1
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Tu K, Li X, Zhang Q, Huang W, Xie D. A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing. Bioinformatics 2024; 40:btae206. [PMID: 38613848 PMCID: PMC11256936 DOI: 10.1093/bioinformatics/btae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
MOTIVATION Identifying chromatin accessibility is one of the key steps in studying the regulation of eukaryotic genomes. The combination of exogenous methyltransferase and nanopore sequencing provides an strategy to identify open chromatin over long genomic ranges at the single-molecule scale. However, endogenous methylation, non-open-chromatin-specific exogenous methylation and base-calling errors limit the accuracy and hinders its application to complex genomes. RESULTS We systematically evaluated the impact of these three influence factors, and developed a model-based computational method, methyltransferase accessible genome region finder (MAGNIFIER), to address the issues. By incorporating control data, MAGNIFIER attenuates the three influence factors with data-adaptive comparison strategy. We demonstrate that MAGNIFIER is not only sensitive to identify the open chromatin with much improved accuracy, but also able to detect the chromatin accessibility of repetitive regions that are missed by NGS-based methods. By incorporating long-read RNA-seq data, we revealed the association between the accessible Alu elements and non-classic gene isoforms. AVAILABILITY AND IMPLEMENTATION Freely available on web at https://github.com/Goatofmountain/MAGNIFIER.
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Affiliation(s)
- Kailing Tu
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xuemei Li
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Qilin Zhang
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Wei Huang
- School of Mathematics and Statistics, Key Laboratory for Applied Statistics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Dan Xie
- National Frontier Center of Disease Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
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2
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Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. Sci Rep 2024; 14:3936. [PMID: 38365907 PMCID: PMC10873509 DOI: 10.1038/s41598-024-54302-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/11/2024] [Indexed: 02/18/2024] Open
Abstract
Regulation of gene expression through enhancers is one of the major processes shaping the structure and function of the human brain during development. High-throughput assays have predicted thousands of enhancers involved in neurodevelopment, and confirming their activity through orthogonal functional assays is crucial. Here, we utilized Massively Parallel Reporter Assays (MPRAs) in stem cells and forebrain organoids to evaluate the activity of ~ 7000 gene-linked enhancers previously identified in human fetal tissues and brain organoids. We used a Gaussian mixture model to evaluate the contribution of background noise in the measured activity signal to confirm the activity of ~ 35% of the tested enhancers, with most showing temporal-specific activity, suggesting their evolving role in neurodevelopment. The temporal specificity was further supported by the correlation of activity with gene expression. Our findings provide a valuable gene regulatory resource to the scientific community.
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Affiliation(s)
- Davide Capauto
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Jessica Mariani
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | | | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA.
- Department of Neuroscience, Yale University, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale University, New Haven, CT, 06520, USA.
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3
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Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553170. [PMID: 37645832 PMCID: PMC10461976 DOI: 10.1101/2023.08.14.553170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Regulation of gene expression through enhancers is one of the major processes shaping the structure and function of the human brain during development. High-throughput assays have predicted thousands of enhancers involved in neurodevelopment, and confirming their activity through orthogonal functional assays is crucial. Here, we utilized Massively Parallel Reporter Assays (MPRAs) in stem cells and forebrain organoids to evaluate the activity of ~7,000 gene-linked enhancers previously identified in human fetal tissues and brain organoids. We used a Gaussian mixture model to evaluate the contribution of background noise in the measured activity signal to confirm the activity of ~35% of the tested enhancers, with most showing temporal-specific activity, suggesting their evolving role in neurodevelopment. The temporal specificity was further supported by the correlation of activity with gene expression. Our findings provide a valuable gene regulatory resource to the scientific community.
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Affiliation(s)
- Davide Capauto
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | | | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University; Kyoto, Japan
| | | | | | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
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4
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Chin HG, Vishnu US, Sun Z, Ponnaluri VKC, Zhang G, Xu SY, Benoukraf T, Cejas P, Spracklin G, Estève PO, Long HW, Pradhan S. Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells. Methods Mol Biol 2023; 2611:39-52. [PMID: 36807062 DOI: 10.1007/978-1-0716-2899-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crosslinking. Here, we describe accessible chromatin library preparation from low numbers of formaldehyde-crosslinked cells using a modified nick translation method, where a nicking enzyme nicks one strand of DNA and DNA polymerase incorporates biotin-conjugated dATP, dCTP, and methyl-dCTP. Once the DNA is labeled, it can be isolated for NGS library preparation. We termed this method as universal NicE-seq (nicking enzyme-assisted sequencing). We also demonstrate a single tube method that enables direct NGS library preparation from low cell numbers without DNA purification. Furthermore, we demonstrated universal NicE-seq on FFPE tissue section sample.
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Affiliation(s)
| | | | - Zhiyi Sun
- New England Biolabs Inc., Ipswich, MA, USA
| | | | | | | | - Touati Benoukraf
- Faculty of Medicine, Craig L. Dobbin Genetics Research Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - George Spracklin
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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5
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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6
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Tang X, Zheng P, Liu Y, Yao Y, Huang G. LangMoDHS: A deep learning language model for predicting DNase I hypersensitive sites in mouse genome. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:1037-1057. [PMID: 36650801 DOI: 10.3934/mbe.2023048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learning-based language model for predicting DHSs, named LangMoDHS. The LangMoDHS mainly comprised the convolutional neural network (CNN), the bi-directional long short-term memory (Bi-LSTM) and the feed-forward attention. The CNN and the Bi-LSTM were stacked in a parallel manner, which was helpful to accumulate multiple-view representations from primary DNA sequences. We conducted 5-fold cross-validations and independent tests over 14 tissues and 4 developmental stages. The empirical experiments showed that the LangMoDHS is competitive with or slightly better than the iDHS-Deep, which is the latest method for predicting DHSs. The empirical experiments also implied substantial contribution of the CNN, Bi-LSTM, and attention to DHSs prediction. We implemented the LangMoDHS as a user-friendly web server which is accessible at http:/www.biolscience.cn/LangMoDHS/. We used indices related to information entropy to explore the sequence motif of DHSs. The analysis provided a certain insight into the DHSs.
