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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. NATURE AGING 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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HDAC inhibitor and proteasome inhibitor induce cleavage and exosome-mediated secretion of HSP90 in mouse pluripotent stem cells. Biochem Biophys Res Commun 2022; 620:29-34. [DOI: 10.1016/j.bbrc.2022.06.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 11/22/2022]
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3
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E C, Dai L, Yu J. Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path. Biophys J 2022; 121:582-595. [PMID: 35031277 PMCID: PMC8874028 DOI: 10.1016/j.bpj.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, we computationally investigated how a viral RNA polymerase (RNAP) from bacteriophage T7 evolves into RNAP variants under lab-directed evolution to switch recognition from T7 promoter to T3 promoter in transcription initiation. We first constructed a closed initiation complex for the wild-type T7 RNAP and then for six mutant RNAPs discovered from phage-assisted continuous evolution experiments. All-atom molecular dynamics simulations up to 1 μs each were conducted on these RNAPs in a complex with the T7 and T3 promoters. Our simulations show notably that protein-DNA electrostatic interactions or stabilities at the RNAP-DNA promoter interface well dictate the promoter recognition preference of the RNAP and variants. Key residues and structural elements that contribute significantly to switching the promoter recognition were identified. Followed by a first point mutation N748D on the specificity loop to slightly disengage the RNAP from the promoter to hinder the original recognition, we found an auxiliary helix (206-225) that takes over switching the promoter recognition upon further mutations (E222K and E207K) by forming additional charge interactions with the promoter DNA and reorientating differently on the T7 and T3 promoters. Further mutations on the AT-rich loop and the specificity loop can fully switch the RNAP-promoter recognition to the T3 promoter. Overall, our studies reveal energetics and structural dynamics details along an exemplary directed evolutionary path of the phage RNAP variants for a rewired promoter recognition function. The findings demonstrate underlying physical mechanisms and are expected to assist knowledge and data learning or rational redesign of the protein enzyme structure function.
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Affiliation(s)
- Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Liqiang Dai
- Beijing Computational Science Research Center, Beijing, China; Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, Guangdong, China
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California.
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Ebersbach C, Beier AMK, Thomas C, Erb HHH. Impact of STAT Proteins in Tumor Progress and Therapy Resistance in Advanced and Metastasized Prostate Cancer. Cancers (Basel) 2021; 13:4854. [PMID: 34638338 PMCID: PMC8508518 DOI: 10.3390/cancers13194854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Signal transducers and activators of transcription (STATs) are a family of transcription factors involved in several biological processes such as immune response, cell survival, and cell growth. However, they have also been implicated in the development and progression of several cancers, including prostate cancer (PCa). Although the members of the STAT protein family are structurally similar, they convey different functions in PCa. STAT1, STAT3, and STAT5 are associated with therapy resistance. STAT1 and STAT3 are involved in docetaxel resistance, while STAT3 and STAT5 are involved in antiandrogen resistance. Expression of STAT3 and STAT5 is increased in PCa metastases, and together with STAT6, they play a crucial role in PCa metastasis. Further, expression of STAT3, STAT5, and STAT6 was elevated in advanced and high-grade PCa. STAT2 and STAT4 are currently less researched in PCa. Since STATs are widely involved in PCa, they serve as potential therapeutic targets. Several inhibitors interfering with STATs signaling have been tested unsuccessfully in PCa clinical trials. This review focuses on the respective roles of the STAT family members in PCa, especially in metastatic disease and provides an overview of STAT-inhibitors evaluated in clinical trials.
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Affiliation(s)
- Celina Ebersbach
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (C.E.); (A.-M.K.B.); (C.T.)
- Mildred Scheel Early Career Center, Department of Urology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Alicia-Marie K. Beier
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (C.E.); (A.-M.K.B.); (C.T.)
- Mildred Scheel Early Career Center, Department of Urology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Christian Thomas
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (C.E.); (A.-M.K.B.); (C.T.)
| | - Holger H. H. Erb
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany; (C.E.); (A.-M.K.B.); (C.T.)
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5
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Park S, Jeon JH, Park JA, Choi JK, Lee Y. Cleavage of HSP90β induced by histone deacetylase inhibitor and proteasome inhibitor modulates cell growth and apoptosis. Cell Stress Chaperones 2021; 26:129-139. [PMID: 32869129 PMCID: PMC7736425 DOI: 10.1007/s12192-020-01161-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022] Open
Abstract
HSP90, one of the molecular chaperones, contributes to protein stability in most living organisms. Previously, we found cleavage of HSP90 by caspase 10 in response to treatment with histone deacetylase inhibitor or proteasome inhibitor in leukemic cell lines. In this study, we investigated this phenomenon in various cell lines and found that HSP90 was cleaved by treatment with SAHA or MG132 in 6 out of 16 solid tumor cell lines. To further investigate the effects of HSP90 cleavage on cells, we introduced mutations to the potential cleavage sites of HSP90β and found that the 294th aspartic acid residue of the protein was mainly cleaved. In the K562 and Mia-PaCa-2 cell lines expressing HSP90β D294A, the cleavage of HSP90 by the treatment with SAHA or MG132 was reduced compared with the K562 and Mia-PaCa-2 cell lines expressing HSP90β WT. Accordingly, cell growth and survival were enhanced by HSP90β D294A expression. Therefore, we suggest that HSP90 cleavage widely occurs in several cell lines, and cleavage of HSP90 may have a potential for one of the mechanisms involved in the anti-tumor effects of known drugs and novel anti-tumor drug candidates.
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Affiliation(s)
- Sangkyu Park
- Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jae-Hyung Jeon
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jeong-A Park
- Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jun-Kyu Choi
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Younghee Lee
- Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, Chungbuk, 28644, Republic of Korea.
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6
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Chen L, Yang R, Kwan T, Tang C, Watt S, Zhang Y, Bourque G, Ge B, Downes K, Frontini M, Ouwehand WH, Lin JW, Soranzo N, Pastinen T, Chen L. Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells. Sci Data 2020; 7:376. [PMID: 33168820 PMCID: PMC7652884 DOI: 10.1038/s41597-020-00719-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Both poly(A) enrichment and ribosomal RNA depletion are commonly used for RNA sequencing. Either has its advantages and disadvantages that may lead to biases in the downstream analyses. To better access these effects, we carried out both ribosomal RNA-depleted and poly(A)-selected RNA-seq for CD4+ T naive cells isolated from 40 healthy individuals from the Blueprint Project. For these 40 individuals, the genomic and epigenetic data were also available. This dataset offers a unique opportunity to understand how library construction influences differential gene expression, alternative splicing and molecular QTL (quantitative loci) analyses for human primary cells.
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Affiliation(s)
- Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ruirui Yang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tony Kwan
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC, H3A 0G1, Canada
| | - Chao Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Yiming Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Guillaume Bourque
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC, H3A 0G1, Canada
| | - Bing Ge
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC, H3A 0G1, Canada
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- East Midlands and East of England Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW, UK
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Willem H Ouwehand
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Jing-Wen Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
| | - Tomi Pastinen
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, 2401 Gilham Rd., Kansas City, 64108 MO, USA.
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Fliedner A, Kirchner P, Wiesener A, van de Beek I, Waisfisz Q, van Haelst M, Scott DA, Lalani SR, Rosenfeld JA, Azamian MS, Xia F, Dutra-Clarke M, Martinez-Agosto JA, Lee H, Noh GJ, Lippa N, Alkelai A, Aggarwal V, Agre KE, Gavrilova R, Mirzaa GM, Straussberg R, Cohen R, Horist B, Krishnamurthy V, McWalter K, Juusola J, Davis-Keppen L, Ohden L, van Slegtenhorst M, de Man SA, Ekici AB, Gregor A, van de Laar I, Zweier C, Nelson SF, Grody WW, Lee H, Deignan JL, Kang SH, Arboleda VA, Senaratne TN, Dorrani N, Dutra-Clarke MS, Kianmahd J, Hinkamp FL, Neustadt AM, Martinez-Agosto JA, Fogel BL, Quintero-Rivera F. Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. Am J Hum Genet 2020; 107:544-554. [PMID: 32730804 DOI: 10.1016/j.ajhg.2020.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/25/2020] [Indexed: 01/14/2023] Open
Abstract
RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.
