA-PET, Hi-C, and their derivatives. However, these methods require millions of input cells for high-quality data and thus are unsuitable for many studies when only limited cells are available. Conversely, epigenomic profiling via transposase digestion in ATAC-seq requires only hundreds to thousands of cells to robustly map open chromatin associated with transcription activity, but it cannot directly connect active genes to their distal enhancers. Here, we combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq into ChIATAC to efficiently map interactions between open chromatin loci in low numbers of input cells. We validate ChIATAC in Drosophila cells and optimize it for mapping 3D epigenomes in human cells robustly. Applying ChIATAC to primary human T cells, we reveal mechanisms that topologically regulate transcriptional programs during T cell activation.
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Affiliation(s)
- Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Liao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chee Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, P. R. China.
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4
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Zhao X, Wang P, Diedrich JD, Smart B, Reyes N, Yoshimura S, Zhang J, Yang W, Barnett K, Xu B, Li Z, Huang X, Yu J, Crews K, Yeoh AEJ, Konopleva M, Wei CL, Pui CH, Savic D, Yang JJ. Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia. Nat Commun 2022; 13:5401. [PMID: 36104354 PMCID: PMC9474531 DOI: 10.1038/s41467-022-33143-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
FLT3 is an attractive therapeutic target in acute lymphoblastic leukemia (ALL) but the mechanism for its activation in this cancer is incompletely understood. Profiling global gene expression in large ALL cohorts, we identify over-expression of FLT3 in ZNF384-rearranged ALL, consistently across cases harboring different fusion partners with ZNF384. Mechanistically, we discover an intergenic enhancer element at the FLT3 locus that is exclusively activated in ZNF384-rearranged ALL, with the enhancer-promoter looping directly mediated by the fusion protein. There is also a global enrichment of active enhancers within ZNF384 binding sites across the genome in ZNF384-rearranged ALL cells. Downregulation of ZNF384 blunts FLT3 activation and decreases ALL cell sensitivity to FLT3 inhibitor gilteritinib in vitro. In patient-derived xenograft models of ZNF384-rearranged ALL, gilteritinib exhibits significant anti-leukemia efficacy as a monotherapy in vivo. Collectively, our results provide insights into FLT3 regulation in ALL and point to potential genomics-guided targeted therapy for this patient population.
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Affiliation(s)
- Xujie Zhao
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan D Diedrich
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon Smart
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Noemi Reyes
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingliao Zhang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kelly Barnett
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Allen Eng Juh Yeoh
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Marina Konopleva
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel Savic
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Zhu Y, Gong L, Wei CL. Guilt by association: EcDNA as a mobile transactivator in cancer. Trends Cancer 2022; 8:747-758. [PMID: 35753910 PMCID: PMC9388558 DOI: 10.1016/j.trecan.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/10/2022] [Accepted: 04/28/2022] [Indexed: 10/17/2022]
Abstract
Extrachromosomal DNA (ecDNA), first described in the 1960s, is emerging as a prevalent but poorly characterized oncogenic alteration in cancer. ecDNA is a reservoir for oncogene amplification and is associated with an aggressive tumor phenotype and poor patient outcome. Despite the long-held knowledge of its existence, little is known about how ecDNA affects tumor cell behavior. Recent data reveal that ecDNA hubs are mobile transcriptional enhancers which can transactivate gene expression through chromatin interactions. Given its prevalence, structural complexity, and unequal segregation into daughter cells, ecDNA can offer selective growth advantages, contribute to intratumor heterogeneity (ITH), and accelerate tumor evolution. Future technology development is expected to transform the current paradigm for studying ecDNA and lead to therapeutic strategies targeting ecDNA vulnerabilities.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang 311121, China
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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6
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Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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7
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Pagin M, Pernebrink M, Giubbolini S, Barone C, Sambruni G, Zhu Y, Chiara M, Ottolenghi S, Pavesi G, Wei CL, Cantù C, Nicolis SK. Sox2 controls neural stem cell self-renewal through a Fos-centered gene regulatory network. Stem Cells 2021; 39:1107-1119. [PMID: 33739574 DOI: 10.1002/stem.3373] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
The Sox2 transcription factor is necessary for the long-term self-renewal of neural stem cells (NSCs). Its mechanism of action is still poorly defined. To identify molecules regulated by Sox2, and acting in mouse NSC maintenance, we transduced, into Sox2-deleted NSC, genes whose expression is strongly downregulated following Sox2 loss (Fos, Jun, Egr2), individually or in combination. Fos alone rescued long-term proliferation, as shown by in vitro cell growth and clonal analysis. Furthermore, pharmacological inhibition by T-5224 of FOS/JUN AP1 complex binding to its targets decreased cell proliferation and expression of the putative target Suppressor of cytokine signaling 3 (Socs3). Additionally, Fos requirement for efficient long-term proliferation was demonstrated by the reduction of NSC clones capable of long-term expansion following CRISPR/Cas9-mediated Fos inactivation. Previous work showed that the Socs3 gene is strongly downregulated following Sox2 deletion, and its re-expression by lentiviral transduction rescues long-term NSC proliferation. Fos appears to be an upstream regulator of Socs3, possibly together with Jun and Egr2; indeed, Sox2 re-expression in Sox2-deleted NSC progressively activates both Fos and Socs3 expression; in turn, Fos transduction activates Socs3 expression. Based on available SOX2 ChIPseq and ChIA-PET data, we propose a model whereby Sox2 is a direct activator of both Socs3 and Fos, as well as possibly Jun and Egr2; furthermore, we provide direct evidence for FOS and JUN binding on Socs3 promoter, suggesting direct transcriptional regulation. These results provide the basis for developing a model of a network of interactions, regulating critical effectors of NSC proliferation and long-term maintenance.
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Affiliation(s)
- Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Mattias Pernebrink
- Wallenberg Centre for Molecular Medicine (WCMM) and Department of Biomedical and Clinical Sciences, Faculty of Health Science, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science, Linköping University, Linköping, Sweden
| | - Simone Giubbolini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Cristiana Barone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Gaia Sambruni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Matteo Chiara
- Department of Biosciences, University of Milano, Milan, Italy
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, Milan, Italy
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine (WCMM) and Department of Biomedical and Clinical Sciences, Faculty of Health Science, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science, Linköping University, Linköping, Sweden
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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8
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Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021; 39:694-707.e7. [PMID: 33836152 PMCID: PMC8119378 DOI: 10.1016/j.ccell.2021.03.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chee-Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Yi-An Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Meihong Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam Mil-Homens
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chris Kuhlberg
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Fanyue Sun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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9
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Wei CL, Shi SF, Zhou WS, Wu XC, Jiang J. [Evaluation of intervention effect in the occupational protection of glass fiber workers by occupational health education]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2021; 39:270-273. [PMID: 33910286 DOI: 10.3760/cma.j.cn121094-20191203-00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To understand the mastery of occupational hygienic knowledge and the implementing of occupational health protection measures in the group which were exposed to the procedure of manufacture and use in glass fiber company, and to explore the feasibility of the prevention of the skin injury by occupational health education in glass fiber workers. Methods: We selected 257 on-the-job employees as the research object in a ceramic enterprise in Nanjing from June 2018 to August 2019, with the method of cluster random sampling. According to Solomon's design, the intervention group in which we took measures with health education was divided into RG(1) (O(1)XO(2)) and RG(3) (XO(5)) group, and the control group where we didn't take any intervention was divided into RG(2) (O(3)-O(4)) and RG(4) (-O(6)) group. The intervention effect of health education on the occupational protection of glass fiber workers was evaluated by the results of questionnaire. Results: After training, the average score of occupational health knowledge in the intervention group was 27.34 points higher than that before training, the intervention index was 1.42, 23.62-27.73 points higher than the control glass fiber workers and 33.62-35.52 points higher than the control glass non-glass fiber workers; Compared with the control group, the positive attitude rate of fiber glass workers in the intervention group increased by 13.28%, 13.51%, 11.68% and 11.48%, and the intervention indexes were 1.18, 1.17, 1.14 and 1.15, which was corresponding to using protective cream, wearing gloves, wearing working clothes, washing hands and bathing after work, respectively; Compared with the control group, the implementation rate of occupational protection measures which were represented by wearing gloves、washing hands and bathing for glass fiber workers in the intervention group increased by 29.25% and 7.27% respectively, and the intervention indexes were 1.43 and 1.08 respectively; The skin injury rate of fiberglass workers in the intervention group was reduced by 11.43% comparing to the control group, the intervention index was 1.67. Conclusion: According to the occupational health education of fiberglass workers, it improves the mastery of occupational health knowledge, positive atti-tude rate and the implementation rate of occupational protection measures, meanwhile, it reduces the skin injury rate of the intervention objects to a certain extent.