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Affiliation(s)
- Xingyu Tang
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
| | - Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
| | - Yuhua Yao
- School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang 422000, China
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7
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Dougherty MW, Jobin C. Intestinal bacteria and colorectal cancer: etiology and treatment. Gut Microbes 2023; 15:2185028. [PMID: 36927206 PMCID: PMC10026918 DOI: 10.1080/19490976.2023.2185028] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
The etiology of colorectal cancer (CRC) is influenced by bacterial communities that colonize the gastrointestinal tract. These microorganisms derive essential nutrients from indigestible dietary or host-derived compounds and activate molecular signaling pathways necessary for normal tissue and immune function. Associative and mechanistic studies have identified bacterial species whose presence may increase CRC risk, including notable examples such as Fusobacterium nucleatum, Enterotoxigenic Bacteroides fragilis, and pks+ E. coli. In recent years this work has expanded in scope to include aspects of host mutational status, intra-tumoral microbial heterogeneity, transient infection, and the cumulative influence of multiple carcinogenic bacteria after sequential or co-colonization. In this review, we will provide an updated overview of how host-bacteria interactions influence CRC development, how this knowledge may be utilized to diagnose or prevent CRC, and how the gut microbiome influences CRC treatment efficacy.
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Affiliation(s)
- Michael W. Dougherty
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Christian Jobin
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Infectious Diseases and Immunology, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
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8
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Li Z, Zhao B, Qin C, Wang Y, Li T, Wang W. Chromatin Dynamics in Digestive System Cancer: Commander and Regulator. Front Oncol 2022; 12:935877. [PMID: 35965507 PMCID: PMC9372441 DOI: 10.3389/fonc.2022.935877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.
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9
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Wang MY, Zhang CM, Zhou HH, Ge ZB, Su CC, Lou ZH, Zhang XY, Xu TT, Li SY, Zhu L, Zhou YL, Wu Y, Ji SR. Identification of a distal enhancer that determines the expression pattern of acute phase marker C-reactive protein. J Biol Chem 2022; 298:102160. [PMID: 35724961 PMCID: PMC9287136 DOI: 10.1016/j.jbc.2022.102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 11/18/2022] Open
Abstract
C-reactive protein (CRP) is a major acute phase protein and inflammatory marker, the expression of which is largely liver specific and highly inducible. Enhancers are regulatory elements critical for the precise activation of gene expression, yet the contributions of enhancers to the expression pattern of CRP have not been well defined. Here, we identify a constitutively active enhancer (E1) located 37.7 kb upstream of the promoter of human CRP in hepatocytes. By using chromatin immunoprecipitation, luciferase reporter assay, in situ genetic manipulation, CRISPRi, and CRISPRa, we show that E1 is enriched in binding sites for transcription factors STAT3 and C/EBP-β and is essential for the full induction of human CRP during the acute phase. Moreover, we demonstrate that E1 orchestrates with the promoter of CRP to determine its varied expression across tissues and species through surveying activities of E1-promoter hybrids and the associated epigenetic modifications. These results thus suggest an intriguing mode of molecular evolution wherein expression-changing mutations in distal regulatory elements initiate subsequent functional selection involving coupling among distal/proximal regulatory mutations and activity-changing coding mutations.
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Affiliation(s)
- Ming-Yu Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Chun-Miao Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Hai-Hong Zhou
- Gansu Provincial Cancer Hospital, Lanzhou 730050, P.R. China
| | - Zhong-Bo Ge
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Chen-Chen Su
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Zi-Hao Lou
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Xin-Yun Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Tao-Tao Xu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Si-Yi Li
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Li Zhu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China; Electron Microscopy Centre of Lanzhou University, Lanzhou 730000, China
| | - Ya-Li Zhou
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China; Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Children's Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.
| | - Shang-Rong Ji
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China.
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10
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Zhang X, Qiu H, Zhang F, Ding S. Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research. Front Cell Dev Biol 2022; 10:883861. [PMID: 35733851 PMCID: PMC9207481 DOI: 10.3389/fcell.2022.883861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
With the development of ever more powerful and versatile high-throughput sequencing techniques and innovative ways to capture single cells, mapping the multicellular tissues at the single-cell level is becoming routine practice. However, it is still challenging to depict the epigenetic landscape of a single cell, especially the genome-wide chromatin accessibility, histone modifications, and DNA methylation. We summarize the most recent methodologies to profile these epigenetic marks at the single-cell level. We also discuss the development and advancement of several multi-omics sequencing technologies from individual cells. Advantages and limitations of various methods to compare and integrate datasets obtained from different sources are also included with specific practical notes. Understanding the heart tissue at single-cell resolution and multi-modal levels will help to elucidate the cell types and states involved in physiological and pathological events during heart development and disease. The rich information produced from single-cell multi-omics studies will also promote the research of heart regeneration and precision medicine on heart diseases.