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Zhang Z, Tu K, Liu F, Liang M, Yu K, Wang Y, Luo Y, Yang B, Qin Y, He D, Jiang G, Huang O, Zou Y. FoxM1 promotes the migration of ovarian cancer cell through KRT5 and KRT7. Gene 2020; 757:144947. [PMID: 32659254 DOI: 10.1016/j.gene.2020.144947] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/28/2022]
Abstract
Forkhead box M1(FoxM1) played an important role in the pathogenesis of ovarian cancer, but its downstream molecular network is mysterious. Here, we combined ChIP-seq with RNA-seq analysis and identified 687 FoxM1-binding regions and 182 genes regulated by FoxM1. The above data pointed out that KRT5 and KRT7 were downstream target genes of FoxM1. Next, we used qPCR and Western blot to verify that FoxM1 knockdown inhibited the expression levels of KRT5 and KRT7. We also demonstrated that FoxM1 regulated KRT5 and KRT7 genes expression through binding a consensus AP-2 cis element, and showed that KRT5 and KRT7 deficiency could prevent the migration but not proliferation of SK-OV-3 cells. Finally, tissue microarray results indicated that KRT5 and KRT7 were highly expressed in ovarian cancer and positively correlated with FoxM1 expression. TCGA database showed that high expression of KRT5 and KRT7 could significantly reduce the survival rate of patients with ovarian cancer. The above results clarify the specific downstream molecular network of FoxM1 to promote the pathogenesis of ovarian cancer, and provide a basis experiment for the judgment of ovarian cancer prognosis and the design of drug targets.
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Affiliation(s)
- Ziyu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Kaijia Tu
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Faying Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Meirong Liang
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Kaihui Yu
- The College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Yaoqing Wang
- The College of Medicine, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Yong Luo
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Bicheng Yang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Yunna Qin
- Department of Pathology, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Deming He
- Department of Pathology, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China
| | - Guoyi Jiang
- Department of Obstetrics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, 330006, PR China
| | - Ouping Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China.
| | - Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China; Central Laboratory, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, PR China.
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Abstract
Chromatin is a highly dynamic structure that closely relates with gene expression in eukaryotes. ATP-dependent chromatin remodelling, histone post-translational modification and DNA methylation are the main ways that mediate such plasticity. The histone variant H2A.Z is frequently encountered in eukaryotes, and can be deposited or removed from nucleosomes by chromatin remodelling complex SWR1 or INO80, respectively, leading to altered chromatin state. H2A.Z has been found to be involved in a diverse range of biological processes, including genome stability, DNA repair and transcriptional regulation. Due to their formidable production of secondary metabolites, filamentous fungi play outstanding roles in pharmaceutical production, food safety and agriculture. During the last few years, chromatin structural changes were proven to be a key factor associated with secondary metabolism in fungi. However, studies on the function of H2A.Z are scarce. Here, we summarize current knowledge of H2A.Z functions with a focus on filamentous fungi. We propose that H2A.Z is a potential target involved in the regulation of secondary metabolite biosynthesis by fungi.
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10
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Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 343] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
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Haijes HA, Koster MJE, Rehmann H, Li D, Hakonarson H, Cappuccio G, Hancarova M, Lehalle D, Reardon W, Schaefer GB, Lehman A, van de Laar IMBH, Tesselaar CD, Turner C, Goldenberg A, Patrier S, Thevenon J, Pinelli M, Brunetti-Pierri N, Prchalová D, Havlovicová M, Vlckova M, Sedláček Z, Lopez E, Ragoussis V, Pagnamenta AT, Kini U, Vos HR, van Es RM, van Schaik RFMA, van Essen TAJ, Kibaek M, Taylor JC, Sullivan J, Shashi V, Petrovski S, Fagerberg C, Martin DM, van Gassen KLI, Pfundt R, Falk MJ, McCormick EM, Timmers HTM, van Hasselt PM. De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. Am J Hum Genet 2019; 105:283-301. [PMID: 31353023 PMCID: PMC6699192 DOI: 10.1016/j.ajhg.2019.06.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/30/2019] [Indexed: 11/26/2022] Open
Abstract
The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.
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Affiliation(s)
- Hanneke A Haijes
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Maria J E Koster
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Holger Rehmann
- Expertise Center for Structural Biology, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Dong Li
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Daphne Lehalle
- Department of Genetics, Centre Hospitalier Universitaire de Dijon, 21000 Dijon, France
| | - Willie Reardon
- Department of Clinical and Medical Genetics, Our Lady's Hospital for Sick Children, D12 N512 Dublin, Ireland
| | - G Bradley Schaefer
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, AR 72223, USA
| | - Anna Lehman
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus Medical University Center Rotterdam, 3000 CA Rotterdam, the Netherlands
| | - Coranne D Tesselaar
- Department of Pediatrics, Amphia Hospital Breda, 4818 CK Breda, the Netherlands
| | - Clesson Turner
- Department of Clinical Genetics and Pediatrics, Walter Reed National Military Medical Center, Bethesda, Maryland, MD 20814, USA
| | - Alice Goldenberg
- Department of Genetics, Rouen University Hospital, Centre de Référence Anomalies du Développement, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
| | - Sophie Patrier
- Department of Pathology, Rouen University Hospital, Centre de Référence Anomalies du Développement, 76000 Rouen, France
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalier Universitaire de Grenoble, 38700 Grenoble, France
| | - Michele Pinelli
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Vlckova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Zdeněk Sedláček
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Elena Lopez
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Vassilis Ragoussis
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Alistair T Pagnamenta
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Usha Kini
- Department of Genomic Medicine, Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, OX3 7LE Oxford, UK
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Richard F M A van Schaik
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Ton A J van Essen
- Department of Clinical Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Maria Kibaek
- H.C. Andersen Children Hospital, Odense University Hospital, 5000 Odense, Denmark
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Slave Petrovski
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, CB4 0WG Cambridge, United Kingdom; Department of Medicine, the University of Melbourne, VIC 3010 Melbourne, Australia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, MI 48109, USA
| | - Koen L I van Gassen
- Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center Nijmegen, 6525 HR Nijmegen, the Netherlands
| | - Marni J Falk
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Department of Urology, University Medical Center Freiburg, University of Freiburg, 79110 Freiburg, Germany
| | - Peter M van Hasselt
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands.
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12
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Feng ZX, Li QZ, Meng JJ. Modeling the relationship of diverse genomic signatures to gene expression levels with the regulation of long-range enhancer-promoter interactions. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-0089-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Long C, E. C, Da LT, Yu J. A Viral T7 RNA Polymerase Ratcheting Along DNA With Fidelity Control. Comput Struct Biotechnol J 2019; 17:638-644. [PMID: 31193497 PMCID: PMC6535458 DOI: 10.1016/j.csbj.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022] Open
Abstract
RNA polymerase (RNAP) from bacteriophage T7 is a representative single-subunit viral RNAP that can transcribe with high promoter activities without assistances from transcription factors. We accordingly studied this small transcription machine computationally as a model system to understand underlying mechanisms of mechano-chemical coupling and fidelity control in the RNAP transcription elongation. Here we summarize our computational work from several recent publications to demonstrate first how T7 RNAP translocates via Brownian alike motions along DNA right after the catalytic product release. Then we show how the backward translocation motions are prevented at post-translocation upon successful nucleotide incorporation, which is also subject to stepwise nucleotide selection and acts as a pawl for "selective ratcheting". The structural dynamics and energetics features revealed from our atomistic molecular dynamics (MD) simulations and related analyses on the single-subunit T7 RNAP thus provided detailed and quantitative characterizations on the Brownian-ratchet working scenario of a prototypical transcription machine with sophisticated nucleotide selectivity for fidelity control. The presented mechanisms can be more or less general for structurally similar viral or mitochondrial RNAPs and some of DNA polymerases, or even for the RNAP engine of the more complicated transcription machinery in higher organisms.
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Affiliation(s)
- Chunhong Long
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Chao E.