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Affiliation(s)
- C L Wei
- Nanjing Prevention and Treatment for Occupational Disease, Nanjing 210042, China
| | - S F Shi
- Nanjing Prevention and Treatment for Occupational Disease, Nanjing 210042, China
| | - W S Zhou
- Nanjing Prevention and Treatment for Occupational Disease, Nanjing 210042, China
| | - X C Wu
- Nanjing Prevention and Treatment for Occupational Disease, Nanjing 210042, China
| | - J Jiang
- Nanjing Prevention and Treatment for Occupational Disease, Nanjing 210042, China
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10
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Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei CL, Ruan Y, Li S. ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Sci Adv 2020; 6:eaay2078. [PMID: 32832596 PMCID: PMC7439456 DOI: 10.1126/sciadv.aay2078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. To enable structural interpretation, ChIA-PIPE calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops. ChIA-PIPE also supports the analysis of other related chromatin-mapping data types.
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Affiliation(s)
- Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jiahui Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yuliang Feng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ahmed Abbas
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
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11
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Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. Genome Biol 2020; 21:110. [PMID: 32393309 PMCID: PMC7212609 DOI: 10.1186/s13059-020-02030-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/27/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis remain largely unknown. RESULTS Using an inducible system, we comprehensively analyze the 3D genome organization in myeloid cells and its reorganization after PML-RARα induction and perform additional analyses in patient-derived APL cells with native PML-RARα. We discover that PML-RARα mediates extensive chromatin interactions genome-wide. Globally, it redefines the chromatin topology of the myeloid genome toward a more condensed configuration in APL cells; locally, it intrudes RNAPII-associated interaction domains, interrupts myeloid-specific transcription factors binding at enhancers and super-enhancers, and leads to transcriptional repression of genes critical for myeloid differentiation and maturation. CONCLUSIONS Our results not only provide novel topological insights for the roles of PML-RARα in transforming myeloid cells into leukemia cells, but further uncover a topological framework of a molecular mechanism for oncogenic fusion proteins in cancers.
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Affiliation(s)
- Ping Wang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Present Address: Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Jacqueline Jufen Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030, USA
| | - Liuyang Cai
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Przemyslaw Szalaj
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Simon Zhongyuan Tian
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06030, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT, 06030, USA.
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12
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Bertolini JA, Favaro R, Zhu Y, Pagin M, Ngan CY, Wong CH, Tjong H, Vermunt MW, Martynoga B, Barone C, Mariani J, Cardozo MJ, Tabanera N, Zambelli F, Mercurio S, Ottolenghi S, Robson P, Creyghton MP, Bovolenta P, Pavesi G, Guillemot F, Nicolis SK, Wei CL. Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance. Cell Stem Cell 2020; 24:462-476.e6. [PMID: 30849367 PMCID: PMC6506828 DOI: 10.1016/j.stem.2019.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/16/2018] [Accepted: 02/06/2019] [Indexed: 11/29/2022]
Abstract
The SOX2 transcription factor is critical for neural stem cell (NSC) maintenance and brain development. Through chromatin immunoprecipitation (ChIP) and chromatin interaction analysis (ChIA-PET), we determined genome-wide SOX2-bound regions and Pol II-mediated long-range chromatin interactions in brain-derived NSCs. SOX2-bound DNA was highly enriched in distal chromatin regions interacting with promoters and carrying epigenetic enhancer marks. Sox2 deletion caused widespread reduction of Pol II-mediated long-range interactions and decreased gene expression. Genes showing reduced expression in Sox2-deleted cells were significantly enriched in interactions between promoters and SOX2-bound distal enhancers. Expression of one such gene, Suppressor of Cytokine Signaling 3 (Socs3), rescued the self-renewal defect of Sox2-ablated NSCs. Our work identifies SOX2 as a major regulator of gene expression through connections to the enhancer network in NSCs. Through the definition of such a connectivity network, our study shows the way to the identification of genes and enhancers involved in NSC maintenance and neurodevelopmental disorders. Sox2-bound enhancers are enriched within long-range interactions in neural stem cells SOX2 loss decreases chromatin interactivity genome-wide Sox2-bound enhancers from interactions activate reporter genes in zebrafish forebrain Socs3, a gene downregulated in Sox2 mutant NSCs, rescues their self-renewal
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Affiliation(s)
- Jessica A Bertolini
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Rebecca Favaro
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chee Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht 3584CT, Utrecht, the Netherlands
| | - Ben Martynoga
- The Francis Crick Institute, Midland Road, London NW 1AT, UK
| | - Cristiana Barone
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Jessica Mariani
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Marcos Julián Cardozo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid and Ciber de Enfermedades Raras (CIBERER), ISCIII Madrid, Spain
| | - Noemi Tabanera
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid and Ciber de Enfermedades Raras (CIBERER), ISCIII Madrid, Spain
| | - Federico Zambelli
- Department of Biosciences, University of Milano, 20133 Milano, Italy
| | - Sara Mercurio
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Stem Cell and Regenerative Biology, Genome Institute of Singapore, Singapore
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht 3584CT, Utrecht, the Netherlands
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid and Ciber de Enfermedades Raras (CIBERER), ISCIII Madrid, Spain
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, 20133 Milano, Italy
| | | | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University Milano-Bicocca, 20126 Milano, Italy.
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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13
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Wei CL, Nicolis SK, Zhu Y, Pagin M. Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. J Exp Neurosci 2019; 13:1179069519868224. [PMID: 31431802 PMCID: PMC6686325 DOI: 10.1177/1179069519868224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 11/16/2022] Open
Abstract
In our article, we asked whether Sox2, a transcription factor important in brain
development and disease, is involved in gene regulation through its action on
long-range interactions between promoters and distant enhancers. Our findings
highlight that Sox2 shapes a genome-wide network of promoter-enhancer
interactions, acting by direct binding to these elements. Sox2 loss affects the
three-dimensional (3D) genome and decreases the activity of a subset of genes
involved in Sox2-bound interactions. At least one of such downregulated genes,
Socs3, is critical for long-term neural stem cell
maintenance. These results point to the possibility of identifying a
transcriptional network downstream to Sox2, and involved in neural stem cell
maintenance. In addition, interacting Sox2-bound enhancers are often connected
to genes which are relevant, in man, to neurodevelopmental disease; this may
facilitate the detection of functionally relevant mutations in regulatory
elements in man, contributing to neural disease.
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Affiliation(s)
- Chia-Lin Wei
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Yanfen Zhu
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
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14
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Abstract
Third generation single-molecule DNA sequencing technologies offer significantly longer read length that can facilitate the assembly of complex genomes and analysis of complex structural variants. Nanopore platforms perform single-molecule sequencing by directly measuring the current changes mediated by DNA passage through the pores and can generate hundreds of kilobase (kb) reads with minimal capital cost. This platform has been adopted by many researchers for a variety of applications. Achieving longer sequencing read lengths is the most critical factor to leverage the value of nanopore sequencing platforms. To generate ultra-long reads, special consideration is required to avoid DNA breakages and gain efficiency to generate productive sequencing templates. Here, we provide the detailed protocol of ultra-long DNA sequencing including high molecular weight (HMW) DNA extraction from fresh or frozen cells, library construction by mechanical shearing or transposase fragmentation, and sequencing on a nanopore device. From 20-25 µg of HMW DNA, the method can achieve N50 read length of 50-70 kb with mechanical shearing and N50 of 90-100 kb read length with transposase mediated fragmentation. The protocol can be applied to DNA extracted from mammalian cells to perform whole genome sequencing for the detection of structural variants and genome assembly. Additional improvements on the DNA extraction and enzymatic reactions will further increase the read length and expand its utility.
