1
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Alkhayer R, Ponath V, Pogge von Strandmann E. Protocol to target a promoter region in human embryonic kidney cells using the CRISPR-dCas9 system for single-locus proteomics. STAR Protoc 2024; 5:103045. [PMID: 38691460 PMCID: PMC11070752 DOI: 10.1016/j.xpro.2024.103045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
The unbiased identification of less-abundant transcription factors, which direct the expression of a target gene, is technically challenging. Here, we present a protocol to analyze the locus-specific chromatin-regulating proteome using in situ capture of chromatin interactions by an inactive Cas9 (dCas9). We describe steps for designing guide RNAs and transfection, followed by precipitation of chromatin and associated proteins. In the last step, we describe the elution of DNA and proteins for PCR and mass spectrometric analysis, respectively. For complete details on the use and execution of this protocol, please refer to Alkhayer et al.1.
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Affiliation(s)
- Reem Alkhayer
- Institute for Tumor Immunology, Philipps University Marburg, 35043 Marburg, Germany
| | - Viviane Ponath
- Institute for Tumor Immunology, Philipps University Marburg, 35043 Marburg, Germany.
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2
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Coutte L, Antoine R, Slupek S, Locht C. Combined transcriptomic and ChIPseq analyses of the Bordetella pertussis RisA regulon. mSystems 2024; 9:e0095123. [PMID: 38470037 PMCID: PMC11019879 DOI: 10.1128/msystems.00951-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of Bordetella pertussis virulence is mediated by the two-component system BvgA/S, which activates the transcription of virulence-activated genes (vags). In the avirulent phase, the vags are not expressed, but instead, virulence-repressed genes (vrgs) are expressed, under the control of another two-component system, RisA/K. Here, we combined transcriptomic and chromatin immunoprecipitation sequencing (ChIPseq) data to examine the RisA/K regulon. We performed RNAseq analyses of RisA-deficient and RisA-phosphoablative B. pertussis mutants cultivated in virulent and avirulent conditions. We confirmed that the expression of most vrgs is regulated by phosphorylated RisA. However, the expression of some, including those involved in flagellum biosynthesis and chemotaxis, requires RisA independently of phosphorylation. Many RisA-regulated genes encode proteins with regulatory functions, suggesting multiple RisA regulation cascades. By ChIPseq analyses, we identified 430 RisA-binding sites, 208 within promoter regions, 201 within open reading frames, and 21 in non-coding regions. RisA binding was demonstrated in the promoter regions of most vrgs and, surprisingly, of some vags, as well as for other genes not identified as vags or vrgs. Unexpectedly, many genes, including some vags, like prn, brpL, bipA, and cyaA, contain a BvgA-binding site and a RisA-binding site, which increases the complexity of the RisAK/BvgAS network in B. pertussis virulence regulation.IMPORTANCEThe expression of virulence-activated genes (vags) of Bordetella pertussis, the etiological agent of whooping cough, is under the transcriptional control of the two-component system BvgA/S, which allows the bacterium to switch between virulent and avirulent phases. In addition, the more recently identified two-component system RisA/K is required for the expression of B. pertussis genes, collectively named vrgs, that are repressed during the virulent phase but activated during the avirulent phase. We have characterized the RisA/K regulon by combined transcriptomic and chromatin immunoprecipitation sequencing analyses. We identified more than 400 RisA-binding sites. Many of them are localized in promoter regions, especially vrgs, but some were found within open reading frames and in non-coding regions. Surprisingly, RisA-binding sites were also found in promoter regions of some vags, illustrating the previously underappreciated complexity of virulence regulation in B. pertussis.