- Beijing Computational Science Research Center, Beijing, 100193, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Jin Yu
- Beijing Computational Science Research Center, Beijing, 100193, China
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14
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Wu TH, Shi L, Lowe AW, Nicolls MR, Kao PN. Inducible expression of immediate early genes is regulated through dynamic chromatin association by NF45/ILF2 and NF90/NF110/ILF3. PLoS One 2019; 14:e0216042. [PMID: 31022259 PMCID: PMC6483252 DOI: 10.1371/journal.pone.0216042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 04/14/2019] [Indexed: 12/11/2022] Open
Abstract
Immediate early gene (IEG) transcription is rapidly activated by diverse stimuli. This transcriptional regulation is assumed to involve constitutively expressed nuclear factors that are targets of signaling cascades initiated at the cell membrane. NF45 (encoded by ILF2) and its heterodimeric partner NF90/NF110 (encoded by ILF3) are chromatin-interacting proteins that are constitutively expressed and localized predominantly in the nucleus. Previously, NF90/NF110 chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) in K562 erythroleukemia cells revealed its enriched association with chromatin at active promoters and strong enhancers. NF90/NF110 specifically occupied the promoters of IEGs. Here, ChIP in serum-starved HEK293 cells demonstrated that NF45 and NF90/NF110 pre-exist and specifically occupy the promoters of IEG transcription factors EGR1, FOS and JUN. Cellular stimulation with phorbol myristyl acetate increased NF90/NF110 chromatin association, while decreasing NF45 chromatin association at promoters of EGR1, FOS and JUN. In HEK293 cells stably transfected with doxycycline-inducible shRNA vectors targeting NF90/NF110 or NF45, doxycycline-mediated knockdown of NF90/NF110 or NF45 attenuated the inducible expression of EGR1, FOS, and JUN at the levels of transcription, RNA and protein. Dynamic chromatin association of NF45 and NF90/NF110 at IEG promoters are observed upon stimulation, and NF45 and NF90/NF110 contribute to inducible transcription of IEGs. NF45 and NF90/NF110 operate as chromatin regulators of the immediate early response.
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Affiliation(s)
- Ting-Hsuan Wu
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lingfang Shi
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Anson W. Lowe
- Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark R. Nicolls
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter N. Kao
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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15
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Zheng Y, Fu X, Wang L, Zhang W, Zhou P, Zhang X, Zeng W, Chen J, Cao Z, Jia K, Li S. Comparative analysis of MicroRNA expression in dog lungs infected with the H3N2 and H5N1 canine influenza viruses. Microb Pathog 2018; 121:252-261. [PMID: 29772263 DOI: 10.1016/j.micpath.2018.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022]
Abstract
MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach. To identify the roles of microRNAs in viral pathogenicity and the host immune response, microRNA target genes were predicted, and their functions were analyzed using bioinformatics software. A total of 229 microRNAs were upregulated in the H5N1 infection group compared with those in the H3N2 infection group, and 166 microRNAs were downregulated. MicroRNA target genes in the H5N1 group were more significantly involved in metabolic pathways, such as glycerolipid metabolism and glycerophospholipid metabolism, than those in the H3N2 group. The inhibition of metabolic pathways may lead to appetite loss, weight loss and weakened immunity. Moreover, miR-485, miR-144, miR-133b, miR-4859-5p, miR-6902-3p, miR-7638, miR-1307-3p and miR-1346 were significantly altered microRNAs that potentially led to the inhibition of innate immune pathways and the heightened pathogenicity of H5N1 compared with that of H3N2 in dogs. This study deepens our understanding of the complex relationships among microRNAs, the influenza virus-mediated immune response and immune injury in dogs.
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Affiliation(s)
- Yun Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Xinliang Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Lifang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Wenyan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Pei Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Xin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Weijie Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China
| | - Jidang Chen
- School of Life Science and Engineering, Foshan University, Guangzhou, People's Republic of China
| | - Zongxi Cao
- Hainan Academy of Agricultural Science, Hainan, People's Republic of China
| | - Kun Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China.
| | - Shoujun Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, Guangdong Province 510642, People's Republic of China; Guangdong Provincial Pet Engineering Technology Research Center, Guangzhou, Guangdong Province 510642, People's Republic of China.
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16
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Wu TH, Shi L, Adrian J, Shi M, Nair RV, Snyder MP, Kao PN. NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells. PLoS One 2018; 13:e0193126. [PMID: 29590119 PMCID: PMC5873942 DOI: 10.1371/journal.pone.0193126] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 11/19/2022] Open
Abstract
NF90 and splice variant NF110 are DNA- and RNA-binding proteins encoded by the Interleukin enhancer-binding factor 3 (ILF3) gene that have been established to regulate RNA splicing, stabilization and export. The roles of NF90 and NF110 in regulating transcription as chromatin-interacting proteins have not been comprehensively characterized. Here, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) identified 9,081 genomic sites specifically occupied by NF90/NF110 in K562 cells. One third of NF90/NF110 peaks occurred at promoters of annotated genes. NF90/NF110 occupancy colocalized with chromatin marks associated with active promoters and strong enhancers. Comparison with 150 ENCODE ChIP-seq experiments revealed that NF90/NF110 clustered with transcription factors exhibiting preference for promoters over enhancers (POLR2A, MYC, YY1). Differential gene expression analysis following shRNA knockdown of NF90/NF110 in K562 cells revealed that NF90/NF110 activates transcription factors that drive growth and proliferation (EGR1, MYC), while attenuating differentiation along the erythroid lineage (KLF1). NF90/NF110 associates with chromatin to hierarchically regulate transcription factors that promote proliferation and suppress differentiation.
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Affiliation(s)
- Ting-Hsuan Wu
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (PNK.); (THW)
| | - Lingfang Shi
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jessika Adrian
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ramesh V. Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter N. Kao
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (PNK.); (THW)
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17
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Maticzka D, Ilik IA, Aktas T, Backofen R, Akhtar A. uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins. Nat Commun 2018; 9:1142. [PMID: 29559621 PMCID: PMC5861125 DOI: 10.1038/s41467-018-03575-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/26/2018] [Indexed: 01/24/2023] Open
Abstract
RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation, and stability of mRNAs. We describe ultraviolet crosslinking and affinity purification (uvCLAP), an easy-to-use, robust, reproducible, and high-throughput method to determine in vivo targets of RBPs. uvCLAP is fast and does not rely on radioactive labeling of RNA. We investigate binding of 15 RBPs from fly, mouse, and human cells to test the method's performance and applicability. Multiplexing of signal and control libraries enables straightforward comparison of samples. Experiments for most proteins achieve high enrichment of signal over background. A point mutation and a natural splice isoform that change the RBP subcellular localization dramatically alter target selection without changing the targeted RNA motif, showing that compartmentalization of RBPs can be used as an elegant means to generate RNA target specificity.
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Affiliation(s)
- Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany
| | - Ibrahim Avsar Ilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Tugce Aktas
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany.
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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18
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Barbosa-Camacho AA, Méndez-Hernández LE, Lara-Chacón B, Peña-Gómez SG, Romero V, González-González R, Guerra-Moreno JA, Robledo-Rivera AY, Sánchez-Olea R, Calera MR. The Gpn3 Q279* cancer-associated mutant inhibits Gpn1 nuclear export and is deficient in RNA polymerase II nuclear targeting. FEBS Lett 2017; 591:3555-3566. [PMID: 28940195 DOI: 10.1002/1873-3468.12856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 11/07/2022]
Abstract
Gpn3 is required for RNA polymerase II (RNAPII) nuclear targeting. Here, we investigated the effect of a cancer-associated Q279* nonsense mutation in Gpn3 cellular function. Employing RNAi, we replaced endogenous Gpn3 by wt or Q279* RNAi-resistant Gpn3R in epithelial model cells. RNAPII nuclear accumulation and transcriptional activity were markedly decreased in cells expressing only Gpn3R Q279*. Wild-type Gpn3R localized to the cytoplasm but a fraction of Gpn3R Q279* entered the cell nucleus and inhibited Gpn1-EYFP nuclear export. This property and the transcriptional deficit in Gpn3R Q279*-expressing cells required a PDZ-binding motif generated by the Q279* mutation. We conclude that an acquired PDZ-binding motif in Gpn3 Q279* caused Gpn3 nuclear entry, and inhibited Gpn1 nuclear export and Gpn3-mediated RNAPII nuclear targeting.