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Affiliation(s)
- Liang Gong
- Genome Technologies, Jackson Laboratory for Genomic Medicine
| | - Chee-Hong Wong
- Genome Technologies, Jackson Laboratory for Genomic Medicine
| | - Jennifer Idol
- Genome Technologies, Jackson Laboratory for Genomic Medicine
| | - Chew Yee Ngan
- Genome Technologies, Jackson Laboratory for Genomic Medicine
| | - Chia-Lin Wei
- Genome Technologies, Jackson Laboratory for Genomic Medicine;
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15
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Lin JH, Wu ZY, Gong L, Wong CH, Chao WC, Yen CM, Wang CP, Wei CL, Huang YT, Liu PY. Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing. J Clin Med 2019; 8:jcm8030351. [PMID: 30871085 PMCID: PMC6462986 DOI: 10.3390/jcm8030351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 02/07/2023] Open
Abstract
Brain abscess is a severe infectious disease with high mortality and mobility. Although culture-based techniques have been widely used for the investigation of microbial composition of brain abscess, these approaches are inherent biased. Recent studies using 16S ribosomal sequencing approaches revealed high complexity of the bacterial community involved in brain abscess but fail to detect fungal and viral composition. In the study, both culture-independent nanopore metagenomic sequencing and culture-based whole-genome sequencing using both the Illumina and the Nanopore platforms were conducted to investigate the microbial composition and genomic characterization in brain abscess. Culture-independent metagenomic sequencing revealed not only a larger taxonomic diversity of bacteria but also the presence of fungi and virus communities. The culture-based whole-genome sequencing identified a novel species in Prevotella and reconstructs a Streptococcus constellatus with a high GC-skew genome. Antibiotic-resistance genes CfxA and ErmF associated with resistance to penicillin and clindamycin were also identified in culture-based and culture-free sequencing. This study implies current understanding of brain abscess need to consider the broader diversity of microorganisms.
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Affiliation(s)
- Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Zong-Yen Wu
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Liang Gong
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chee-Hong Wong
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Wen-Cheng Chao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Chun-Ming Yen
- Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
- Department of Neurosurgery, Neurological Institute, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Ching-Ping Wang
- Department of Otolaryngology-Head and Neck Surgery, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
| | - Chia-Lin Wei
- Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan.
| | - Po-Yu Liu
- Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan.
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16
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Zheng M, Tian SZ, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu JJ, Li Z, Wong CH, Ngan CY, Wang P, Ruan X, Wei CL, Ruan Y. Multiplex chromatin interactions with single-molecule precision. Nature 2019; 566:558-562. [PMID: 30778195 DOI: 10.1038/s41586-019-0949-1] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 01/16/2019] [Indexed: 12/25/2022]
Abstract
The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus1. Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C)2, and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)3, have revealed topologically associating domains4 with frequent chromatin contacts, and have identified chromatin loops mediated by specific protein factors for insulation and regulation of transcription5-7. However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C8 potentially overcomes this issue, this method may be limited by the sparsity of data that is inherent to current single-cell assays. Recent advances in microfluidics have opened opportunities for droplet-based genomic analysis9 but this approach has not yet been adapted for chromatin interaction analysis. Here we describe a strategy for multiplex chromatin-interaction analysis via droplet-based and barcode-linked sequencing, which we name ChIA-Drop. We demonstrate the robustness of ChIA-Drop in capturing complex chromatin interactions with single-molecule precision, which has not been possible using methods based on population-level pairwise contacts. By applying ChIA-Drop to Drosophila cells, we show that chromatin topological structures predominantly consist of multiplex chromatin interactions with high heterogeneity; ChIA-Drop also reveals promoter-centred multivalent interactions, which provide topological insights into transcription.
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Affiliation(s)
- Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Daniel Capurso
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Emaly Piecuch
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jacqueline Jufen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Zhihui Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.,School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Chee Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. .,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA. .,Huazhong Agricultural University, Wuhan, China.
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17
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Bachy C, Charlesworth CJ, Chan AM, Finke JF, Wong CH, Wei CL, Sudek S, Coleman ML, Suttle CA, Worden AZ. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 2018; 20:2898-2912. [PMID: 29749714 DOI: 10.1111/1462-2920.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.
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Affiliation(s)
- Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Christina J Charlesworth
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jan F Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chee-Hong Wong
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.,Departments of Botany, and Microbiology & Immunology, and Institute of Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
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18
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Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ, Worden AZ. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nat Microbiol 2018; 3:781-790. [PMID: 29946165 DOI: 10.1038/s41564-018-0178-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/16/2018] [Indexed: 01/05/2023]
Abstract
Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients1,2. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification3,4. Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical5,6. We used advanced photo-bioreactors to investigate how the widespread marine green alga Micromonas commoda grows under transitions from replete nutrients to chronic phosphate limitation and subsequent relief, analysing photosystem changes and broad cellular responses using proteomics, transcriptomics and biophysical measurements. We find that physiological and protein expression responses previously attributed to stress are critical to supporting stable exponential growth when phosphate is limiting. Unexpectedly, the abundance of most proteins involved in light harvesting does not change, but an ancient light-harvesting-related protein, LHCSR, is induced and dissipates damaging excess absorbed light as heat throughout phosphate limitation. Concurrently, a suite of uncharacterized proteins with narrow phylogenetic distributions increase multifold. Notably, of the proteins that exhibit significant changes, 70% are not differentially expressed at the mRNA transcript level, highlighting the importance of post-transcriptional processes in microbial eukaryotes. Nevertheless, transcript-protein pairs with concordant changes were identified that will enable more robust interpretation of eukaryotic phytoplankton responses in the field from metatranscriptomic studies. Our results show that P-limited Micromonas responds quickly to a fresh pulse of phosphate by rapidly increasing replication, and that the protein network associated with this ability is composed of both conserved and phylogenetically recent proteome systems that promote dynamic phosphate homeostasis. That an ancient mechanism for mitigating light stress is central to sustaining growth during extended phosphate limitation highlights the possibility of interactive effects arising from combined stressors under ocean change, which could reduce the efficacy of algal strategies for optimizing marine photosynthesis.
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Affiliation(s)
- Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Susanne Wilken
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, the Netherlands
| | - Valeria Jimenez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Chang Jae Choi
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Charles Ansong
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard Dannebaum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | | | - Denis Klimov
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Chia-Lin Wei
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.,The Jackson Laboratory, Farmington, CT, USA
| | - Govindarajan Kunde-Ramamoorthy
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.,The Jackson Laboratory, Farmington, CT, USA
| | | | | | | | | | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.
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19
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Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL. Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods 2018; 15:455-460. [PMID: 29713081 PMCID: PMC5990454 DOI: 10.1038/s41592-018-0002-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/14/2018] [Indexed: 12/11/2022]
Abstract
Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.
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Affiliation(s)
- Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chee-Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- China Medical University, Taichung, Taiwan.
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20
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Cerrato V, Mercurio S, Leto K, Fucà E, Hoxha E, Bottes S, Pagin M, Milanese M, Ngan CY, Concina G, Ottolenghi S, Wei CL, Bonanno G, Pavesi G, Tempia F, Buffo A, Nicolis SK. Sox2 conditional mutation in mouse causes ataxic symptoms, cerebellar vermis hypoplasia, and postnatal defects of Bergmann glia. Glia 2018; 66:1929-1946. [PMID: 29732603 DOI: 10.1002/glia.23448] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/07/2022]
Abstract
Sox2 is a transcription factor active in the nervous system, within different cell types, ranging from radial glia neural stem cells to a few specific types of differentiated glia and neurons. Mutations in the human SOX2 transcription factor gene cause various central nervous system (CNS) abnormalities, involving hippocampus and eye defects, as well as ataxia. Conditional Sox2 mutation in mouse, with different Cre transgenes, previously recapitulated different essential features of the disease, such as hippocampus and eye defects. In the cerebellum, Sox2 is active from early embryogenesis in the neural progenitors of the cerebellar primordium; Sox2 expression is maintained, postnatally, within Bergmann glia (BG), a differentiated cell type essential for Purkinje neurons functionality and correct motor control. By performing Sox2 Cre-mediated ablation in the developing and postnatal mouse cerebellum, we reproduced ataxia features. Embryonic Sox2 deletion (with Wnt1Cre) leads to reduction of the cerebellar vermis, known to be commonly related to ataxia, preceded by deregulation of Otx2 and Gbx2, critical regulators of vermis development. Postnatally, BG is progressively disorganized, mislocalized, and reduced in mutants. Sox2 postnatal deletion, specifically induced in glia (with GLAST-CreERT2), reproduces the BG defect, and causes (milder) ataxic features. Our results define a role for Sox2 in cerebellar function and development, and identify a functional requirement for Sox2 within postnatal BG, of potential relevance for ataxia in mouse mutants, and in human patients.