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Affiliation(s)
- Loïc Coutte
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Rudy Antoine
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Stephanie Slupek
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Camille Locht
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
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3
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Willemin G, Mange F, Praz V, Lorrain S, Cousin P, Roger C, Willis IM, Hernandez N. Contrasting effects of whole-body and hepatocyte-specific deletion of the RNA polymerase III repressor Maf1 in the mouse. Front Mol Biosci 2023; 10:1297800. [PMID: 38143800 PMCID: PMC10746880 DOI: 10.3389/fmolb.2023.1297800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
MAF1 is a nutrient-sensitive, TORC1-regulated repressor of RNA polymerase III (Pol III). MAF1 downregulation leads to increased lipogenesis in Drosophila melanogaster, Caenorhabditis elegans, and mice. However, Maf1 -/- mice are lean as increased lipogenesis is counterbalanced by futile pre-tRNA synthesis and degradation, resulting in increased energy expenditure. We compared Chow-fed Maf1 -/- mice with Chow- or High Fat (HF)-fed Maf1 hep-/- mice that lack MAF1 specifically in hepatocytes. Unlike Maf1 -/- mice, Maf1 hep-/- mice become heavier and fattier than control mice with old age and much earlier under a HF diet. Liver ChIPseq, RNAseq and proteomics analyses indicate increased Pol III occupancy at Pol III genes, very few differences in mRNA accumulation, and protein accumulation changes consistent with increased lipogenesis. Futile pre-tRNA synthesis and degradation in the liver, as likely occurs in Maf1 hep-/- mice, thus seems insufficient to counteract increased lipogenesis. Indeed, RNAseq and metabolite profiling indicate that liver phenotypes of Maf1 -/- mice are strongly influenced by systemic inter-organ communication. Among common changes in the three phenotypically distinct cohorts, Angiogenin downregulation is likely linked to increased Pol III occupancy of tRNA genes in the Angiogenin promoter.
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Affiliation(s)
- Gilles Willemin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - François Mange
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Lausanne Genomic Technologies Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Séverine Lorrain
- Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Catherine Roger
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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4
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Gong H, Li M, Ji M, Zhang X, Yuan Z, Zhang S, Yang Y, Li C, Chen Y. Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell line. STAR Protoc 2023; 4:102188. [PMID: 37000618 PMCID: PMC10068612 DOI: 10.1016/j.xpro.2023.102188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 04/01/2023] Open
Abstract
Here, we present a protocol for calculating the spatial density of regulatory chromatin interactions (SD-RCI) using Hi-C, ATAC-seq, and ChIP-seq datasets from the same cell line. We describe steps for selecting and preprocessing datasets, training and predicting a model to obtain regulatory chromatin interactions, and evaluating model performance. We then detail calculation of SD-RCI and visualization of the correlation between SD-RCI and gene expression. This protocol is applicable to Hi-C, ATAC-seq, and ChIP-seq data from the human cell line. For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1.
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Affiliation(s)
- Haiyan Gong
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Minghong Li
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Mengdie Ji
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Xiaotong Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China; Shunde Innovation School, University of Science and Technology Beijing, Foshan 528399, China.
| | - Zan Yuan
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Sichen Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yi Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Chun Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
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5
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Das S, Mukherjee S, Ali N. Purification of immune-active macrophage super enhancers by chemical cross-linked chromatin immune precipitation. STAR Protoc 2023; 4:102004. [PMID: 36638018 PMCID: PMC9852664 DOI: 10.1016/j.xpro.2022.102004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/08/2022] [Accepted: 12/18/2022] [Indexed: 01/12/2023] Open
Abstract
Isolation of extraordinarily long-length super-enhancers (SEs) using typical chromatin immune precipitation (ChIP) techniques can lead to DNA breakage due to uncontrolled cross-linking. We present a redefined ChIP technique for SE purification. After controlled paraformaldehyde-based cross-linking, glycine was used to quench the cross-linker followed by mild sonication. The sonication produced ideal fragment length of long-length SE chromatin. Presently, miR146a-5p SE of macrophages was pulled using BRD4 protein. Our protocol can reproducibly simplify the SE element isolation issues, in a quality-controlled manner. For complete details on the use and execution of this protocol, please refer to Das et al. (2021).1.
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Affiliation(s)
- Sonali Das
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India.