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Affiliation(s)
| | | | | | | | - Violeta Romero
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Mexico
| | | | | | | | | | - Mónica R Calera
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Mexico
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19
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Sdano MA, Fulcher JM, Palani S, Chandrasekharan MB, Parnell TJ, Whitby FG, Formosa T, Hill CP. A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. eLife 2017; 6:28723. [PMID: 28826505 PMCID: PMC5599234 DOI: 10.7554/elife.28723] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/11/2017] [Indexed: 01/01/2023] Open
Abstract
We determined that the tandem SH2 domain of S. cerevisiae Spt6 binds the linker region of the RNA polymerase II subunit Rpb1 rather than the expected sites in its heptad repeat domain. The 4 nM binding affinity requires phosphorylation at Rpb1 S1493 and either T1471 or Y1473. Crystal structures showed that pT1471 binds the canonical SH2 pY site while pS1493 binds an unanticipated pocket 70 Å distant. Remarkably, the pT1471 phosphate occupies the phosphate-binding site of a canonical pY complex, while Y1473 occupies the position of a canonical pY side chain, with the combination of pT and Y mimicking a pY moiety. Biochemical data and modeling indicate that pY1473 can form an equivalent interaction, and we find that pT1471/pS1493 and pY1473/pS1493 combinations occur in vivo. ChIP-seq and genetic analyses demonstrate the importance of these interactions for recruitment of Spt6 to sites of transcription and for the maintenance of repressive chromatin.
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Affiliation(s)
- Matthew A Sdano
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - James M Fulcher
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Timothy J Parnell
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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20
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Chen S, Wang H, Huang YF, Li ML, Cheng JH, Hu P, Lu CH, Zhang Y, Liu N, Tzeng CM, Zhang ZM. WW domain-binding protein 2: an adaptor protein closely linked to the development of breast cancer. Mol Cancer 2017; 16:128. [PMID: 28724435 PMCID: PMC5518133 DOI: 10.1186/s12943-017-0693-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/10/2017] [Indexed: 01/27/2023] Open
Abstract
The WW domain is composed of 38 to 40 semi-conserved amino acids shared with structural, regulatory, and signaling proteins. WW domain-binding protein 2 (WBP2), as a binding partner of WW domain protein, interacts with several WW-domain-containing proteins, such as Yes kinase-associated protein (Yap), paired box gene 8 (Pax8), WW-domain-containing transcription regulator protein 1 (TAZ), and WW-domain-containing oxidoreductase (WWOX) through its PPxY motifs within C-terminal region, and further triggers the downstream signaling pathway in vitro and in vivo. Studies have confirmed that phosphorylated form of WBP2 can move into nuclei and activate the transcription of estrogen receptor (ER) and progesterone receptor (PR), whose expression were the indicators of breast cancer development, indicating that WBP2 may participate in the progression of breast cancer. Both overexpression of WBP2 and activation of tyrosine phosphorylation upregulate the signal cascades in the cross-regulation of the Wnt and ER signaling pathways in breast cancer. Following the binding of WBP2 to the WW domain region of TAZ which can accelerate migration, invasion and is required for the transformed phenotypes of breast cancer cells, the transformation of epithelial to mesenchymal of MCF10A is activated, suggesting that WBP2 is a key player in regulating cell migration. When WBP2 binds with WWOX, a tumor suppressor, ER transactivation and tumor growth can be suppressed. Thus, WBP2 may serve as a molecular on/off switch that controls the crosstalk between E2, WWOX, Wnt, TAZ, and other oncogenic signaling pathways. This review interprets the relationship between WBP2 and breast cancer, and provides comprehensive views about the function of WBP2 in the regulation of the pathogenesis of breast cancer and endocrine therapy in breast cancer treatment.
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Affiliation(s)
- Shuai Chen
- Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China
| | - Han Wang
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China
| | - Yu-Fan Huang
- Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361005, People's Republic of China
| | - Ming-Li Li
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China
| | - Jiang-Hong Cheng
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China
| | - Peng Hu
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China.,INNOVA Cell Theranostics/Clinics and TRANSLA Health Group, Yangzhou, Jiangsu, People's Republic of China
| | - Chuan-Hui Lu
- Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361005, People's Republic of China
| | - Ya Zhang
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China.,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China
| | - Na Liu
- Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361005, People's Republic of China
| | - Chi-Meng Tzeng
- Translational Medicine Research Center (TMRC), School of Pharmaceutical Science, Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. .,Key Laboratory for Cancer T-Cell Therapeutics and Clinical Translation (CTCTCT), Xiamen, Fujian, 361005, People's Republic of China. .,INNOVA Cell Theranostics/Clinics and TRANSLA Health Group, Yangzhou, Jiangsu, People's Republic of China.
| | - Zhi-Ming Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361005, People's Republic of China. .,Teaching Hospital of Fujian Medical University, Fuzhou, Fujian, 350004, People's Republic of China.
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21
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Large normal-range TBP and ATXN7 CAG repeat lengths are associated with increased lifetime risk of depression. Transl Psychiatry 2017; 7:e1143. [PMID: 28585930 PMCID: PMC5534943 DOI: 10.1038/tp.2017.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 04/20/2017] [Indexed: 01/27/2023] Open
Abstract
Depression is one of the most prevalent and debilitating psychiatric disorders worldwide. Recently, we showed that both relatively short and relatively long cytosine-adenine-guanine (CAG) repeats in the huntingtin gene (HTT) are associated with an increased risk of lifetime depression. However, to what extent the variations in CAG repeat length in the other eight polyglutamine disease-associated genes (PDAGs) are associated with depression is still unknown. We determined the CAG repeat sizes of ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1 and AR in two well-characterized Dutch cohorts-the Netherlands Study of Depression and Anxiety and the Netherlands Study of Depression in Older Persons-including 2165 depressed and 1058 non-depressed individuals-aged 18-93 years. The association between PDAG CAG repeat size and the risk for depression was assessed via binary logistic regression. We found that the odds ratio (OR) for lifetime depression was significantly higher for individuals with >10, compared with subjects with ≤10, CAG repeats in both ATXN7 alleles (OR=1.90, confidence interval (CI) 1.26-2.85). For TBP we found a similar association: A CAG repeat length exceeding the median in both alleles was associated with an increased risk for lifetime depression (OR=1.33, CI 1.00-1.76). In conclusion, we observed that carriers of either ATXN7 or TBP alleles with relatively large CAG repeat sizes in both alleles had a substantially increased risk of lifetime depression. Our findings provide critical evidence for the notion that repeat polymorphisms can act as complex genetic modifiers of depression.
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22
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You Q, Yan H, Liu Y, Yi X, Zhang K, Xu W, Su Z. A systemic identification approach for primary transcription start site of Arabidopsis miRNAs from multidimensional omics data. Funct Integr Genomics 2016; 17:353-363. [PMID: 28032247 DOI: 10.1007/s10142-016-0541-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023]
Abstract
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts. Here, we used the model plant Arabidopsis thaliana to improve the ability to identify candidate promoter locations in intergenic miRNAs and to determine rules for identifying primary transcription start sites of miRNAs by integrating high-throughput omics data, such as the DNase I hypersensitive sites, chromatin immunoprecipitation-sequencing of polymerase II and H3K4me3, as well as high throughput transcriptomic data. As a result, 93% of refined primary transcripts could be confirmed by the primer pairs from a previous study. Cis-element and secondary structure analyses also supported the feasibility of our results. This work will contribute to the primary transcriptional regulatory analysis of miRNAs, and the conserved regulatory pattern may be a suitable miRNA characteristic in other plant species.