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Affiliation(s)
- Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Sara Mercurio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, Milano, 20126, Italy
| | - Ketty Leto
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Elisa Fucà
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Eriola Hoxha
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Sara Bottes
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, Milano, 20126, Italy
| | - Miriam Pagin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, Milano, 20126, Italy
| | - Marco Milanese
- Department of Pharmacy, Pharmacology and Toxicology Unit and Center of Excellence for Biomedical Research, University of Genova, Viale Cembrano 4, Genoa, 16148, Italy
| | - Chew-Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Giulia Concina
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Sergio Ottolenghi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, Milano, 20126, Italy
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Giambattista Bonanno
- Department of Pharmacy, Pharmacology and Toxicology Unit and Center of Excellence for Biomedical Research, University of Genova, Viale Cembrano 4, Genoa, 16148, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, 20100, Italy
| | - Filippo Tempia
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Torino, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole, 10, Orbassano, (Torino), 10043, Italy
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, piazza della Scienza 2, Milano, 20126, Italy
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21
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Wei CL, Cheng JL, Khan MA, Yang LQ, Imani S, Chen HC, Fu JJ. An improved DNA marker technique for genetic characterization using RAMP-PCR with high-GC primers. Genet Mol Res 2016; 15:gmr8721. [PMID: 27706740 DOI: 10.4238/gmr.15038721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Random amplified polymorphic DNA (RAPD) is a widely used molecular marker technique. As traditional RAPD has poor reproducibility and productivity, we previously developed an improved RAPD method (termed RAMP-PCR), which increased the reproducibility, number of bands, and efficiency of studies on polymorphism. To further develop the efficiency of this method, we used high-GC content primers for improved RAMP-PCR with DNA samples from Lonicera japonica. Comparison of amplification profiles obtained by standard RAPD primers with those obtained by regular PCR and RAMP-PCR, and high-GC primers with regular PCR and RAMP-PCR showed that the average number of bands and polymorphisms per primer gradually and significantly increased (from 6.4 to 15.0 and from 4.6 to 10.2, respectively). Cluster dendrograms showed similar results, indicating that this new method is consistent and reproducible. A total of 22 samples from different species, including plants, animals, and humans, were used for RAMP-PCR with high-GC primers. Multiple bands were successfully amplified from all samples, demonstrating that this method is a reliable technique with consistent results and may be of general interest in studies on different genera and species. We developed highly effective DNA markers, which can provide a more effective and potentially valuable approach than traditional RAPD for the genetic identification of various organisms, particularly of medicinal plants.
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Affiliation(s)
- C L Wei
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China.,The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China
| | - J L Cheng
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China
| | - M A Khan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China
| | - L Q Yang
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China
| | - S Imani
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China
| | - H C Chen
- Department of Biochemistry, School of Life Sciences & the State Key Laboratory of Medical Genetics, Central South University, Changsha City, Hunan Province, China
| | - J J Fu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China .,The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province, China .,Judicial Authentication Center, Southwest Medical University, Luzhou City, Sichuan Province, China
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22
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Cheng JL, Yin ZC, Mei ZQ, Wei CL, Chen HC, Wu XS, Fu JJ. Development and significance of SCAR marker QG12-5 for Canarium album (Lour.) Raeusch by molecular cloning from improved RAPD amplification. Genet Mol Res 2016; 15:gmr8347. [PMID: 27706623 DOI: 10.4238/gmr.15038347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sequence-characterized amplified region (SCAR) is a valuable molecular marker for the genetic identification of any species. This marker is mainly derived from molecular cloning of random amplified polymorphic DNA (RAPD). We have previously reported the use of an improved RAPD technique for the genetic characterization of different samples of Canarium album (Lour.) Raeusch (C. album). In this study, DNA fragments were amplified using improved RAPD amplified from different samples of C. album. The amplified DNA fragment was excised, purified from an agarose gel and cloned into a pGM-T vector; subsequently, a positive clone, called QG12-5 was identified by PCR amplification and enzymatic digestion and sequenced by Sanger di-deoxy sequencing method. This clone was revealed consisting of 510 nucleotides of C. album. The SCAR marker QG12-5 was developed using specifically designed PCR primers and optimized PCR conditions. This SCAR marker expressed seven continuous "TATG" [(TATG)n] tandem repeats, which was found to characterize C. album. Subsequently, this novel SCAR marker was deposited in GenBank with accession No. KT359568. Therefore, we successfully developed a C. album-specific SCAR marker for the identification and authentication of different C. album species in this study.
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Affiliation(s)
- J L Cheng
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Z C Yin
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, Hunan, China.,Key Lab of MOE for Development Biology and Protein Chemistry, Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Z Q Mei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - C L Wei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - H C Chen
- Department of Biochemistry, School of Life Sciences & the State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - X S Wu
- Key Lab of MOE for Development Biology and Protein Chemistry, Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - J J Fu
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.,Judicial Authentication Center, Southwest Medical University, Luzhou, Sichuan, China
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23
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Khan MA, Cheng JL, Mei ZQ, Wei CL, Fu JJ. Development of two novel specific SCAR markers by cloning improved RAPD fragments from the medicinal mushroom Ganoderma lucidium (Leysser: Fr) Karst. Genet Mol Res 2016; 15:gmr8536. [PMID: 27706590 DOI: 10.4238/gmr.15038536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Development of sequence-characterized amplified region (SCAR) markers from random-amplified polymorphic DNA (RAPD) fragments is a valuable molecular approach for the genetic identification of different species. By using SCAR markers, molecular analysis is reduced to a simple polymerase chain reaction (PCR) analysis using primers designed from the amplicon sequence of RAPD. In this study, the DNA fragments from an improved RAPD amplification of Ganoderma species were cloned into a pGM-T vector; positive clones were identified by PCR amplification and enzymatic digestion, and finally, DNA fragments were sequenced using the Sanger sequencing method for developing the SCAR markers. Two SCAR markers, named LZ4-1 with 534 nucleotides, and LZ5-2 with 337 nucleotides were identified, which are specific to Ganoderma lucidium (Leysser: Fr) Karst species. BLAST of these two nucleotide sequences in the GenBank database showed no identity to other species. We deposited these sequences into the GenBank database (LZ4-1 accession No. KM391933, LZ5-2 accession No. KM391934). PCR assays confirmed them as novel molecular markers for G. lucidium (Leysser: Fr) Karst, which might be used for genetic authentication of adulterant samples. Thus, our study developed two specific SCAR markers for identifying and distinguishing the medicinal mushroom G. lucidium (Leysser: Fr) Karst from other Ganoderma species.
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Affiliation(s)
- M A Khan
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - J L Cheng
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Z Q Mei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - C L Wei
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - J J Fu
- Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan, China .,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China .,Judicial Authentication Center, Southwest Medical University, Luzhou, Sichuan, China
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24
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Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ. Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. PLoS One 2016; 11:e0155839. [PMID: 27434306 PMCID: PMC4951065 DOI: 10.1371/journal.pone.0155839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/05/2016] [Indexed: 11/18/2022] Open
Abstract
Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (<2 μm diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3’ UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.