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6
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Groelly FJ, Dagg RA, Mailler J, Halazonetis TD, Tarsounas M. High-resolution mapping of mitotic DNA synthesis under conditions of replication stress in cultured cells. STAR Protoc 2023; 4:101970. [PMID: 36598851 PMCID: PMC9826876 DOI: 10.1016/j.xpro.2022.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/13/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Cells experiencing DNA replication stress enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here we describe a protocol to identify at genome wide and at high resolution the genomic sites where MiDAS occurs in cells exposed to aphidicolin. We use EdU incorporation to label nascent DNA in mitotic cells, followed by isolation of the EdU-labeled DNA and next-generation sequencing. For complete details on the use and execution of this protocol, please refer to Groelly et al. (2022)1 and Macheret et al. (2020).2.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Jonathan Mailler
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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7
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Lee H, Sanidas I, Dyson NJ, Lawrence MS. Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP. STAR Protoc 2023; 4:101991. [PMID: 36607812 PMCID: PMC9826822 DOI: 10.1016/j.xpro.2022.101991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/16/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns. For complete details on the use and execution of this protocol, please refer to Sanidas et al. (2022).1.
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Affiliation(s)
- Hanjun Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Ioannis Sanidas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY 14203, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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8
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Moutsopoulos I, Williams EC, Mohorianu II. bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data. Brief Bioinform 2023; 24:6965538. [PMID: 36583521 PMCID: PMC9851288 DOI: 10.1093/bib/bbac591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
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Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
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9
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Höllbacher B, Strickland B, Greulich F, Uhlenhaut NH, Heinig M. Machine learning reveals STAT motifs as predictors for GR-mediated gene repression. Comput Struct Biotechnol J 2023; 21:1697-1710. [PMID: 36879886 PMCID: PMC9984779 DOI: 10.1016/j.csbj.2023.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/13/2023] Open
Abstract
Glucocorticoids are potent immunosuppressive drugs, but long-term treatment leads to severe side-effects. While there is a commonly accepted model for GR-mediated gene activation, the mechanism behind repression remains elusive. Understanding the molecular action of the glucocorticoid receptor (GR) mediated gene repression is the first step towards developing novel therapies. We devised an approach that combines multiple epigenetic assays with 3D chromatin data to find sequence patterns predicting gene expression change. We systematically tested> 100 models to evaluate the best way to integrate the data types and found that GR-bound regions hold most of the information needed to predict the polarity of Dex-induced transcriptional changes. We confirmed NF-κB motif family members as predictors for gene repression and identified STAT motifs as additional negative predictors.
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Affiliation(s)
- Barbara Höllbacher
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Munich 85764, Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, 85748 Garching, Germany
| | - Benjamin Strickland
- Metabolic Programming, TUM School of Life Sciences, Weihenstephan & ZIEL-Institute for Food & Health, Freising, Germany
| | - Franziska Greulich
- Metabolic Programming, TUM School of Life Sciences, Weihenstephan & ZIEL-Institute for Food & Health, Freising, Germany.,Institute for Diabetes and Endocrinology (IDE), Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) and German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - N Henriette Uhlenhaut
- Metabolic Programming, TUM School of Life Sciences, Weihenstephan & ZIEL-Institute for Food & Health, Freising, Germany.,Institute for Diabetes and Endocrinology (IDE), Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) and German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Munich 85764, Neuherberg, Germany.,Department of Computer Science, TUM School of Computation, Information and Technology, Technical University Munich, 85748 Garching, Germany
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10
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Ji F, Van Rechem C, Whetstine JR, Sadreyev RI. Computational workflow for integrative analyses of DNA replication timing, epigenomic, and transcriptomic data. STAR Protoc 2022; 3:101827. [PMID: 36386876 PMCID: PMC9647704 DOI: 10.1016/j.xpro.2022.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Temporal profiling of DNA replication timing (RT) in combination with chromatin modifications, chromatin accessibility, and gene expression provides new insights into the causal relationships between chromatin and RT during cell cycle. Here, we describe a protocol for in-depth integrative computational analyses of Repli-seq, ATAC-seq, RNA-seq, and ChIP-seq or CUT&RUN data for multiple marks at various time points across cell cycle and changes in their interrelationships upon an experimental perturbation (e.g., knockdown or overexpression of a regulatory protein). For complete details on the use and execution of this protocol, please refer to Van Rechem et al. (2021).