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Affiliation(s)
- Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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23
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Cho WK, Jayanth N, Mullen S, Tan TH, Jung YJ, Cissé II. Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing. Sci Rep 2016; 6:35949. [PMID: 27782203 PMCID: PMC5080603 DOI: 10.1038/srep35949] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/07/2016] [Indexed: 12/19/2022] Open
Abstract
Live cell imaging of mammalian RNA polymerase II (Pol II) has previously relied on random insertions of exogenous, mutant Pol II coupled with the degradation of endogenous Pol II using a toxin, α-amanitin. Therefore, it has been unclear whether over-expression of labeled Pol II under an exogenous promoter may have played a role in reported Pol II dynamics in vivo. Here we label the endogenous Pol II in mouse embryonic fibroblast (MEF) cells using the CRISPR/Cas9 gene editing system. Using single-molecule based super-resolution imaging in the living cells, we captured endogenous Pol II clusters. Consistent with previous studies, we observed that Pol II clusters were short-lived (cluster lifetime ~8 s) in living cells. Moreover, dynamic responses to serum-stimulation, and drug-mediated transcription inhibition were all in agreement with previous observations in the exogenous Pol II MEF cell line. Our findings suggest that previous exogenously tagged Pol II faithfully recapitulated the endogenous polymerase clustering dynamics in living cells, and our approach may in principle be used to directly label transcription factors for live cell imaging.
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Affiliation(s)
- Won-Ki Cho
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Namrata Jayanth
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Susan Mullen
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Tzer Han Tan
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yoon J Jung
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ibrahim I Cissé
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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24
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Chizzali C, Gusberti M, Schouten HJ, Gessler C, Broggini GAL. Cisgenic Rvi6 scab-resistant apple lines show no differences in Rvi6 transcription when compared with conventionally bred cultivars. PLANTA 2016; 243:635-644. [PMID: 26586177 DOI: 10.1007/s00425-015-2432-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
The expression of the apple scab resistance gene Rvi6 in different apple cultivars and lines is not modulated by biotic or abiotic factors. All commercially important apple cultivars are susceptible to Venturia inaequalis, the causal organism of apple scab. A limited number of apple cultivars were bred to express the resistance gene Vf from the wild apple genotype Malus floribunda 821. Positional cloning of the Vf locus allowed the identification of the Rvi6 (formerly HcrVf2) scab resistance gene that was subsequently used to generate cisgenic apple lines. It is important to understand and compare how this resistance gene is transcribed and modulated during infection in conventionally bred cultivars and in cisgenic lines. The aim of this work was to study the transcription pattern of Rvi6 in three classically bred apple cultivars and six lines of 'Gala' genetically modified to express Rvi6. Rvi6 transcription was analyzed at two time points using quantitative real-time PCR (RT-qPCR) following inoculation with V. inaequalis conidia or water. Rvi6 transcription was assessed in relation to five reference genes. β-Actin, RNAPol, and UBC were the most suited to performing RT-qPCR experiments on Malus × domestica. Inoculation with V. inaequalis conidia under conditions conducive to scab infection failed to produce any significant changes to the transcription level of Rvi6. Rvi6 expression levels were inconsistent in response to external treatments in the different apple cultivars, and transgenic, intragenic or cisgenic lines.
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Affiliation(s)
- Cornelia Chizzali
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745, Jena, Germany.
| | - Michele Gusberti
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Henk J Schouten
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Cesare Gessler
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Giovanni A L Broggini
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
- Agroscope, Institute for Plant Production Sciences, Schloss 1, 8820, Wädenswil, Switzerland
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25
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MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A 2015; 112:E3457-65. [PMID: 26080409 DOI: 10.1073/pnas.1424804112] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.
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26
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Frege T, Uversky VN. Intrinsically disordered proteins in the nucleus of human cells. Biochem Biophys Rep 2015; 1:33-51. [PMID: 29124132 PMCID: PMC5668563 DOI: 10.1016/j.bbrep.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the disordered nuclear proteins.
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Affiliation(s)
- Telma Frege
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- GenomeNext LLC, 175 South 3rd Street, Suite 200, Columbus OH 43215, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer׳s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Department of Biology, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Correspondence to: Department of Molecular, Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC07, Tampa, FL 33612, USA. Tel.: +1 813 974 5816; fax: +1 813 974 7357.
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27
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Schubert V, Weisshart K. Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1687-98. [PMID: 25740920 PMCID: PMC4357323 DOI: 10.1093/jxb/erv091] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
RNA polymerase II (RNAPII) is responsible for the transcription of most eukaryotic protein-coding genes. Analysing the topological distribution and quantification of RNAPII can contribute to understanding its function in interphase nuclei. Previously it was shown that RNAPII molecules in plant nuclei form reticulate structures within euchromatin of differentiated Arabidopsis thaliana nuclei rather than being organized in distinct 'transcription factories' as observed in mammalian nuclei. Immunosignal intensity measurements based on specific antibody labelling in maximum intensity projections of image stacks acquired by structured illumination microscopy (SIM) suggested a relative proportional increase of RNAPII in endopolyploid plant nuclei. Here, photoactivated localization microscopy (PALM) was applied to determine the absolute number and distribution of active and inactive RNAPII molecules in differentiated A. thaliana nuclei. The proportional increase of RNAPII during endopolyploidization is confirmed, but it is also shown that PALM measurements are more reliable than those based on SIM in terms of quantification. The single molecule localization results show that, although RNAPII molecules are globally dispersed within plant euchromatin, they also aggregate within smaller distances as described for mammalian transcription factories.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
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28
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Park S, Park JA, Kim YE, Song S, Kwon HJ, Lee Y. Suberoylanilide hydroxamic acid induces ROS-mediated cleavage of HSP90 in leukemia cells. Cell Stress Chaperones 2015; 20:149-57. [PMID: 25119188 PMCID: PMC4255254 DOI: 10.1007/s12192-014-0533-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 07/03/2014] [Accepted: 07/29/2014] [Indexed: 12/20/2022] Open
Abstract
Heat shock protein 90 (HSP90) is a molecular chaperone that supports stability of client proteins. We found that HSP90 was cleaved to 55 kDa protein after treatment with histone deacetylase (HDAC) inhibitors including suberoylanilide hydroxamic acid (SAHA) in several leukemia cell lines. We further analyzed molecular changes induced by SAHA in K562 cells. The SAHA-induced cleavage of HSP90 was blocked by a pan-caspase inhibitor, z-VAD-fmk, implying that the process is dependent on caspase activity. However, the experiments using antagonistic and agonistic Fas antibodies revealed that the cleavage of HSP90 was not dependent on Fas signaling. SAHA induced generation of reactive oxygen species (ROS), and the cleavage of HSP90 was blocked by a ROS scavenger N-acetylcystein (NAC). We also confirmed that hydrogen peroxide (H2O2) induced cleavage of HSP90 in a similar manner. Caspase 2, 3, 4, 6, 8, and 10 were activated by treatment with SAHA, and the activities were reduced by the pretreatment of NAC. Treatment of the cells with caspase 10 inhihitor, but not other inhibitors of caspases activated by SAHA, prevented cleavage of HSP90 by SAHA. SAHA-induced ROS generation and HSP90 cleavage were dependent on newly synthesized unknown proteins. Taken together, our results suggest that the cleavage of HSP90 by SAHA is mediated by ROS generation and caspase 10 activation. HSP90 cleavage may provide an additional mechanism involved in anti-cancer effects of HDAC inhibitors.
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Affiliation(s)
- Sangkyu Park
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Jeong-A Park
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Young-Eun Kim
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Sukgil Song
- />College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Hyung-Joo Kwon
- />Center for Medical Science Research, Hallym University, Chuncheon, 200-720 Republic of Korea
- />Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 200-720 Republic of Korea
| | - Younghee Lee
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Biotechnology Research Institute, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- />Department of Biochemistry, College of Natural Sciences, Chungbuk National University, 52 Naesudong-Ro, Heungduk-Gu, Cheongju, Chungbuk 361-763 Republic of Korea
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29
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Yu J, Da LT, Huang X. Constructing kinetic models to elucidate structural dynamics of a complete RNA polymerase II elongation cycle. Phys Biol 2014; 12:016004. [DOI: 10.1088/1478-3975/12/1/016004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development 2014; 142:118-27. [PMID: 25480920 DOI: 10.1242/dev.114843] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We show here that the chromatin remodeler Chd1 is required for transcriptional output and development of the mouse epiblast. Chd1(-/-) embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5 and fail to grow, to become patterned or to gastrulate. Removal of p53 allows progression of Chd1(-/-) mutants only to E7.0-8.0, highlighting the crucial requirement for Chd1 during early post-implantation development. Chd1(-/-) embryonic stem cells (ESCs) have a self-renewal defect and a genome-wide reduction in transcriptional output at both known mRNAs and intergenic transcripts. These transcriptional defects were only uncovered when cell number-normalized approaches were used, and correlate with a lower engagement of RNAP II with transcribed genes in Chd1(-/-) ESCs. We further show that Chd1 directly binds to ribosomal DNA, and that both Chd1(-/-) epiblast cells in vivo and ESCs in vitro express significantly lower levels of ribosomal RNA. In agreement with these findings, mutant cells in vivo and in vitro exhibit smaller and more elongated nucleoli. Thus, the RNA output by both Pol I and II is reduced in Chd1(-/-) cells. Our data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinctly rapid growth of the mouse epiblast.