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Affiliation(s)
- Xingwu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
| | - Hui Qiu
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Fengzhi Zhang
- First Hospital of Tsinghua University, Beijing, China
| | - Shuangyuan Ding
- Center for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing, China
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11
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Wu T, Li G. An Improved EMSA-based Method to Prioritize Candidate cis-REs for Further Functional Validation. Bio Protoc 2022; 12:e4397. [PMID: 35800102 PMCID: PMC9081477 DOI: 10.21769/bioprotoc.4397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/19/2022] [Accepted: 03/14/2022] [Indexed: 12/29/2022] Open
Abstract
Cells are the complex product of gene expression programs that involve the coordinated transcription of thousands of genes controlled by cis-regulatory elements (cis-REs). Therefore, identification of cis-REs is the key to decipher the mechanisms underlying the regulation of gene expression. Here, we describe a simple and time-effective protocol of fine-mapping cis-REs by using an electrophoresis mobility shift assay (EMSA)-based, in vitro, high-throughput (HTP) technique called regulatory element-sequencing (Reel-seq). Reel-seq can be applied to identify cis-REs at a high resolution and sensitivity over large genome regions, in a systematic and continuous manner. It can be used to prioritize candidate cis-REs as a complement to the existing approaches, such as massive parallel reporter assay (MPRA), chromatin immunoprecipitation DNA-sequencing (ChIP-seq), and the assay for transposase-accessible chromatin sequencing (ATAC-seq). Graphical abstract: Generation of the Reel-seq Library 1 and 2 (A) and identification of cis-REs by an electrophoresis mobility shift assay (EMSA)-based Reel-seq screen (B). NE: nuclear extract; NGS: next generation sequencing.
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Affiliation(s)
- Ting Wu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Medicine, Xiangya School of Medicine, Central South University, Changsha, 410083, China
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15223, USA
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12
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iDHS-DT: Identifying DNase I hypersensitive sites by integrating DNA dinucleotide and trinucleotide information. Biophys Chem 2021; 281:106717. [PMID: 34798459 DOI: 10.1016/j.bpc.2021.106717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023]
Abstract
DNase I hypersensitive sites (DHSs) is important for identifying the location of gene regulatory elements, such as promoters, enhancers, silencers, and so on. Thus, it is crucial for discriminating DHSs from non-DHSs. Although some traditional methods, such as Southern blots and DNase-seq technique, have the ability to identify DHSs, these approaches are time-consuming, laborious, and expensive. To address these issues, researchers paid their attention on computational approaches. Therefore, in this study, we developed a novel predictor called iDHS-DT to identify DHSs. In this predictor, the DNA sequences were firstly denoted by physicochemical properties (PC) of DNA dinucleotide and trinucleotide. Then, three different descriptors, including auto-covariance, cross-covariance, and discrete wavelet transform were used to collect related features from the PC matrix. Next, the least absolute shrinkage and selection operator (LASSO) algorithm was employed to remove these irrelevant and redundant features. Finally, these selected features were fed into support vector machine (SVM) for distinguishing DHSs from non-DHSs. The proposed method achieved 97.64% and 98.22% classification accuracy on dataset S1 and S2, respectively. Compared with the existing predictors, our proposed model has significantly improvement in classification performance. Experimental results demonstrated that the proposed method is powerful in identifying DHSs.
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13
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Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021; 22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
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Affiliation(s)
- Anjali Chawla
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
| | - Corina Nagy
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
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14
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Wang J, Chen L, Zhang X, Tong Y, Zheng T. OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data. Int J Mol Sci 2021; 22:ijms22115802. [PMID: 34071577 PMCID: PMC8198695 DOI: 10.3390/ijms22115802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Open chromatin regions (OCRs) are special regions of the human genome that can be accessed by DNA regulatory elements. Several studies have reported that a series of OCRs are associated with mechanisms involved in human diseases, such as cancers. Identifying OCRs using ATAC-seq or DNase-seq is often expensive. It has become popular to detect OCRs from plasma cell-free DNA (cfDNA) sequencing data, because both the fragmentation modes of cfDNA and the sequencing coverage in OCRs are significantly different from those in other regions. However, it is a challenging computational problem to accurately detect OCRs from plasma cfDNA-seq data, as multiple factors—e.g., sequencing and mapping bias, insufficient read depth, etc.—often mislead the computational model. In this paper, we propose a novel bioinformatics pipeline, OCRDetector, for detecting OCRs from whole-genome cfDNA sequencing data. The pipeline calculates the window protection score (WPS) waveform and the cfDNA sequencing coverage. To validate the proposed pipeline, we compared the percentage overlap of our OCRs with those obtained by other methods. The experimental results show that 81% of the TSS regions of housekeeping genes are detected, and our results have obvious tissue specificity. In addition, the overlap percentage between our OCRs and the high-confidence OCRs obtained by ATAC-seq or DNase-seq is greater than 70%.
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15
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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16
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O’Garro C, Igbineweka L, Ali Z, Mezei M, Mujtaba S. The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics. Biomolecules 2021; 11:biom11030455. [PMID: 33803759 PMCID: PMC8003229 DOI: 10.3390/biom11030455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 01/13/2023] Open
Abstract
The molecular interplay between nucleosomal packaging and the chromatin landscape regulates the transcriptional programming and biological outcomes of downstream genes. An array of epigenetic modifications plays a pivotal role in shaping the chromatin architecture, which controls DNA access to the transcriptional machinery. Acetylation of the amino acid lysine is a widespread epigenetic modification that serves as a marker for gene activation, which intertwines the maintenance of cellular homeostasis and the regulation of signaling during stress. The biochemical horizon of acetylation ranges from orchestrating the stability and cellular localization of proteins that engage in the cell cycle to DNA repair and metabolism. Furthermore, lysine acetyltransferases (KATs) modulate the functions of transcription factors that govern cellular response to microbial infections, genotoxic stress, and inflammation. Due to their central role in many biological processes, mutations in KATs cause developmental and intellectual challenges and metabolic disorders. Despite the availability of tools for detecting acetylation, the mechanistic knowledge of acetylation-mediated cellular processes remains limited. This review aims to integrate molecular and structural bases of KAT functions, which would help design highly selective tools for understanding the biology of KATs toward developing new disease treatments.