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Affiliation(s)
- Peter H. Waltman
- University of California at Santa Cruz, Baskin School of Engineering, Santa Cruz, California, 95064, United States of America
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Emily Nahas Reistetter
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Samuel Purvine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Charles K. Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Marijke J. van Baren
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Chee-Hong Wong
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, 94598, United States of America
| | - Chia-Lin Wei
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, 94598, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
| | - Stephen J. Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, United States of America
- * E-mail: (SJC); (JMS); (AZW)
| | - Joshua M. Stuart
- University of California at Santa Cruz, Baskin School of Engineering, Santa Cruz, California, 95064, United States of America
- * E-mail: (SJC); (JMS); (AZW)
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
- University of California Santa Cruz, Department of Ocean Sciences, Santa Cruz, California, 95064, United States of America
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, Canada, M5G 1Z8
- * E-mail: (SJC); (JMS); (AZW)
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25
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Yang C, Zhang YQ, Tang X, Gao P, Wei CL, Hu YH. [Retrospective cohort study for the impact on readmission of patients with ischemic stroke after treatment of aspirin plus clopidogrel or aspirin mono-therapy]. Beijing Da Xue Xue Bao Yi Xue Ban 2016; 48:442-447. [PMID: 27318905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To see the influence of different antiplatelet therapies on stroke patients' readmission by performing a deep data-mining into Beijing Healthcare Insuring Database, based on a large sample size. METHODS Aretrospective cohort study, was adopted to extract patients primarily diagnosed as ischemic stroke from healthcare database. The first hospital records were considered as the patient's baseline in this study, who were divided into MAPT (aspirin) and DAPT (aspirin and clopidogrel) according to the patient's baseline medications. A follow-up was conducted to see whether the patients would have rehospitalization record because of major result events after medication. The major result events, included: (1) recurrence of ischemic stroke; (2) hemorrhagic transformation of ischemic stroke; (3) myocardial infarction; (4) the digestive hemorrhage. The Kaplan-Meier figure was used to compare the survival situations between these two groups, the log-rank test was used to test the difference of the survival curve, and 1:1 propensity score matching was calculated from the patients' baseline data. Cox proportional hazards model was used to calculate the hazard ratio (HR). RESULTS A total of 27 695 patients From January 2010 to September 2013 were included, 4 047 with DAPT, and 23 648 with MAPT. Because the baseline characteristics of the patients was disequilibrium, so we used 1:1 propensity score matching, after which, the number of the two groups was 4 046 each. Adjusted for the general demographic characteristics such as age, sex, nationality, complication and drug combination, no statistical significance was observed between the survival curves of the two groups (P=0.06). HR value of major result events between the groups was 0.91 (0.82-1.01, P=0.07), which was not statistically significant. The covariate gender HR=1.36 (1.20-1.55, P<0.05), accompanied by diabetes HR= 1.36 (1.20-1.54, P<0.05), dyslipidemia HR=1.13 (1.00-1.27, P=1.13), heart disease HR=1.39 (1.22-1.58, P<0.05) was statistically significant. Drug combination with other antiplatelet agents HR=1.05 (0.95-1.17, P>1.05) did not increase the risk of readmission. CONCLUSION There was no difference in prevention of readmission between patients with DAPT and MAPT. Patients with complications should actively treat the complications at the same time as they prevent recurrence after first attack.
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Affiliation(s)
- C Yang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - Y Q Zhang
- Department of Education, Peking University Health Science Center, Beijing 100191, China
| | - X Tang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - P Gao
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - C L Wei
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - Y H Hu
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
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26
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Cheng JL, Li J, Qiu YM, Wei CL, Yang LQ, Fu JJ. Development of novel SCAR markers for genetic characterization of Lonicera japonica from high GC-RAMP-PCR and DNA cloning. Genet Mol Res 2016; 15:gmr7737. [PMID: 27173286 DOI: 10.4238/gmr.15027737] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Sequence-characterized amplified region (SCAR) markers were further developed from high-GC primer RAMP-PCR-amplified fragments from Lonicera japonica DNA by molecular cloning. The four DNA fragments from three high-GC primers (FY-27, FY-28, and FY-29) were successfully cloned into a pGM-T vector. The positive clones were sequenced; their names, sizes, and GenBank numbers were JYHGC1-1, 345 bp, KJ620024; YJHGC2-1, 388 bp, KJ620025; JYHGC7-2, 1036 bp, KJ620026; and JYHGC6-2, 715 bp, KJ620027, respectively. Four novel SCAR markers were developed by designing specific primers, optimizing conditions, and PCR validation. The developed SCAR markers were used for the genetic authentication of L. japonica from its substitutes. This technique provides another means of developing DNA markers for the characterization and authentication of various organisms including medicinal plants and their substitutes.
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Affiliation(s)
- J L Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China
| | - J Li
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China
| | - Y M Qiu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China.,Maternal and Child Health Care Hospital of Zigong, Zigong, Sichuan, China
| | - C L Wei
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - L Q Yang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China
| | - J J Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.,Judicial Authentication Center, Sichuan Medical University, Luzhou City, Sichuan, China
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27
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van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Deerinck TJ, Kuo A, Grigoriev IV, Wong CH, Smith RD, Callister SJ, Wei CL, Schmutz J, Worden AZ. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics 2016; 17:267. [PMID: 27029936 PMCID: PMC4815162 DOI: 10.1186/s12864-016-2585-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/11/2016] [Indexed: 01/26/2023] Open
Abstract
Background Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2585-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marijke J van Baren
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Charles Bachy
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Emily Nahas Reistetter
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Samuel O Purvine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jane Grimwood
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Hang Yu
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.,Now at: Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Thomas J Deerinck
- Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, La Jolla, San Diego, California, 92093, USA
| | - Alan Kuo
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Chee-Hong Wong
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Stephen J Callister
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chia-Lin Wei
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Hudson Alpha, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA. .,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.
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28
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Yang WC, Zhu L, Qiu YM, Zhou BX, Cheng JL, Wei CL, Chen HC, Li LY, Fu XD, Fu JJ. Isolation and analysis of cell-free fetal DNA from maternal peripheral blood in Chinese women. Genet Mol Res 2015; 14:18078-89. [PMID: 26782455 DOI: 10.4238/2015.december.22.34] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Non-invasive prenatal diagnosis is used to detect the genetic material of the fetus by isolating the cell-free fetal DNA (cffDNA) from maternal peripheral blood. In order to establish an isolation method for cffDNA from maternal peripheral blood in Chinese women, the cffDNA was acquired with a two-step centrifugation using a QlAamp DNA Blood mini kit. The SRY gene of plasma DNA was amplified by polymerase chain reaction (PCR). Real-time quantitative PCR was used to measure the concentration of cffDNA in maternal peripheral blood in different pregnant women. The results of the SRY gene amplification of plasma DNA from pregnant women was the same as that of the amniocyte DNA. The average concentration of cffDNA in maternal peripheral blood of pregnant women in different gestational stages was 0.98 ng/mL (0.26-1.49 ng/mL), 1.43 ng/mL (0.46- 2.34 ng/mL), and 1.95 ng/mL (0.65-6.81 ng/mL) from early, middle, and late gestational stages, respectively. The mean of cffDNA from total DNA in plasma in different stages of gestation was 22.28% (9.86-27.81%). The lowest concentration of DNA amplified by nested-PCR in our research was 10-4-10-3 ng/μL. The isolation method for cffDNA from maternal peripheral blood was successfully established and further research into its applications will be conducted.
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Affiliation(s)
- W C Yang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China
| | - L Zhu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China
| | - Y M Qiu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China.,Maternal and Child Health Care Hospital of Zigong, Zigong, Sichuan Province, China
| | - B X Zhou
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China
| | - J L Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China
| | - C L Wei
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China
| | - H C Chen
- Department of Biochemistry, School of Life Sciences & the State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan Province, China
| | - L Y Li
- Institute of Reproduction and Stem Cell Engineering, Central South University Xiangya School of Medicine, Changsha, Hunan Province, China
| | - X D Fu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Sichuan Medical University, Luzhou, Sichuan Province, China
| | - J J Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou City, Sichuan Province, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR), China.,Department of Obstetrics and Gynecology, First Affiliated Hospital of Sichuan Medical University, Luzhou, Sichuan Province, China
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29
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Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell 2015; 163:1611-27. [PMID: 26686651 PMCID: PMC4734140 DOI: 10.1016/j.cell.2015.11.024] [Citation(s) in RCA: 637] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/12/2015] [Accepted: 11/10/2015] [Indexed: 01/09/2023]
Abstract
Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.