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Affiliation(s)
- Marcela Guzman-Ayala
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Michael Sachs
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Fong Ming Koh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Courtney Onodera
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Institute for Human Genetics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Department of Epidemiology and Biostatistics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Priscilla Wong
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Rachel Nitta
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Jun S Song
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Institute for Human Genetics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Department of Epidemiology and Biostatistics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
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31
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Schubert V. RNA polymerase II forms transcription networks in rye and Arabidopsis nuclei and its amount increases with endopolyploidy. Cytogenet Genome Res 2014; 143:69-77. [PMID: 25060696 DOI: 10.1159/000365233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RNA polymerase II (RNAPII) is responsible for the transcription of most eukaryotic genes. In mammalian nuclei, RNAPII is mainly localized in relatively few distinct transcription factories. In this study--applying super-resolution microscopy--it is shown that in plants, inactive (non-phosphorylated) and active (phosphorylated) RNAPII modifications compose distinct 'transcription networks' within the euchromatin. These reticulate structures sometimes attach to each other, but they are absent from heterochromatin and nucleoli. The global RNAPII distribution within nuclei is not influenced by interphase chromatin organization such as Rabl (rye) versus non-Rabl (Arabidopsis thaliana) orientation. Replication of sister chromatids without cell division causes endopolyploidy, a phenomenon widespread in plants and animals. Endopolyploidy raises the number of gene copies per nucleus. Here, it is shown that the amounts of active and inactive RNAPII enzymes in differentiated 2-32C leaf nuclei of A. thaliana proportionally increase with rising endopolyploidy. Thus, increasing the transcriptional activity of cells and tissues seems to be an important function of endopolyploidy.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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32
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Programming biological operating systems: genome design, assembly and activation. Nat Methods 2014; 11:521-6. [PMID: 24781325 DOI: 10.1038/nmeth.2894] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/22/2014] [Indexed: 12/21/2022]
Abstract
The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.
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Wang B, Predeus AV, Burton ZF, Feig M. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J 2014; 105:767-75. [PMID: 23931324 DOI: 10.1016/j.bpj.2013.05.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022] Open
Abstract
An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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Cross-talk of phosphorylation and prolyl isomerization of the C-terminal domain of RNA Polymerase II. Molecules 2014; 19:1481-511. [PMID: 24473209 PMCID: PMC4350670 DOI: 10.3390/molecules19021481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/06/2014] [Accepted: 01/21/2014] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications of the heptad repeat sequences in the C-terminal domain (CTD) of RNA polymerase II (Pol II) are well recognized for their roles in coordinating transcription with other nuclear processes that impinge upon transcription by the Pol II machinery; and this is primarily achieved through CTD interactions with the various nuclear factors. The identification of novel modifications on new regulatory sites of the CTD suggests that, instead of an independent action for all modifications on CTD, a combinatorial effect is in operation. In this review we focus on two well-characterized modifications of the CTD, namely serine phosphorylation and prolyl isomerization, and discuss the complex interplay between the enzymes modifying their respective regulatory sites. We summarize the current understanding of how the prolyl isomerization state of the CTD dictates the specificity of writers (CTD kinases), erasers (CTD phosphatases) and readers (CTD binding proteins) and how that correlates to transcription status. Subtle changes in prolyl isomerization states cannot be detected at the primary sequence level, we describe the methods that have been utilized to investigate this mode of regulation. Finally, a general model of how prolyl isomerization regulates the phosphorylation state of CTD, and therefore transcription-coupled processes, is proposed.
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Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keleş S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 2013; 9:e1003565. [PMID: 23818864 PMCID: PMC3688515 DOI: 10.1371/journal.pgen.1003565] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/29/2013] [Indexed: 01/05/2023] Open
Abstract
FNR is a well-studied global regulator of anaerobiosis, which is widely conserved across bacteria. Despite the importance of FNR and anaerobiosis in microbial lifestyles, the factors that influence its function on a genome-wide scale are poorly understood. Here, we report a functional genomic analysis of FNR action. We find that FNR occupancy at many target sites is strongly influenced by nucleoid-associated proteins (NAPs) that restrict access to many FNR binding sites. At a genome-wide level, only a subset of predicted FNR binding sites were bound under anaerobic fermentative conditions and many appeared to be masked by the NAPs H-NS, IHF and Fis. Similar assays in cells lacking H-NS and its paralog StpA showed increased FNR occupancy at sites bound by H-NS in WT strains, indicating that large regions of the genome are not readily accessible for FNR binding. Genome accessibility may also explain our finding that genome-wide FNR occupancy did not correlate with the match to consensus at binding sites, suggesting that significant variation in ChIP signal was attributable to cross-linking or immunoprecipitation efficiency rather than differences in binding affinities for FNR sites. Correlation of FNR ChIP-seq peaks with transcriptomic data showed that less than half of the FNR-regulated operons could be attributed to direct FNR binding. Conversely, FNR bound some promoters without regulating expression presumably requiring changes in activity of condition-specific transcription factors. Such combinatorial regulation may allow Escherichia coli to respond rapidly to environmental changes and confer an ecological advantage in the anaerobic but nutrient-fluctuating environment of the mammalian gut. Regulation of gene expression by transcription factors (TFs) is key to adaptation to environmental changes. Our comprehensive, genome-scale analysis of a prototypical global TF, the anaerobic regulator FNR from Escherichia coli, leads to several novel and unanticipated insights into the influences on FNR binding genome-wide and the complex structure of bacterial regulons. We found that binding of NAPs restricts FNR binding at a subset of sites, suggesting that the bacterial genome is not freely accessible for FNR binding. Our finding that less than half of the predicted FNR binding sites were occupied in vivo further challenges the utility of using bioinformatic searches alone to predict regulon structure, reinforcing the need for experimental determination of TF binding. By correlating the occupancy data with transcriptomic data, we confirm that FNR serves as a global signal of anaerobiosis but expression of some operons in the FNR regulon require other regulators sensitive to alternative environmental stimuli. Thus, FNR binding and regulation appear to depend on both the nucleoprotein structure of the chromosome and on combinatorial binding of FNR with other regulators. Both of these phenomena are typical of TF binding in eukaryotes; our results establish that they are also features of bacterial TF binding.
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Affiliation(s)
- Kevin S. Myers
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Huihuang Yan
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Irene M. Ong
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Dongjun Chung
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kun Liang
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Frances Tran
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
| | - Patricia J. Kiley
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (RL); (PJK)
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Pandey P, Houben A, Kumlehn J, Melzer M, Rutten T. Chromatin alterations during pollen development in Hordeum vulgare. Cytogenet Genome Res 2013; 141:50-7. [PMID: 23735538 DOI: 10.1159/000351211] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2013] [Indexed: 11/19/2022] Open
Abstract
The dynamics of posttranslational histone modifications in relation to nuclear architecture has been analyzed during pollen development in Hordeum vulgare L. cv. Igri. Notwithstanding the asymmetry of cytokinesis associated with pollen mitosis I, immunolabeling revealed that the vegetative and generative nuclei initially display identical chromatin modification patterns. Yet, differential chromatin modification patterns between vegetative and generative nuclei emerge with the development of conspicuous differences in nuclear morphology as visualized by 4',6-diamidino-2-phenylindole staining. The temporal and spatial distribution of most histone modifications observed is in agreement with reduced gene activity in the generative nucleus and increased expression in the vegetative nucleus as indicated by immunolabeling of active RNA polymerase II. Signals of trimethylation of histone H3 lysine 27 proved to be particularly enriched in euchromatic domains of subtelomeric regions. In the context of nuclear differentiation in bicellular pollen, this modification became restricted to the vegetative nucleus, indicating a role in activating rather than suppressing gene expression. The presence of acetylated histone H3 at lysine 9 in the cytoplasm of the generative cell is indicative of a more complex, still unknown function of this particular modification.