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Affiliation(s)
- Chenise O’Garro
- Department of Biology, Medgar Evers College, City University of New York, Brooklyn, NY 11225, USA; (C.O.); (L.I.); (Z.A.)
| | - Loveth Igbineweka
- Department of Biology, Medgar Evers College, City University of New York, Brooklyn, NY 11225, USA; (C.O.); (L.I.); (Z.A.)
| | - Zonaira Ali
- Department of Biology, Medgar Evers College, City University of New York, Brooklyn, NY 11225, USA; (C.O.); (L.I.); (Z.A.)
| | - Mihaly Mezei
- Department of Pharmaceutical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Shiraz Mujtaba
- Department of Biology, Medgar Evers College, City University of New York, Brooklyn, NY 11225, USA; (C.O.); (L.I.); (Z.A.)
- Correspondence:
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17
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Zhou L, Huang Y, Wang Q, Guo D. Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua. Molecules 2021; 26:molecules26041194. [PMID: 33672342 PMCID: PMC7926469 DOI: 10.3390/molecules26041194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 11/21/2022] Open
Abstract
Glandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Several critical genes involved in artemisinin biosynthesis are specifically expressed in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules are able to interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, we investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique. We identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR2 and CYP71AV1, showed higher accessible regions in GT compared to that in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the highly accessible chromatin regions associated with artemisinin biosynthetic genes in glandular trichomes. Finally, we proposed a working model illustrating the chromatin accessibility dynamics in regulating artemisinin biosynthetic gene expression. This work provided new insights into epigenetic regulation of gene expression in GT.
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Affiliation(s)
- Limeng Zhou
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
| | - Yingzhang Huang
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
| | - Qi Wang
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510000, China;
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology, School of Life Science, The Chinese University of Hong Kong, Hong Kong 999077, China; (L.Z.); (Y.H.)
- Correspondence: ; Tel.: +852-3943-6298
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18
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Abstract
Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is a method to investigate the accessibility of chromatin in a genome-wide fashion. In this chapter, we provide a brief history of the chromatin accessibility field followed by a detailed protocol to perform ATAC-Seq assay.
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Affiliation(s)
| | - Amitava Basu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, UK.
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19
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Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp J, Naughton C, Shapiro B, Green RE. A novel NGS library preparation method to characterize native termini of fragmented DNA. Nucleic Acids Res 2020; 48:e47. [PMID: 32112100 PMCID: PMC7192605 DOI: 10.1093/nar/gkaa128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 12/22/2022] Open
Abstract
Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5′ and 3′) of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80–90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
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Affiliation(s)
| | - Nathan K Schaefer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Varsha Rao
- Claret Bioscience LLC, Santa Cruz, CA 95060, USA
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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20
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Spracklin G, Pradhan S. Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin. Nucleic Acids Res 2020; 48:e16. [PMID: 31819993 PMCID: PMC7026637 DOI: 10.1093/nar/gkz1150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/11/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022] Open
Abstract
In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin via resistance to nuclease degradation followed by next-generation sequencing (NGS). We performed Protect-seq on the human colon cancer cell line HCT-116 and observed overlap with previously curated LADs. We provide evidence that these protected regions are enriched for and can distinguish between the repressive histone modification H3K9me3, H3K9me2 and H3K27me3. Moreover, in human cells the loss of H3K9me3 leads to an increase in chromatin accessibility and loss of Protect-seq signal. For further validation, we performed Protect-seq in the fibrosarcoma cell line HT1080 and found a similar correlation with previously curated LADs and repressive histone modifications. In sum, Protect-seq is an efficient technique that allows rapid identification of nuclease resistant chromatin, which correlate with heterochromatin and radial positioning.
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Affiliation(s)
- George Spracklin
- Genome Biology Division, New England Biolabs, Inc, Ipswich, MA 01938, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc, Ipswich, MA 01938, USA
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21
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Zhou J, Li Y, Cao H, Yang M, Chu L, Li T, Yu Z, Yu R, Qiu B, Wang Q, Li X, Xie J. CATA: a comprehensive chromatin accessibility database for cancer. Database (Oxford) 2020; 2022:6520815. [PMID: 35134148 PMCID: PMC9246274 DOI: 10.1093/database/baab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL: CATA is available at http://www.xiejjlab.bio/cata/.
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Affiliation(s)
- Jianyuan Zhou
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong
- First Medical University, and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan 250000, China
| | | | | | - Min Yang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Lingyu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Taisong Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
| | - Zhengmin Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Rui Yu
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Bo Qiu
- Central Laboratory of Molecular Biology, Medical College of Jiaying University, 146 Huangtang Road, Meizhou 514031, China
| | - Qiuyu Wang
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Xuecang Li
- School of Medical Informatics, Harbin Medical University, Daqing Campus, Daqing 163319, China
| | - Jianjun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou 515041, China
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22
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Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 2019; 28:69-85. [PMID: 31776829 PMCID: PMC7125251 DOI: 10.1007/s10577-019-09619-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
Abstract
Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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23
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Chen Y, Chen A. Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites. Biomed Rep 2019; 11:87-97. [PMID: 31423302 PMCID: PMC6684942 DOI: 10.3892/br.2019.1233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/03/2019] [Indexed: 01/18/2023] Open
Abstract
DNase I-hypersensitive sites (DHSs) serve key roles in the regulation of gene transcription as markers of cis-regulatory elements (CREs). Recent advances in next-generation sequencing have enabled the genome-wide location and annotation of DHSs in a variety of cells. Numerous studies have confirmed that DHSs are involved in several processes in cell fate decision and development. DHSs have also been indicated in cancer and inherited diseases as driver distal regulatory elements. Here, the definition of DHSs is reviewed, in addition to high-throughput methods of DHS identification. Furthermore, the function of DHSs in gene expression is probed. The roles of DHSs in disease occurrence are also reviewed and discussed. Concomitant advances in the identification of essential roles of DHSs will assist in disclosing the underlying molecular mechanisms, supplementing gene transcription and enlarging the molecular basis of DHS-related bioprocesses, phenotypes, distinct traits and diseases.