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Affiliation(s)
- Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Harvard Medical School Department of Medicine, 13th Street Bldg. 149, Charlestown, MA 02129, USA; Stanford Medicine Department of Pathology, 269 Campus Drive, Stanford, CA 94305, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Harvard Medical School Department of Medicine, 13th Street Bldg. 149, Charlestown, MA 02129, USA; Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue West 260, Philadelphia, PA 19111, USA; Cancer Epigenetics Institute, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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11
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Williams EC, Chazarra-Gil R, Shahsavari A, Mohorianu I. The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes. Genes (Basel) 2022; 13:genes13122265. [PMID: 36553532 PMCID: PMC9777937 DOI: 10.3390/genes13122265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The advances in high-throughput sequencing (HTS) have enabled the characterisation of biological processes at an unprecedented level of detail; most hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains a main challenge. Although variability in results may be introduced at various stages, e.g., alignment, summarisation or detection of differential expression, one source of variability was systematically omitted: the sequencing design, which propagates through analyses and may introduce an additional layer of technical variation. We illustrate qualitative and quantitative differences arising from splitting samples across lanes on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling and the peaks' properties. At the single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10× data are presented. The observed reduction in the number of unique sequenced fragments limits the level of detail on which the different prediction approaches depend. Furthermore, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias. Subsequently, we observe an overall reduction in sequencing complexity and a distortion in the biological signal across technologies, experimental contexts, organisms and tissues.
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Affiliation(s)
- Eleanor C. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ruben Chazarra-Gil
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Life Sciences-Transcriptomics and Functional Genomics Lab, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Arash Shahsavari
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Correspondence:
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Abstract
Classic approaches to characterizing cell cycle leverage chemicals or altered nucleotide pools, which could impact chromatin states at specific phases of the cell cycle. Such approaches could induce metabolic alterations and/or DNA damage, which could reshape protein recruitment and histone modifications. In this protocol, we describe ways to fix and sort cells across the cell cycle based on their DNA content. We further detail immunoprecipitation and library preparation, allowing analysis of the epigenome by chromatin immunoprecipitation sequencing (ChIP-seq) for small numbers of cells. For complete details on the use and execution of this protocol, please refer to Van Rechem et al. (2021). Drugs are not used to arrest cells at different cell cycle phases This protocol is adapted to small amounts of chromatin for ChIP-seq This protocol can be adapted to separate additional cell cycle phases This protocol can be adapted to any cycling cells and other histone modifications
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13
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Cholico GN, Nault R, Zacharewski TR. Genome-Wide ChIPseq Analysis of AhR, COUP-TF, and HNF4 Enrichment in TCDD-Treated Mouse Liver. Int J Mol Sci 2022; 23:1558. [PMID: 35163483 PMCID: PMC8836158 DOI: 10.3390/ijms23031558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 02/01/2023] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor known for mediating the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds. Although the canonical mechanism of AhR activation involves heterodimerization with the aryl hydrocarbon receptor nuclear translocator, other transcriptional regulators that interact with AhR have been identified. Enrichment analysis of motifs in AhR-bound genomic regions implicated co-operation with COUP transcription factor (COUP-TF) and hepatocyte nuclear factor 4 (HNF4). The present study investigated AhR, HNF4α and COUP-TFII genomic binding and effects on gene expression associated with liver-specific function and cell differentiation in response to TCDD. Hepatic ChIPseq data from male C57BL/6 mice at 2 h after oral gavage with 30 µg/kg TCDD were integrated with bulk RNA-sequencing (RNAseq) time-course (2-72 h) and dose-response (0.01-30 µg/kg) datasets to assess putative AhR, HNF4α and COUP-TFII interactions associated with differential gene expression. Functional enrichment analysis of differentially expressed genes (DEGs) identified differential binding enrichment for AhR, COUP-TFII, and HNF4α to regions within liver-specific genes, suggesting intersections associated with the loss of liver-specific functions and hepatocyte differentiation. Analysis found that the repression of liver-specific, HNF4α target and hepatocyte differentiation genes, involved increased AhR and HNF4α binding with decreased COUP-TFII binding. Collectively, these results suggested TCDD-elicited loss of liver-specific functions and markers of hepatocyte differentiation involved interactions between AhR, COUP-TFII and HNF4α.