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Affiliation(s)
- Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Oscar Junhong Luo
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Xingwang Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Meizhen Zheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Jacqueline Jufen Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
| | - Przemyslaw Szalaj
- Center for Bioinformatics and Data Analysis, Medical University of Bialystok, ul. Jana Kilinskiego 1, 15-089 Bialystok, Poland; I-BioStat, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium; Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Pawel Trzaskoma
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Adriana Magalska
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Jakub Wlodarczyk
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Blazej Ruszczycki
- Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Paul Michalski
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Emaly Piecuch
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Danjuan Wang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Simon Zhongyuan Tian
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - May Penrad-Mobayed
- Université Paris-Diderot-Paris 7, Centre National de la Recherche Scientifique and Institut Jacques Monod, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Laurent M Sachs
- Centre National de la Recherche Scientifique and Muséum National d'Histoire Naturelle, 57 Rue Cuvier, 75231 Paris Cedex, France
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | - Chia-Lin Wei
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA
| | | | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
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30
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Wei CL, Cheng JL, Yang WC, Li LY, Cheng HC, Fu JJ. Identification of the origin of marker chromosomes by two-color fluorescence in situ hybridization and polymerase chain reaction in azoospermic patients. Genet Mol Res 2015; 14:14488-95. [PMID: 26600507 DOI: 10.4238/2015.november.18.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Y chromosomal microdeletions at the azoospermia factor locus and chromosome abnormalities have been implicated as the major causes of idiopathic male infertility. A marker chromosome is a structurally abnormal chromosome in which no part can be identified by cytogenetics. In this study, to identify the origin of the marker chromosomes and to perform a genetic diagnosis of patients with azoospermia, two-color fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques were carried out. The marker chromosomes for the two patients with azoospermia originated in the Y chromosome; it was ascertained that the karyotype of both patients was 46,X, ish del(Y)(q11)(DYZ3+, DXZ1-). The combination of two-color FISH and PCR techniques is an important method for the identification of the origin of marker chromosomes. Thus, genetic counseling and a clear genetic diagnosis of patients with azoospermia before intracytoplasmic sperm injection or other clinical managements are important.
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Affiliation(s)
- C L Wei
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan Province, China
| | - J L Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan Province, China
| | - W C Yang
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan Province, China
| | - L Y Li
- Insistitute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - H C Cheng
- Insistitute of Reproduction and Stem Cell Engineering, Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - J J Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Sichuan Medical University, Luzhou, Sichuan Province, China
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31
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. Plant J 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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32
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Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, García-Cerdán JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL. Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nat Plants 2015; 1:15107. [PMID: 27250540 DOI: 10.1038/nplants.2015.107] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/22/2015] [Indexed: 05/09/2023]
Abstract
Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify transcriptional regulators of lipid accumulation, we performed an integrative chromatin signature and transcriptomic analysis to decipher the regulation of lipid biosynthesis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between the algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor, PSR1, as a pivotal switch that triggers cytosolic lipid accumulation. Dissection of the PSR1-induced lipid profiles corroborates its role in coordinating multiple lipid-inducing stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a transcriptional regulator of algal lipid metabolism will facilitate targeted engineering strategies to mediate high lipid production in microalgae.
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Affiliation(s)
- Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Chee-Hong Wong
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Katherine Louie
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Jing Jia
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Benjamin Bowen
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Haoyu Cheng
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Lauriebeth Leonelli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rita Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Richard Baran
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - José G García-Cerdán
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Abhishek Pratap
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Joanne Lim
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Hope Tice
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jian Xu
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Trent Northen
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Axel Visel
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - James Bristow
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Krishna K Niyogi
- School of Natural Sciences, University of California, Merced, California 95343, USA
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Chia-Lin Wei
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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33
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Tsai YS, Jou YC, Tsai YP, Liu BD, Lin HI, Wei CL, Chen SY, Tsai HT, Ou CH, Yang WH, Tzai TS. Development of 3-Hydroxyanthranilic acid-based Integrated Non-invasive Biosensor for Bladder Cancer Detection. Urological Science 2015. [DOI: 10.1016/j.urols.2015.06.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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34
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Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW. A genome-wide map of adeno-associated virus-mediated human gene targeting. Nat Struct Mol Biol 2014; 21:969-75. [PMID: 25282150 PMCID: PMC4405182 DOI: 10.1038/nsmb.2895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/27/2014] [Indexed: 02/03/2023]
Abstract
To determine which genomic features promote homologous recombination, we created a genome-wide map of gene targeting sites. We used an adeno-associated virus vector to target identical loci introduced as transcriptionally active retroviral vectors. A comparison of ~2,000 targeted and untargeted sites showed that targeting occurred throughout the human genome and was not influenced by the presence of nearby CpG islands, sequence repeats or DNase I-hypersensitive sites. Targeted sites were preferentially located within transcription units, especially when the target loci were transcribed in the opposite orientation to their surrounding chromosomal genes. We determined the impact of DNA replication by mapping replication forks, which revealed a preference for recombination at target loci transcribed toward an incoming fork. Our results constitute the first genome-wide screen of gene targeting in mammalian cells and demonstrate a strong recombinogenic effect of colliding polymerases.
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Affiliation(s)
- David R Deyle
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - R Scott Hansen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anda M Cornea
- Department of Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Li B Li
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amber A Burt
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Chia-Lin Wei
- Genomic Technologies Department, Joint Genome Institute, Walnut Creek, California, USA
| | - David W Russell
- 1] Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA
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35
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Walz S, Lorenzin F, Morton J, Wiese KE, von Eyss B, Herold S, Rycak L, Dumay-Odelot H, Karim S, Bartkuhn M, Roels F, Wüstefeld T, Fischer M, Teichmann M, Zender L, Wei CL, Sansom O, Wolf E, Eilers M. Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature 2014; 511:483-7. [PMID: 25043018 PMCID: PMC6879323 DOI: 10.1038/nature13473] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022]
Abstract
In mammalian cells, the MYC oncoprotein binds to thousands of promoters. During mitogenic stimulation of primary lymphocytes, MYC promotes an increase in the expression of virtually all genes. In contrast, MYC-driven tumour cells differ from normal cells in the expression of specific sets of up- and downregulated genes that have considerable prognostic value. To understand this discrepancy, we studied the consequences of inducible expression and depletion of MYC in human cells and murine tumour models. Changes in MYC levels activate and repress specific sets of direct target genes that are characteristic of MYC-transformed tumour cells. Three factors account for this specificity. First, the magnitude of response parallels the change in occupancy by MYC at each promoter. Functionally distinct classes of target genes differ in the E-box sequence bound by MYC, suggesting that different cellular responses to physiological and oncogenic MYC levels are controlled by promoter affinity. Second, MYC both positively and negatively affects transcription initiation independent of its effect on transcriptional elongation. Third, complex formation with MIZ1 (also known as ZBTB17) mediates repression of multiple target genes by MYC and the ratio of MYC and MIZ1 bound to each promoter correlates with the direction of response.