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Affiliation(s)
- P Pandey
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
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37
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Strenkert D, Schmollinger S, Schroda M. Heat shock factor 1 counteracts epigenetic silencing of nuclear transgenes in Chlamydomonas reinhardtii. Nucleic Acids Res 2013; 41:5273-89. [PMID: 23585280 PMCID: PMC3664811 DOI: 10.1093/nar/gkt224] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We found previously that the Chlamydomonas HSP70A promoter counteracts transcriptional silencing of downstream promoters in a transgene setting. To elucidate the underlying mechanisms, we analyzed chromatin state and transgene expression in transformants containing HSP70A-RBCS2-ble (AR-ble) constructs harboring deletions/mutations in the A promoter. We identified histone modifications at transgenic R promoters indicative for repressive chromatin, i.e. low levels of histone H3/4 acetylation and H3-lysine 4 trimethylation and high levels of H3-lysine 9 monomethylation. Transgenic A promoters also harbor lower levels of active chromatin marks than the native A promoter, but levels were higher than those at transgenic R promoters. Strikingly, in AR promoter fusions, the chromatin state at the A promoter was transferred to R. This effect required intact HSE4, HSE1/2 and TATA-box in the A promoter and was mediated by heat shock factor (HSF1). However, time-course analyses in strains inducibly depleted of HSF1 revealed that a transcriptionally competent chromatin state alone was not sufficient for activating the R promoter, but required constitutive HSF1 occupancy at transgenic A. We propose that HSF1 constitutively forms a scaffold at the transgenic A promoter, presumably containing mediator and TFIID, from which local chromatin remodeling and polymerase II recruitment to downstream promoters is realized.
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Affiliation(s)
- Daniela Strenkert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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38
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Cai G, Chaban YL, Imasaki T, Kovacs JA, Calero G, Penczek PA, Takagi Y, Asturias FJ. Interaction of the mediator head module with RNA polymerase II. Structure 2012; 20:899-910. [PMID: 22579255 DOI: 10.1016/j.str.2012.02.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 02/09/2023]
Abstract
Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the activity of the preinitiation complex. However, the precise mode of interaction between Mediator and RNA polymerase II (RNAPII), and the mechanism of regulation by Mediator remain elusive. We used cryo-electron microscopy and reconstituted in vitro transcription assays to characterize a transcriptionally-active complex including the Mediator Head module and components of a minimum preinitiation complex (RNAPII, TFIIF, TFIIB, TBP, and promoter DNA). Our results reveal how the Head interacts with RNAPII, affecting its conformation and function.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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39
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Abstract
The transcription initiation factor TFIIH is a remarkable protein complex that has a fundamental role in the transcription of protein-coding genes as well as during the DNA nucleotide excision repair pathway. The detailed understanding of how TFIIH functions to coordinate these two processes is also providing an explanation for the phenotypes observed in patients who bear mutations in some of the TFIIH subunits. In this way, studies of TFIIH have revealed tight molecular connections between transcription and DNA repair and have helped to define the concept of 'transcription diseases'.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, BP 163, 67404 Illkirch Cedex, C. U., Strasbourg, France.
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40
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Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): An inference from nuclear protein-coding genes. Mol Phylogenet Evol 2011; 61:628-38. [DOI: 10.1016/j.ympev.2011.07.022] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 07/13/2011] [Accepted: 07/28/2011] [Indexed: 11/20/2022]
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41
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Emerging functions of transcription factors in malaria parasite. J Biomed Biotechnol 2011; 2011:461979. [PMID: 22131806 PMCID: PMC3216465 DOI: 10.1155/2011/461979] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 08/30/2011] [Accepted: 08/30/2011] [Indexed: 12/31/2022] Open
Abstract
Transcription is a process by which the genetic information stored in DNA is converted into mRNA by enzymes known as RNA polymerase. Bacteria use only one RNA polymerase to transcribe all of its genes while eukaryotes contain three RNA polymerases to transcribe the variety of eukaryotic genes. RNA polymerase also requires other factors/proteins to produce the transcript. These factors generally termed as transcription factors (TFs) are either associated directly with RNA polymerase or add in building the actual transcription apparatus. TFs are the most common tools that our cells use to control gene expression. Plasmodium falciparum is responsible for causing the most lethal form of malaria in humans. It shows most of its characteristics common to eukaryotic transcription but it is assumed that mechanisms of transcriptional control in P. falciparum somehow differ from those of other eukaryotes. In this article we describe the studies on the main TFs such as myb protein, high mobility group protein and ApiA2 family proteins from malaria parasite. These studies show that these TFs are slowly emerging to have defined roles in the regulation of gene expression in the parasite.
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42
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Gibson DG. Gene and genome construction in yeast. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2011; Chapter 3:Unit3.22. [PMID: 21472698 DOI: 10.1002/0471142727.mb0322s94] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The yeast Saccharomyces cerevisiae has the capacity to take up and assemble dozens of different overlapping DNA molecules in one transformation event. These DNA molecules can be single-stranded oligonucleotides, to produce gene-sized fragments, or double-stranded DNA fragments, to produce molecules up to hundreds of kilobases in length, including complete bacterial genomes. This unit presents protocols for designing the DNA molecules to be assembled, transforming them into yeast, and confirming their assembly.
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43
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Phosphoinositide [PI(3,5)P2] lipid-dependent regulation of the general transcriptional regulator Tup1. Genes Dev 2011; 25:984-95. [PMID: 21536737 DOI: 10.1101/gad.1998611] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Transcriptional activity of a gene is governed by transcriptional regulatory complexes that assemble/disassemble on the gene and control the chromatin architecture. How cytoplasmic components influence the assembly/disassembly of transcriptional regulatory complexes is poorly understood. Here we report that the budding yeast Saccharomyces cerevisiae has a chromatin architecture-modulating mechanism that is dependent on the endosomal lipid PI(3,5)P(2). We identified Tup1 and Cti6 as new, highly specific PI(3,5)P(2) interactors. Tup1--which associates with multiple transcriptional regulators, including the HDAC (histone deacetylase) and SAGA complexes--plays a crucial role in determining an activated or repressed chromatin state of numerous genes, including GAL1. We show that, in the context that the Gal4 activation pathway is compromised, PI(3,5)P(2) plays an essential role in converting the Tup1-driven repressed chromatin structure into a SAGA-containing activated chromatin structure at the GAL1 promoter. Biochemical and cell biological experiments suggest that PI(3,5)P(2) recruits Cti6 and the Cyc8-Tup1 corepressor complex to the late endosomal/vacuolar membrane and mediates the assembly of a Cti6-Cyc8-Tup1 coactivator complex that functions to recruit the SAGA complex to the GAL1 promoter. Our findings provide important insights toward understanding how the chromatin architecture and epigenetic status of a gene are regulated by cytoplasmic components.
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44
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Feig M, Burton ZF. RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J 2011; 99:2577-86. [PMID: 20959099 DOI: 10.1016/j.bpj.2010.08.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/28/2010] [Accepted: 08/10/2010] [Indexed: 10/18/2022] Open
Abstract
RNA polymerase II is the central eukaryotic enzyme in transcription from DNA to RNA. The dynamics of RNA polymerase II is described from molecular-dynamics simulations started from two crystal structures with open and closed trigger loop (TL) forms. Dynamic transitions between neutral and forward translocated states were observed, especially for the downstream DNA duplex. Dynamic rearrangements were also seen in the active site environment, including conformations in which the active site nucleotide assumed a possibly precatalytic conformation in close proximity to the terminal 3'-hydroxyl of the nascent RNA. Because nucleic acid translocation was observed primarily in the simulations with an open TL structure, whereas close approach of the active site nucleotide to the terminal RNA ribose predominantly occurred in the closed TL structure, a modified Brownian ratchet mechanism is proposed whereby thermally driven translocation is only possible with an open TL, and fidelity control and catalysis require TL closing.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA.