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Affiliation(s)
- Ying Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ailing Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
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24
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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25
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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26
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Lu Y, Wang X, Yu H, Li J, Jiang Z, Chen B, Lu Y, Wang W, Han C, Ouyang Y, Huang L, Chen C, Tian W, Ling F. Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes. Front Genet 2019; 10:152. [PMID: 30930929 PMCID: PMC6423895 DOI: 10.3389/fgene.2019.00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/13/2019] [Indexed: 11/23/2022] Open
Abstract
How the human brain differs from those of non-human primates is largely unknown and the complex drivers underlying such differences at the genomic level remain unclear. In this study, we selected 243 brain-related genes, based on Gene Ontology, and identified 184,113 DNaseI hypersensitive sites (DHSs) within their regulatory regions. To performed comprehensive evolutionary analyses, we set strict filtering criteria for alignment quality and filtered 39,132 DHSs for inclusion in the investigation and found that 2,397 (~6%) exhibited evidence of accelerated evolution (aceDHSs), which was a much higher proportion that DHSs genome-wide. Target genes predicted to be regulated by brain-aceDHSs were functionally enriched for brain development and exhibited differential expression between human and chimpanzee. Alignments indicated 61 potential human-specific transcription factor binding sites in brain-aceDHSs, including for CTCF, FOXH1, and FOXQ1. Furthermore, based on GWAS, Hi-C, and eQTL data, 16 GWAS SNPs, and 82 eQTL SNPs were in brain-aceDHSs that regulate genes related to brain development or disease. Among these brain-aceDHSs, we confirmed that one enhanced the expression of GPR133, using CRISPR-Cas9 and western blotting. The GPR133 gene is associated with glioblastoma, indicating that SNPs within DHSs could be related to brain disorders. These findings suggest that brain-related gene regulatory regions are under adaptive evolution and contribute to the differential expression profiles among primates, providing new insights into the genetic basis of brain phenotypes or disorders between humans and other primates.
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Affiliation(s)
- Yueer Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiao Wang
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hang Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jianlin Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhiqiang Jiang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Bangwei Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yueqi Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Wei Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chongyin Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Ouyang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Chunbo Chen
- Department of Critical Care Medicine, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Fei Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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27
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Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG. Identification of transcription factor binding sites using ATAC-seq. Genome Biol 2019; 20:45. [PMID: 30808370 PMCID: PMC6391789 DOI: 10.1186/s13059-019-1642-2] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 01/25/2019] [Indexed: 01/07/2023] Open
Abstract
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
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Affiliation(s)
- Zhijian Li
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, 52074 Germany
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, Aachen, 52074 Germany
| | - Marcel H. Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany
| | - Thomas Look
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, Aachen, 52074 Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, RWTH Aachen University Medical School, Aachen, Germany
| | - Martin Zenke
- Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, Aachen, 52074 Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Ivan G. Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, 52074 Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
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28
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Cremer M, Cremer T. Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences. Genes Chromosomes Cancer 2019; 58:427-436. [DOI: 10.1002/gcc.22714] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marion Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
| | - Thomas Cremer
- Biocenter, Department Biology II; Ludwig Maximilians-Universität (LMU Munich); Munich Germany
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29
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Abstract
Venous endothelial cells are molecularly and functionally distinct from their arterial counterparts. Although veins are often considered the default endothelial state, genetic manipulations can modulate both acquisition and loss of venous fate, suggesting that venous identity is the result of active transcriptional regulation. However, little is known about this process. Here we show that BMP signalling controls venous identity via the ALK3/BMPR1A receptor and SMAD1/SMAD5. Perturbations to TGF-β and BMP signalling in mice and zebrafish result in aberrant vein formation and loss of expression of the venous-specific gene Ephb4, with no effect on arterial identity. Analysis of a venous endothelium-specific enhancer for Ephb4 shows enriched binding of SMAD1/5 and a requirement for SMAD binding motifs. Further, our results demonstrate that BMP/SMAD-mediated Ephb4 expression requires the venous-enriched BMP type I receptor ALK3/BMPR1A. Together, our analysis demonstrates a requirement for BMP signalling in the establishment of Ephb4 expression and the venous vasculature. The establishment of functional vasculatures requires the specification of newly formed vessels into veins and arteries. Here, Neal et al. use a combination of genetic approaches in mice and zebrafish to show that BMP signalling, via ALK3 and SMAD1/5, is required for venous specification during blood vessel development.
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30
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Zhang S, Lin J, Su L, Zhou Z. pDHS-DSET: Prediction of DNase I hypersensitive sites in plant genome using DS evidence theory. Anal Biochem 2019; 564-565:54-63. [DOI: 10.1016/j.ab.2018.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
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31
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Jänes J, Dong Y, Schoof M, Serizay J, Appert A, Cerrato C, Woodbury C, Chen R, Gemma C, Huang N, Kissiov D, Stempor P, Steward A, Zeiser E, Sauer S, Ahringer J. Chromatin accessibility dynamics across C. elegans development and ageing. eLife 2018; 7:37344. [PMID: 30362940 PMCID: PMC6231769 DOI: 10.7554/elife.37344] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here, we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one Caenorhabditis elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, more than 1000 promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements changes during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.