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Affiliation(s)
| | | | - Tim R. Zacharewski
- Biochemistry & Molecular Biology, Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA; (G.N.C.); (R.N.)
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14
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Malabarba J, Chen Z, Windels D, Verdier J. Chromatin Immunoprecipitation dataset of H3ac and H3K27me3 histone marks followed by DNA sequencing of Medicago truncatula embryos during control and heat stress conditions to decipher epigenetic regulation of desiccation tolerance acquisition. Data Brief 2022; 40:107793. [PMID: 35036490 PMCID: PMC8749208 DOI: 10.1016/j.dib.2022.107793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022] Open
Abstract
Desiccation tolerance (DT) is one of the most important processes that seeds need to acquire during seed maturation because it will ensure survival until seeds have favourable conditions for germinating. Moreover, in the current climate warming context, heat stress and its impact on seed maturation and quality has been increasingly studied by the scientific community. Even if the transcriptomic changes enrolled in DT acquisition and seed heat stress response are fairly known, its epigenetic control has not yet been investigated. Medicago truncatula is a model legume for studying seed molecular mechanisms, which is known to display a delay in the acquisition of seed maturation mechanisms under heat conditions, except for desiccation acquisition. Our aim was to evaluate the role of two histone marks during embryo development under control and heat stress conditions on seed maturation processes, including the DT acquisition. These histone marks have either repressive (H3K27me3) or inducible (H3ac) effects on gene transcription, respectively corresponding to markers of packed and accessible chromatins. We identified all genomic regions bound to the H3K27me3 histones at four developmental stages and to the H3ac histones at the two earlier developmental stages during seed maturation, from seed filling to mature dry seeds, collected under optimal and heat stress conditions in the model legume, Medicago truncatula (reference genotype A17). A list of genes and promoters potentially linked to these two histone marks is reported and could provide clues about the epigenetic regulation of seed maturation between control and heat stress conditions, including the desiccation tolerance acquisition.
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Affiliation(s)
- Jaiana Malabarba
- University Angers, Institute Agro, INRAE, IRHS, SFR QUASAV, Angers F-49000, France
| | - Zhijuan Chen
- University Angers, Institute Agro, INRAE, IRHS, SFR QUASAV, Angers F-49000, France
| | - David Windels
- University Angers, Institute Agro, INRAE, IRHS, SFR QUASAV, Angers F-49000, France
| | - Jerome Verdier
- University Angers, Institute Agro, INRAE, IRHS, SFR QUASAV, Angers F-49000, France
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15
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Yao C, Shao X, Li J, Deng X. Optimized protocols for ChIP-seq and deletion mutant construction in Pseudomonas syringae. STAR Protoc 2021; 2:100776. [PMID: 34485942 PMCID: PMC8406033 DOI: 10.1016/j.xpro.2021.100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chromatin immunoprecipitation sequencing (ChIP-seq) is an efficient technique to identify the binding sites of transcription factors (TFs) in both eukaryotes and prokaryotes. However, its application in bacteria is very heterogeneous. In this protocol, we optimized the methods of ChIP-seq that can be widely applied to plant pathogens. We used homologous recombination to construct pK18mobsacB-Psph plasmid instead of restriction site ligation and replaced transconjugation with electroporation transformation in Pseudomonas syringae deletion mutant construction, which is more efficient and faster than previous methods. For complete details on the use and execution of this protocol, please refer to Shao et al. (2021). This approach can be used to construct TF-overexpressed Pseudomonas syringae strain Protocols for ChIP-seq library construction of Pseudomonas syringae A simplified procedure to construct a deletion mutant of Pseudomonas syringae
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Affiliation(s)
- Chunyan Yao
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Xiaolong Shao
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jingwei Li
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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16