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45
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Magorivska IB, Bilyy RO, Havrylyuk AM, Chop'yak VV, Stoika RS, Kit YY. Anti-histone H1 IgGs from blood serum of systemic lupus erythematosus patients are capable of hydrolyzing histone H1 and myelin basic protein. J Mol Recognit 2010; 23:495-502. [PMID: 20583146 DOI: 10.1002/jmr.1033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Novel hydrolytic activity of the anti-histone H1 antibodies (Ab) toward histone H1 and myelin basic protein (MBP) was shown. Blood serum of ten patients with clinically diagnosed systemic lupus erythematosus (SLE), and nine healthy donors (control) were screened for the anti-histone H1 antibody- and anti-MBP antibody-mediated specific proteolytic activity. IgGs were isolated by chromatography on Protein G-Sepharose, and four of ten SLE patients appeared to possess IgGs that were capable of cleaving both histone H1 and MBP. Such activity was confirmed to be an intrinsic property of the IgG molecule, since it was preserved at gel filtration at alkaline and acidic pH. At the same time, proteolytic activity was absent in the sera-derived Ab of all healthy donors under control. Anti-histone IgGs were purified by the affinity chromatography on histone H1-Sepharose. Their cross-reactivity toward cationic proteins (histones, lysozyme, and MBP) and their capability of hydrolyzing histone H1 and MBP were detected. However, these IgGs were not cleaving core histones, lysozyme, or albumin. Capability of cleaving histone H1 and MBP was preserved after additional purification of anti-histone H1 IgGs by the HPLC gel filtration. The protease activity of anti-histone H1 IgG Ab was inhibited by serine protease inhibitors.
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Affiliation(s)
- Irina B Magorivska
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Drahomanov Street 14/16, Lviv 79005, Ukraine
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46
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Rothman S. How is the balance between protein synthesis and degradation achieved? Theor Biol Med Model 2010; 7:25. [PMID: 20573219 PMCID: PMC2909984 DOI: 10.1186/1742-4682-7-25] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 06/23/2010] [Indexed: 12/19/2022] Open
Abstract
Unlike most substances that cells manufacture, proteins are not produced and broken down by a common series of chemical reactions, but by completely different (independent and disconnected) mechanisms that possess no intrinsic means of making the rates of the two processes equal and attaining steady state concentrations. Balance between them is achieved extrinsically and is often imagined today to be the result of the actions of chemical feedback agents. But however instantiated, chemical feedback or any similar mechanism can only rectify induced imbalances in a system previously balanced by other means. Those "other means" necessarily involve reversible mass action or equilibrium-based interactions between native and altered forms of protein molecules somewhere in time and space between their synthesis and degradation.
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Affiliation(s)
- Stephen Rothman
- University of California, San Francisco, San Francisco, CA 94143, USA.
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47
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Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, Chuang RY, Carrera W, Moodie M, Algire MA, Phan Q, Alperovich N, Vashee S, Merryman C, Venter JC, Smith HO, Glass JI, Hutchison CA. Cloning whole bacterial genomes in yeast. Nucleic Acids Res 2010; 38:2558-69. [PMID: 20211840 PMCID: PMC2860123 DOI: 10.1093/nar/gkq119] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/08/2010] [Accepted: 02/09/2010] [Indexed: 01/21/2023] Open
Abstract
Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation.
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Affiliation(s)
- Gwynedd A Benders
- Synthetic Biology and Bioenergy Group, The J. Craig Venter Institute, San Diego, CA 92121, USA.
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48
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Cao Y, Vo T, Millien G, Tagne JB, Kotton D, Mason RJ, Williams MC, Ramirez MI. Epigenetic mechanisms modulate thyroid transcription factor 1-mediated transcription of the surfactant protein B gene. J Biol Chem 2009; 285:2152-64. [PMID: 19906647 DOI: 10.1074/jbc.m109.039172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Epigenetic regulation of transcription plays an important role in cell-specific gene expression by altering chromatin structure and access of transcriptional regulators to DNA binding sites. Surfactant protein B (Sftpb) is a developmentally regulated lung epithelial gene critical for lung function. Thyroid transcription factor 1 (Nkx2-1) regulates Sftpb gene expression in various species. We show that Nkx2-1 binds to the mouse Sftpb (mSftpb) promoter in the lung. In a mouse lung epithelial cell line (MLE-15), Nkx2-1 knockdown reduces Sftpb expression, and mutation of Nkx2-1 cis-elements significantly reduces mSftpb promoter activity. Whether chromatin structure modulates Nkx2-1 regulation of Sftpb transcription is unknown. We found that DNA methylation of the mSftpb promoter inversely correlates with known patterns of Sftpb expression in vivo. The mSftpb promoter activity can be manipulated by altering its cytosine methylation status in vitro. Nkx2-1 activation of the mSftpb promoter is impaired by DNA methylation. The unmethylated Sftpb promoter shows an active chromatin structure enriched in the histone modification H3K4me3 (histone 3-lysine 4 trimethylated). The ATP-dependent chromatin remodeling protein Brg1 is recruited to the Sftpb promoter in Sftpb-expressing, but not in non-expressing tissues and cell lines. Brg1 knockdown in MLE-15 cells greatly decreases H3K4me3 levels at the Sftpb promoter region and expression of the Sftpb gene. Brg1 can be co-immunoprecipitated with Nkx2-1 protein. Last, Nkx2-1 and Brg1 with intact ATPase activity are required for mSftpb promoter activation in vitro. Our findings suggest that DNA methylation and chromatin modifications cooperate with Nkx2-1 to regulate Sftpb gene cell specific expression.
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Affiliation(s)
- Yuxia Cao
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA.
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49
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Gopalakrishnan AM, Nyindodo LA, Ross Fergus M, López-Estraño C. Plasmodium falciparum: Preinitiation complex occupancy of active and inactive promoters during erythrocytic stage. Exp Parasitol 2008; 121:46-54. [PMID: 18951895 DOI: 10.1016/j.exppara.2008.09.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 07/22/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
Over 80% of Plasmodium falciparum genes are developmentally regulated during the parasite's life cycle with most genes expressed in a "just in time" fashion. However, the molecular mechanisms of gene regulation are still poorly understood. Analysis of P. falciparum genome shows that the parasite appears to encode relatively few transcription factors homologous to those in other eukaryotes. We used Chromatin immunoprecipitation (ChIP) to study interaction of PfTBP and PfTFIIE with stage specific Plasmodium promoters. Our results indicate that PfTBP and PfTFIIE are bound to their cognate sequence in active and inactive erythrocytic-expressed promoters. In addition, TF occupancy appears to extend beyond the promoter regions, since PfTBP interaction with the coding and 3' end regions was also detected. No PfTBP or PfTFIIE interaction was detected on csp and pfs25 genes which are not active during the erythrocytic asexual stage. Furthermore, PfTBP and PfTFIIE binding did not appear to correlate with histone 3 and/or 4 acetylation, suggesting that histone acetylation may not be a prerequisite for PfTBP or PfTFIIE promoter interaction. Based on our observations we concluded that the PfTBP/PfTFIIE-containing preinitiation complex (PIC) would be preassembled on promoters of all erythrocytic-expressed genes in a fashion independent of histone acetylation, providing support for the "poised" model. Contrary to the classical model of eukaryotic gene regulation, PIC interaction with Plasmodium promoters occurred independent of transcriptional activity and to the notion that chromatin acetylation leads to PIC assembly.
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Affiliation(s)
- Anusha M Gopalakrishnan
- Department of Biology, Life Sciences Building, Room 409B, The University of Memphis, 3774 Walker Avenue, Memphis, TN 38152, USA
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50
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Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS One 2008; 3:e2803. [PMID: 18665230 PMCID: PMC2481391 DOI: 10.1371/journal.pone.0002803] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 07/04/2008] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. METHODOLOGY/PRINCIPAL FINDINGS We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. CONCLUSION/SIGNIFICANCE Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.
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Affiliation(s)
- Qingfa Wu
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yeong C. Kim
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Jian Lu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Zhenyu Xuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jun Chen
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yonglan Zheng
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tom Zhou
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michael Q. Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chung-I Wu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - San Ming Wang
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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