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Affiliation(s)
- Jürgen Jänes
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Yan Dong
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael Schoof
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jacques Serizay
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Alex Appert
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Cerrato
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Carson Woodbury
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ron Chen
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Carolina Gemma
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Ni Huang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Djem Kissiov
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Przemyslaw Stempor
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Annette Steward
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Eva Zeiser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Otto-Warburg Laboratories, Berlin, Germany
| | - Julie Ahringer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.,The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
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32
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Whitley SK, Balasubramani A, Zindl CL, Sen R, Shibata Y, Crawford GE, Weathington NM, Hatton RD, Weaver CT. IL-1R signaling promotes STAT3 and NF-κB factor recruitment to distal cis-regulatory elements that regulate Il17a/f transcription. J Biol Chem 2018; 293:15790-15800. [PMID: 30093408 DOI: 10.1074/jbc.ra118.002721] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Interleukin (IL)-1β plays a critical role in IL-6β- and transforming growth factor β (TGFβ)-initiated Th17 differentiation and induction of Th17-mediated autoimmunity. However, the means by which IL-1 regulates various aspects of Th17 development remain poorly understood. We recently reported that IL-1β enhances STAT3 phosphorylation via NF-κB-mediated repression of SOCS3 to facilitate Il17 transcription and Th17 differentiation, identifying an effect of IL-1 signaling on proximal events of STAT3 signaling. Here, we show that IL-1β promotes STAT3 binding to key cis-elements that control IL-17 expression. Additionally, we demonstrate that the IL-1-induced NF-κB factor RelA directly regulates the Il17a/f loci in cooperation with STAT3. Our findings reveal that IL-1 impacts both proximal signaling events and downstream interactions between transcription factors and cis-regulatory elements to promote Il17a/f transcription and Th17 differentiation.
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Affiliation(s)
| | | | - Carlene L Zindl
- Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Ranjan Sen
- the Laboratory of Cellular and Molecular Biology, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Yoichiro Shibata
- the Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, and
| | - Gregory E Crawford
- the Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, and
| | - Nathaniel M Weathington
- the Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15261
| | - Robin D Hatton
- Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Casey T Weaver
- From the Departments of Microbiology and.,Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294
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33
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Chen A, Chen D, Chen Y. Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals. Gene 2018; 667:83-94. [DOI: 10.1016/j.gene.2018.05.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/04/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
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34
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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35
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Cooper J, Ding Y, Song J, Zhao K. Genome-wide mapping of DNase I hypersensitive sites in rare cell populations using single-cell DNase sequencing. Nat Protoc 2017; 12:2342-2354. [PMID: 29022941 PMCID: PMC11005227 DOI: 10.1038/nprot.2017.099] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Increased chromatin accessibility is a feature of cell-type-specific cis-regulatory elements; therefore, mapping of DNase I hypersensitive sites (DHSs) enables the detection of active regulatory elements of transcription, including promoters, enhancers, insulators and locus-control regions. Single-cell DNase sequencing (scDNase-seq) is a method of detecting genome-wide DHSs when starting with either single cells or <1,000 cells from primary cell sources. This technique enables genome-wide mapping of hypersensitive sites in a wide range of cell populations that cannot be analyzed using conventional DNase I sequencing because of the requirement for millions of starting cells. Fresh cells, formaldehyde-cross-linked cells or cells recovered from formalin-fixed paraffin-embedded (FFPE) tissue slides are suitable for scDNase-seq assays. To generate scDNase-seq libraries, cells are lysed and then digested with DNase I. Circular carrier plasmid DNA is included during subsequent DNA purification and library preparation steps to prevent loss of the small quantity of DHS DNA. Libraries are generated for high-throughput sequencing on the Illumina platform using standard methods. Preparation of scDNase-seq libraries requires only 2 d. The materials and molecular biology techniques described in this protocol should be accessible to any general molecular biology laboratory. Processing of high-throughput sequencing data requires basic bioinformatics skills and uses publicly available bioinformatics software.
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Affiliation(s)
- James Cooper
- Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
- Hematology Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yi Ding
- Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Keji Zhao
- Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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36
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Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters. Epigenetics Chromatin 2017; 10:39. [PMID: 28784182 PMCID: PMC5547466 DOI: 10.1186/s13072-017-0146-0] [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: 04/18/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks. RESULTS Using 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[-] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[-]) are enriched toward the compacted interior of CDCs (INC). CONCLUSIONS Our results add further evidence in support of the ANC-INC network model. The different 3D topographies of DHS[+] and DHS[-] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an 'open,' active and 'closed,' inactive state.
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37
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Jung S, Angarica VE, Andrade-Navarro MA, Buckley NJ, Del Sol A. Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data. Sci Rep 2017; 7:4660. [PMID: 28680085 PMCID: PMC5498635 DOI: 10.1038/s41598-017-04929-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 01/01/2023] Open
Abstract
The epigenetics landscape of cells plays a key role in the establishment of cell-type specific gene expression programs characteristic of different cellular phenotypes. Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq. However, current downstream computational tools fail to reliably determine regulatory region accessibility from the analysis of these experimental data. In particular, currently available peak calling algorithms are very sensitive to their parameter settings and show highly heterogeneous results, which hampers a trustworthy identification of accessible chromatin regions. Here, we present a novel method that predicts accessible and, more importantly, inaccessible gene-regulatory chromatin regions solely relying on transcriptomics data, which complements and improves the results of currently available computational methods for chromatin accessibility assays. We trained a hierarchical classification tree model on publicly available transcriptomics and DNase-seq data and assessed the predictive power of the model in six gold standard datasets. Our method increases precision and recall compared to traditional peak calling algorithms, while its usage is not limited to the prediction of accessible and inaccessible gene-regulatory chromatin regions, but constitutes a helpful tool for optimizing the parameter settings of peak calling methods in a cell type specific manner.