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Affiliation(s)
- Susanne Walz
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2]
| | - Francesca Lorenzin
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2]
| | - Jennifer Morton
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Katrin E Wiese
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Björn von Eyss
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lukas Rycak
- Institute for Molecular Biology and Tumor Research (IMT), Emil-Mannkopff-Str.2, 35033 Marburg, Germany
| | - Hélène Dumay-Odelot
- University of Bordeaux, IECB, ARNA laboratory, Equipe Labellisée Contre le Cancer, 33600 Pessac, France
| | - Saadia Karim
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35390 Giessen, Germany
| | - Frederik Roels
- University Children's Hospital of Cologne, and Cologne Center for Molecular Medicine (CMMC), University of Cologne, Kerpener Str. 62, 50924 Cologne, Germany
| | - Torsten Wüstefeld
- University Hospital Tübingen, Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, Otfried-Mueller-Strasse 10, 72076 Tübingen, Germany
| | - Matthias Fischer
- University Children's Hospital of Cologne, and Cologne Center for Molecular Medicine (CMMC), University of Cologne, Kerpener Str. 62, 50924 Cologne, Germany
| | - Martin Teichmann
- University of Bordeaux, IECB, ARNA laboratory, Equipe Labellisée Contre le Cancer, 33600 Pessac, France
| | - Lars Zender
- 1] University Hospital Tübingen, Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, Otfried-Mueller-Strasse 10, 72076 Tübingen, Germany [2] Translational Gastrointestinal Oncology Group within the German Center for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Chia-Lin Wei
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Owen Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Elmar Wolf
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2] Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str.2, 97080 Würzburg, Germany [3]
| | - Martin Eilers
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2] Comprehensive Cancer Center Mainfranken, University of Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany [3]
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36
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Reeve W, Ardley J, Tian R, De Meyer S, Terpolilli J, Melino V, Tiwari R, Yates R, O’Hara G, Howieson J, Ninawi M, Zhang X, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N. Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). Stand Genomic Sci 2014; 9:540-50. [PMID: 25197439 PMCID: PMC4149032 DOI: 10.4056/sigs.4548266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microvirga lotononidis is a recently described species of root-nodule bacteria that is an effective nitrogen- (N2) fixing microsymbiont of the symbiotically specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr. M. lotononidis possesses several properties that are unusual in root-nodule bacteria, including pigmentation and the ability to grow at temperatures of up to 45°C. Strain WSM3557(T) is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a L. angolensis root nodule collected in Chipata, Zambia in 1963. This is the first report of a complete genome sequence for the genus Microvirga. Here we describe the features of Microvirga lotononidis strain WSM3557(T), together with genome sequence information and annotation. The 7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs, contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
- Department of Agriculture and Food, Western Australia, Australia
| | - Graham O’Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Xiaojing Zhang
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ernest Szeto
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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37
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Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z. A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Sci Rep 2014; 4:4519. [PMID: 24682209 PMCID: PMC3970191 DOI: 10.1038/srep04519] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 02/26/2014] [Indexed: 02/04/2023] Open
Abstract
RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.
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Affiliation(s)
- Jeffrey A Martin
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nicole V Johnson
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Stephen M Gross
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - James Schnable
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Xiandong Meng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Mei Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Devin Coleman-Derr
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Erika Lindquist
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Shawn Kaeppler
- Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | - Feng Chen
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Zhong Wang
- 1] Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA [2] Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
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38
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Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2014; 155:1507-20. [PMID: 24360274 DOI: 10.1016/j.cell.2013.11.039] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/01/2013] [Accepted: 11/25/2013] [Indexed: 12/31/2022]
Abstract
A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.
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Affiliation(s)
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Ewy Mathe
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Qian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guoliang Li
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Wolfgang Resch
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathanael Pruett
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Vian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steevenson Nelson
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ofir Hakim
- Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotaka Nakahashi
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander L Kovalchuk
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jizhong Zou
- Laboratory of Stem Cell Biology, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
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Reeve W, De Meyer S, Terpolilli J, Melino V, Ardley J, Tian R, Tiwari R, Howieson J, Yates R, O'Hara G, Ninawi M, Lu M, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Ivanova N, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N. Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471. Stand Genomic Sci 2013; 9:254-63. [PMID: 24976882 PMCID: PMC4062639 DOI: 10.4056/sigs.4498256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen- (N2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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40
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Reeve W, De Meyer S, Terpolilli J, Melino V, Ardley J, Rui T, Tiwari R, Howieson J, Yates R, O’Hara G, Lu M, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Ovchinnikova G, Pagani I, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Kyrpides N. Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005(T.). Stand Genomic Sci 2013; 9:385-94. [PMID: 24976894 PMCID: PMC4062628 DOI: 10.4056/sigs.4558268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
"Burkholderia sprentiae" strain WSM5005(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of "Burkholderia sprentiae" strain WSM5005(T), together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Tian Rui
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ron Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
- Department of Agriculture and Food, Western Australia, Australia
| | - Graham O’Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Victor Markowitz
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Ernest Szeto
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lin Peters
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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41
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Reeve W, Terpolilli J, Melino V, Ardley J, Tian R, De Meyer S, Tiwari R, Yates R, O'Hara G, Howieson J, Ninawi M, Teshima H, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavrommatis K, Markowitz V, Ivanova N, Ovchinnikova G, Pagani I, Pati A, Goodwin L, Peters L, Woyke T, Kyrpides N. Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417. Stand Genomic Sci 2013; 9:273-82. [PMID: 24976884 PMCID: PMC4062640 DOI: 10.4056/sigs.4518260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Hazuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lin Peters
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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42
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Reeve W, Melino V, Ardley J, Tian R, De Meyer S, Terpolilli J, Tiwari R, Yates R, O'Hara G, Howieson J, Ninawi M, Held B, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N. Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012. Stand Genomic Sci 2013; 9:283-93. [PMID: 24976885 PMCID: PMC4062638 DOI: 10.4056/sigs.4528262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an ineffective root nodule recovered from the roots of the annual clover Trifolium rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host range for N2-fixation. Here we describe the features of R. leguminosarum bv. trifolii strain WSM2012, together with genome sequence information and annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6 scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Brittany Held
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ernest Szeto
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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43
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Reeve W, Tian R, De Meyer S, Melino V, Terpolilli J, Ardley J, Tiwari R, Howieson J, Yates R, O'Hara G, Ninawi M, Teshima H, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Ivanova N, Ovchinnikova G, Pagani I, Pati A, Goodwin L, Pitluck S, Woyke T, Kyrpides N. Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1. Stand Genomic Sci 2013; 9:243-53. [PMID: 24976881 PMCID: PMC4062637 DOI: 10.4056/sigs.4488254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, non-spore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Hazuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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44
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Reeve W, Terpolilli J, Melino V, Ardley J, Tian R, De Meyer S, Tiwari R, Yates R, O'Hara G, Howieson J, Ninawi M, Held B, Bruce D, Detter C, Tapia R, Han C, Wei CL, Huntemann M, Han J, Chen IM, Mavromatis K, Markowitz V, Ivanova N, Ovchinnikova G, Pagani I, Pati A, Goodwin L, Woyke T, Kyrpides N. Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597. Stand Genomic Sci 2013; 9:264-72. [PMID: 24976883 PMCID: PMC4062625 DOI: 10.4056/sigs.4508258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a root nodule of the annual clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembó, Uruguay. This strain is generally ineffective for nitrogen (N2) fixation with clovers of Mediterranean, North American and African origin, but is effective on the South American perennial clover T. polymorphum Poir. Here we describe the features of R. leguminosarum bv. trifolii strain WSM597, together with genome sequence information and annotation. The 7,634,384 bp high-quality-draft genome is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Jason Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Vanessa Melino
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ravi Tiwari
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Ronald Yates
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia ; Department of Agriculture and Food, Western Australia, Australia
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Mohamed Ninawi
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Brittany Held
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - I-Min Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
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45
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Kruse T, Maillard J, Goodwin L, Woyke T, Teshima H, Bruce D, Detter C, Tapia R, Han C, Huntemann M, Wei CL, Han J, Chen A, Kyrpides N, Szeto E, Markowitz V, Ivanova N, Pagani I, Pati A, Pitluck S, Nolan M, Holliger C, Smidt H. Complete genome sequence of Dehalobacter restrictus PER-K23(T.). Stand Genomic Sci 2013; 8:375-88. [PMID: 24501624 PMCID: PMC3910700 DOI: 10.4056/sigs.3787426] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, coupling the oxidation of H2 to the reductive dechlorination of tetra- or trichloroethene. Growth has not been observed with any other electron donor or acceptor, nor has fermentative growth been shown. Here we introduce the first full genome of a pure culture within the genus Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82 RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25 predicted reductive dehalogenase genes, the majority of which appear to be full length. The reductive dehalogenase genes are mainly located in two clusters, suggesting a much larger potential for organohalide respiration than previously anticipated.