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Affiliation(s)
- Sascha Jung
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | | | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes-Gutenberg University of Mainz, Mainz, Germany.,Institute of Molecular Biology, Mainz, Germany
| | - Noel J Buckley
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, United Kingdom
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
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38
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Wu Y, Xing X, You T, Liang R, Liu J. RT-qPCR with chimeric dU stem-loop primer is efficient for the detection of bacterial small RNAs. Appl Microbiol Biotechnol 2017; 101:4561-4568. [PMID: 28314872 DOI: 10.1007/s00253-017-8181-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/30/2017] [Accepted: 02/04/2017] [Indexed: 01/18/2023]
Abstract
Small non-coding RNAs are considered be involved in the regulation of multiple cellular processes. Quantitative reverse transcription PCR (RT-qPCR) is widely used in the detection of eukaryotic microRNA, and the stem-loop primers can improve the specificity and efficiency of reverse transcription. However, the loop structure of primers probably influence the next quantitative amplification due to the base stacking and steric hindrance. Here, we designed a chimeric stem-loop primer with a deoxyuracil (dU) base located near the RNA matching part. After the reverse transcription, uracil-DNA glycosylase (UDG) treatment was used to remove the dU base and destroy the stem-loop structure of RT product. Enzymatic assay confirmed that the recombinant UDG could efficiently eliminate the dU base in the oligonucleotide. Transcriptions of two small RNAs (TFF and ryeA) in Escherichia coli were detected by RT-qPCR with different primers. Results showed that the use of the chimeric dU stem-loop primer and UDG treatment could enhance the detection specificity and sensitivity about 1.1- to 3.4-fold, compared to those with traditional stem-loop primer and linear primer. Total RNA of 1-10 pg was enough for efficient detection with the chimeric stem-loop primers. In a word, this strategy could promote the RT-qPCR detection efficiency on the transcription of bacterial small RNAs even in trace samples and can facilitate the detection of exiguous change in cellular metabolism.
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Affiliation(s)
- Yangfan Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xuejiao Xing
- School of Pharmacy, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ting You
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Jianhua Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
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39
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Bottini S, Del Tordello E, Fagnocchi L, Donati C, Muzzi A. PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes. Front Mol Biosci 2017; 3:82. [PMID: 28066774 PMCID: PMC5167695 DOI: 10.3389/fmolb.2016.00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/30/2016] [Indexed: 11/13/2022] Open
Abstract
PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions. Finally, the pipeline includes anno-chipSAD a method to annotate the detected transcripts in comparison to the genome annotation. Overall, our pipeline allows transcriptional profile analysis of both coding and non-coding portions of the chromosome in a single framework. Importantly, due to its versatile characteristics, it will be of wide applicability to analyse, not only microarray signals, but also data from other high throughput technologies such as RNA-sequencing. The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.
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Affiliation(s)
| | | | | | - Claudio Donati
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach San Michele all'Adige, Italy
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40
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Dong X, Wang X, Zhang F, Tian W. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome. Mol Biol Evol 2016; 33:2565-75. [PMID: 27401230 PMCID: PMC5026254 DOI: 10.1093/molbev/msw128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Accelerated evolution of regulatory sequence can alter the expression pattern of target genes, and cause phenotypic changes. In this study, we used DNase I hypersensitive sites (DHSs) to annotate putative regulatory sequences in the human genome, and conducted a genome-wide analysis of the effects of accelerated evolution on regulatory sequences. Working under the assumption that local ancient repeat elements of DHSs are under neutral evolution, we discovered that ∼0.44% of DHSs are under accelerated evolution (ace-DHSs). We found that ace-DHSs tend to be more active than background DHSs, and are strongly associated with epigenetic marks of active transcription. The target genes of ace-DHSs are significantly enriched in neuron-related functions, and their expression levels are positively selected in the human brain. Thus, these lines of evidences strongly suggest that accelerated evolution on regulatory sequences plays important role in the evolution of human-specific phenotypes.
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Affiliation(s)
- Xinran Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Xiao Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Weidong Tian
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, P.R. China Children's Hospital of Fudan University, Shanghai, P.R. China
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41
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Abstract
A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential.
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Affiliation(s)
- Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
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42
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Blocker AW, Airoldi EM. Template-Based Models for Genome-Wide Analysis of Next-Generation Sequencing Data at Base-Pair Resolution. J Am Stat Assoc 2016. [DOI: 10.1080/01621459.2016.1141095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Wegner MS, Schiffmann S, Parnham MJ, Geisslinger G, Grösch S. The enigma of ceramide synthase regulation in mammalian cells. Prog Lipid Res 2016; 63:93-119. [PMID: 27180613 DOI: 10.1016/j.plipres.2016.03.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/17/2016] [Accepted: 03/27/2016] [Indexed: 12/20/2022]
Abstract
Ceramide synthases (CerS) are key enzymes in the lipid metabolism of eukaryotic cells. Their products, ceramides (Cer), are components of cellular membranes but also mediate signaling functions in physiological processes such as proliferation, skin barrier function and cerebellar development. In pathophysiological processes such as multiple sclerosis and tumor progression, ceramide levels are altered, which can be ascribed, partly, to dysregulation of CerS gene transcription. Most publications deal with the effects of altered ceramide levels on physiological and pathophysiological processes, but the regulation of the appropriate CerS is frequently not investigated. This is insufficient for the clarification of the role of ceramides, because most ceramide species are generated by at least two CerS. The mechanisms of CerS regulation are manifold and it seems that each CerS isoform is regulated individually. For this reason, we discuss the different CerS separately in this review. From transcriptional regulation to alteration of protein activity, the possibilities to influence CerS are diverse. Furthermore, CerS are influenced by a variety of molecules including hormones and lipids. Without claiming completeness, we provide a résumé of the regulatory mechanisms for each CerS in mammalian cells and how dysregulation of these mechanisms during physiological processes may lead to pathophysiological processes.
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Affiliation(s)
- Marthe-Susanna Wegner
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann- Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Susanne Schiffmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology (TMP), Frankfurt am Main, Germany
| | - Michael John Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology (TMP), Frankfurt am Main, Germany
| | - Gerd Geisslinger
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann- Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Sabine Grösch
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann- Wolfgang Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Abstract
Although deoxyribonuclease I (DNase I) was used to probe the structure of the nucleosome in the 1960s and 1970s, in the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions devoid of nucleosomes. Here, we reveal for the first time that DNase I can be used to precisely map the (translational) positions of in vivo nucleosomes genome-wide. Specifically, exploiting a distinctive DNase I cleavage profile within nucleosome-associated DNA—including a signature 10.3 base pair oscillation that corresponds to accessibility of the minor groove as DNA winds around the nucleosome—we develop a Bayes-factor–based method that can be used to map nucleosome positions along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables us to identify translational positioning details not apparent in MNase digestion of linker DNA. Because the oscillatory pattern corresponds to nucleosome rotational positioning, it also reveals the rotational context of transcription factor (TF) binding sites. We show that potential binding sites within nucleosome-associated DNA are often centered preferentially on an exposed major or minor groove. This preferential localization may modulate TF interaction with nucleosome-associated DNA as TFs search for binding sites.
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Zhang T, Marand AP, Jiang J. PlantDHS: a database for DNase I hypersensitive sites in plants. Nucleic Acids Res 2015; 44:D1148-53. [PMID: 26400163 PMCID: PMC4702941 DOI: 10.1093/nar/gkv962] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/11/2015] [Indexed: 01/24/2023] Open
Abstract
Gene expression is regulated by orchestrated binding of regulatory proteins to promoters and other cis-regulatory DNA elements (CREs). Several plant databases have been developed for mapping promoters or DNA motifs associated with promoters. However, there is a lack of databases that allow investigation for all CREs. Here we present PlantDHS (http://plantdhs.org), a plant DNase I hypersensitive site (DHS) database that integrates histone modification, RNA sequencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence within an easily navigated user interface. DHSs are indicative of all CREs, including promoters, enhancers, silencers, insulators and transcription factor binding sites; all of which play immense roles in global gene expression regulation. PlantDHS provides a platform to predict all CREs associated with individual genes from three model plant species, including Arabidopsis thaliana, Brachypodium distachyon and rice (Oryza sativa). PlantDHS is especially valuable in the detection of distant CREs that are located away from promoters.
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Affiliation(s)
- Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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46
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Bowman SK. Discovering enhancers by mapping chromatin features in primary tissue. Genomics 2015; 106:140-144. [DOI: 10.1016/j.ygeno.2015.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/04/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
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47
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Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN. Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation. PLoS One 2015; 10:e0135410. [PMID: 26305327 PMCID: PMC4549251 DOI: 10.1371/journal.pone.0135410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 12/22/2022] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1’s role in gene regulation.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Taha Al-jumaily
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Abdallah M. Eteleeb
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert M. Flight
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shao Xiaorong
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Hunter Moseley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
| | - Yvonne N. Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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Chromatin Dynamics in the Regulation of CFTR Expression. Genes (Basel) 2015; 6:543-58. [PMID: 26184320 PMCID: PMC4584316 DOI: 10.3390/genes6030543] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/31/2022] Open
Abstract
The contribution of chromatin dynamics to the regulation of human disease-associated loci such as the cystic fibrosis transmembrane conductance regulator (CFTR) gene has been the focus of intensive experimentation for many years. Recent technological advances in the analysis of transcriptional mechanisms across the entire human genome have greatly facilitated these studies. In this review we describe the complex machinery of tissue-specific regulation of CFTR expression, and put earlier observations in context by incorporating them into datasets generated by the most recent genomics methods. Though the gene promoter is required for CFTR expression, cell-type specific regulatory elements are located elsewhere in the gene and in flanking intergenic regions. Probably within its own topological domain established by the architectural proteins CTCF and cohesin, the CFTR locus utilizes chromatin dynamics to remodel nucleosomes, recruit cell-selective transcription factors, and activate intronic enhancers. These cis-acting elements are then brought to the gene promoter by chromatin looping mechanisms, which establish long-range interactions across the locus. Despite its complexity, the CFTR locus provides a paradigm for elucidating the critical role of chromatin dynamics in the transcription of individual human genes.
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Recent advances in functional assays of transcriptional enhancers. Genomics 2015; 106:137-139. [PMID: 26100358 DOI: 10.1016/j.ygeno.2015.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/08/2015] [Indexed: 01/23/2023]
Abstract
In this special edition of Genomics, we present reviews of the current state of the field in identifying and functionally understanding transcriptional enhancers in cells and developing tissues. Typically several enhancers coordinate the expression of an individual target gene, each controlling that gene's expression in specific cell types at specific times. Until recently, identifying each gene's enhancers had been challenging because enhancers do not occupy prescribed locations relative to their target genes. Recently there have been powerful advances in DNA sequencing and other technologies that make it possible to identify the majority of enhancers in virtually any cell type of interest. The reviews in this edition of Genomics highlight some of these new and powerful approaches.
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50
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Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat Chem 2015; 7:394-402. [PMID: 25901817 PMCID: PMC4617616 DOI: 10.1038/nchem.2224] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/27/2015] [Indexed: 12/12/2022]
Abstract
Post-translational modification of the histone proteins in chromatin plays a central role in epigenetic control of DNA-templated processes in eukaryotic cells. Developing methods that enable the structure of histones to be manipulated is therefore essential to understand the biochemical mechanisms underlying genomic regulation. Here we present a synthetic biology method to engineer histones bearing site-specific modifications on cellular chromatin using protein trans-splicing. We genetically fused the N-terminal fragment of ultrafast split-intein to the C-terminus of histone H2B, which upon reaction with a complementary synthetic C-intein, generated labeled histone. Using this approach, we incorporated various non-native chemical modifications to chromatin in vivo with temporal control. Furthermore, the time and concentration dependence of protein trans-splicing performed in nucleo enabled us to examine differences in the accessibility of the euchromatin and heterochromatin regions of the epigenome. Finally, we used protein trans-splicing to semi-synthesize a native histone modification, H2BK120 ubiquitination, in isolated nuclei, and show that this can trigger downstream epigenetic cross-talk of H3K79 methylation.
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