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Affiliation(s)
- Thomas Kruse
- Wageningen University, Agrotechnology and Food Sciences, Laboratory of Microbiology, Dreijenplein 10, NL-6703 HB Wageningen, The Netherlands
| | - Julien Maillard
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, CH-1015 Lausanne, Switzerland
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hazuki Teshima
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Chris Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Chia-Lin Wei
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Ernest Szeto
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Christof Holliger
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, CH-1015 Lausanne, Switzerland
| | - Hauke Smidt
- Wageningen University, Agrotechnology and Food Sciences, Laboratory of Microbiology, Dreijenplein 10, NL-6703 HB Wageningen, The Netherlands
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46
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Wall LG, Beauchemin N, Cantor MN, Chaia E, Chen A, Detter JC, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Hua SX, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nordberg HP, Nouioui I, Ovchinnikova G, Pagani I, Pati A, Sen A, Sur S, Szeto E, Thakur S, Wei CL, Woyke T, Tisa LS. Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis. Genome Announc 2013; 1:e00503-13. [PMID: 23846281 PMCID: PMC3709158 DOI: 10.1128/genomea.00503-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 11/20/2022]
Abstract
Frankia forms a nitrogen-fixing symbiosis with actinorhizal plants. We report a draft genome sequence for Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis grown in the Patagonia region of Argentina.
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Affiliation(s)
| | | | | | | | - Amy Chen
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | - Teal Furnholm
- University of New Hampshire, Durham, New Hampshire, USA
| | - Faten Ghodhbane-Gtari
- University of New Hampshire, Durham, New Hampshire, USA
- University of Tunis–El Manar, Tunis, Tunisia
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Maher Gtari
- University of New Hampshire, Durham, New Hampshire, USA
- University of Tunis–El Manar, Tunis, Tunisia
| | - Cliff Han
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - James Han
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Marcel Huntemann
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Xinyu Hua
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Natalia Ivanova
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Nikos Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Victor Markowitz
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Kostas Mavrommatis
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Natalia Mikhailova
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Galina Ovchinnikova
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Ioanna Pagani
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Arnab Sen
- University of North Bengal, Siliguri, India
| | | | - Ernest Szeto
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | - Chia-Lin Wei
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Louis S. Tisa
- University of New Hampshire, Durham, New Hampshire, USA
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47
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Murugapiran SK, Huntemann M, Wei CL, Han J, Detter JC, Han C, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Pati A, Goodwin L, Peters L, Pitluck S, Lam J, McDonald AI, Dodsworth JA, Woyke T, Hedlund BP. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Stand Genomic Sci 2013; 7:449-68. [PMID: 24019992 PMCID: PMC3764938 DOI: 10.4056/sigs.3667269] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18 chromosome with those from other strains of T. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequenced Thermus strains. Phylogenomic analyses using a concatenated set of conserved proteins confirmed the phylogenetic and taxonomic assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus glucosidases, glycosidases, proteases, and peptidases, highlighting highly versatile heterotrophic capabilities. Megaplasmids of both strains contained a gene cluster encoding enzymes predicted to catalyze the sequential reduction of nitrate to nitrous oxide; however, the nitrous oxide reductase required for the terminal step in denitrification was absent, consistent with their incomplete denitrification phenotypes. A sox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.
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Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK. BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol 2012; 13:R82. [PMID: 23034162 PMCID: PMC3491410 DOI: 10.1186/gb-2012-13-10-r82] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 10/03/2012] [Indexed: 12/20/2022] Open
Abstract
DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.
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Yao F, Ariyaratne PN, Hillmer AM, Lee WH, Li G, Teo ASM, Woo XY, Zhang Z, Chen JP, Poh WT, Zawack KFB, Chan CS, Leong ST, Neo SC, Choi PSD, Gao S, Nagarajan N, Thoreau H, Shahab A, Ruan X, Cacheux-Rataboul V, Wei CL, Bourque G, Sung WK, Liu ET, Ruan Y. Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS One 2012; 7:e46152. [PMID: 23029419 PMCID: PMC3461012 DOI: 10.1371/journal.pone.0046152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/28/2012] [Indexed: 01/23/2023] Open
Abstract
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10–20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.
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Affiliation(s)
- Fei Yao
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pramila N. Ariyaratne
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Axel M. Hillmer
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wah Heng Lee
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Guoliang Li
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Audrey S. M. Teo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Xing Yi Woo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Zhenshui Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jieqi P. Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wan Ting Poh
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kelson F. B. Zawack
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chee Seng Chan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - See Ting Leong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Say Chuan Neo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Poh Sum D. Choi
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Song Gao
- Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Hervé Thoreau
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Atif Shahab
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Xiaoan Ruan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Valère Cacheux-Rataboul
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Chia-Lin Wei
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Guillaume Bourque
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wing-Kin Sung
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Edison T. Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Yijun Ruan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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Heisig J, Weber D, Englberger E, Winkler A, Kneitz S, Sung WK, Wolf E, Eilers M, Wei CL, Gessler M. Target gene analysis by microarrays and chromatin immunoprecipitation identifies HEY proteins as highly redundant bHLH repressors. PLoS Genet 2012; 8:e1002728. [PMID: 22615585 PMCID: PMC3355086 DOI: 10.1371/journal.pgen.1002728] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 04/05/2012] [Indexed: 01/03/2023] Open
Abstract
HEY bHLH transcription factors have been shown to regulate multiple key steps in cardiovascular development. They can be induced by activated NOTCH receptors, but other upstream stimuli mediated by TGFß and BMP receptors may elicit a similar response. While the basic and helix-loop-helix domains exhibit strong similarity, large parts of the proteins are still unique and may serve divergent functions. The striking overlap of cardiac defects in HEY2 and combined HEY1/HEYL knockout mice suggested that all three HEY genes fulfill overlapping function in target cells. We therefore sought to identify target genes for HEY proteins by microarray expression and ChIPseq analyses in HEK293 cells, cardiomyocytes, and murine hearts. HEY proteins were found to modulate expression of their target gene to a rather limited extent, but with striking functional interchangeability between HEY factors. Chromatin immunoprecipitation revealed a much greater number of potential binding sites that again largely overlap between HEY factors. Binding sites are clustered in the proximal promoter region especially of transcriptional regulators or developmental control genes. Multiple lines of evidence suggest that HEY proteins primarily act as direct transcriptional repressors, while gene activation seems to be due to secondary or indirect effects. Mutagenesis of putative DNA binding residues supports the notion of direct DNA binding. While class B E-box sequences (CACGYG) clearly represent preferred target sequences, there must be additional and more loosely defined modes of DNA binding since many of the target promoters that are efficiently bound by HEY proteins do not contain an E-box motif. These data clearly establish the three HEY bHLH factors as highly redundant transcriptional repressors in vitro and in vivo, which explains the combinatorial action observed in different tissues with overlapping expression. NOTCH signaling is a central developmental pathway that influences a multitude of cell fate decisions and differentiation steps as well as later tissue homeostasis and regeneration. The three HEY genes encode basic helix-loop-helix transcription factors that are critical effectors to convey signaling by NOTCH receptors and similar signaling systems. This is underscored by the multitude of developmental defects observed in HEY single- and double-mutant mice. The mode of action of HEY proteins remained largely unexplored, however. By gene expression analysis and chromatin immunoprecipitation we have now identified a large set of HEY target genes. While only 500–2,000 mRNAs are regulated by HEY1 or HEY2, there are around 10,000 binding sites in the genome. HEY proteins act as transcriptional repressors that bind close to transcriptional start sites in all cases tested. In contrast, gene activation seems to be mediated by indirect/secondary mechanisms. The extent of regulation is rather limited, implicating HEY genes in modulating rather than switching on or off target gene expression. All our in vitro and in vivo data point to a high degree of redundancy between the three HEY genes, suggesting that tissue specific patterns and expression levels determine the final outcome of HEY induced cellular responses.
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Affiliation(s)
- Julia Heisig
- Developmental Biochemistry, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - David Weber
- Developmental Biochemistry, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Eva Englberger
- Developmental Biochemistry, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Anja Winkler
- Developmental Biochemistry, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Laboratory for Microarray Applications, and Physiological Chemistry I, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | - Elmar Wolf
- Biochemistry and Molecular Biology, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Martin Eilers
- Biochemistry and Molecular Biology, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore, Singapore
| | - Manfred Gessler
- Developmental Biochemistry, Theodor-Boveri-Institute, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- * E-mail:
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