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Li Y, Nakka K, Olender T, Gingras-Gelinas P, Wong MMK, Robinson DCL, Bandukwala H, Palii CG, Neyret O, Brand M, Blais A, Dilworth FJ. Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag. STAR Protoc 2021; 2:100751. [PMID: 34467227 PMCID: PMC8384913 DOI: 10.1016/j.xpro.2021.100751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Muscle stem cells (MuSCs) are a rare stem cell population that provides myofibers with a remarkable capacity to regenerate after tissue injury. Here, we have adapted the Cleavage Under Target and Tagmentation technology to the mapping of the chromatin landscape and transcription factor binding in 50,000 activated MuSCs isolated from injured mouse hindlimb muscles. We have applied this same approach to human CD34+ hematopoietic stem and progenitor cells. This protocol could be adapted to any rare stem cell population. For complete details on the use and execution of this protocol, please refer to Robinson et al. (2021). Isolation of muscle stem cells from cardiotoxin-injured tissue CUT&Tag-based mapping of epigenetic landscape and transcription factor enrichment Adaptation of a synthetic spike-in DNA for effective normalization across samples Pipeline for efficient analysis of CUT&Tag sequencing data hosted on Git-hub
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Affiliation(s)
- Yuefeng Li
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kiran Nakka
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Matthew Man-Kin Wong
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Daniel C L Robinson
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hina Bandukwala
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Odile Neyret
- Molecular Biology Platform, Institut de Recherche Clinique de Montreal, Montreal, QC, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Alexandre Blais
- Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,CI3, University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, ON, Canada
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, ON, Canada
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17
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Greulich F, Mechtidou A, Horn T, Uhlenhaut NH. Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation. STAR Protoc 2021; 2:100609. [PMID: 34189474 PMCID: PMC8220248 DOI: 10.1016/j.xpro.2021.100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Quantifying differential genome occupancy by chromatin immunoprecipitation (ChIP) remains challenging due to variation in chromatin fragmentation, immunoprecipitation efficiencies, and intertube variability. In this protocol, we add heterologous spike-ins from Drosophila chromatin as an internal control to the mice chromatin before immunoprecipitation to normalize for technical variation in ChIP-qPCR or ChIP-seq. The choice of spike-in depends on the evolutionary conservation of the protein of interest and the antibody used. For complete details on the use and execution of this protocol, please refer to Greulich et al. (2021).
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Affiliation(s)
- Franziska Greulich
- Metabolic Programming, School of Life Sciences Weihenstephan, ZIEL-Institute for Food & Health, Technische Universitaet Muenchen (TUM), 85354 Freising, Germany
| | - Aikaterini Mechtidou
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany
| | - Teresa Horn
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany
| | - Nina Henriette Uhlenhaut
- Metabolic Programming, School of Life Sciences Weihenstephan, ZIEL-Institute for Food & Health, Technische Universitaet Muenchen (TUM), 85354 Freising, Germany.,Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany
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18
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Lismer A, Lambrot R, Lafleur C, Dumeaux V, Kimmins S. ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance. STAR Protoc 2021; 2:100602. [PMID: 34159325 PMCID: PMC8202352 DOI: 10.1016/j.xpro.2021.100602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In the field of epigenetic inheritance, delineating molecular mechanisms implicated in the transfer of paternal environmental conditions to descendants has been elusive. This protocol details how to track sperm chromatin intergenerationally. We describe mouse model design to probe chromatin states in single mouse sperm and techniques to assess pre-implantation embryo chromatin and gene expression. We place emphasis on how to obtain high-quality and quantifiable data sets in sperm and embryos, as well as highlight the limitations of working with low input. For complete details on the use and execution of this protocol, please refer to Lismer et al. (2021). Assessment of paternal environmental exposure effects on sperm chromatin by ChIP-seq Tracking chromatin changes in sperm to embryos using ultra-low-input (ULI)-ChIP-seq Identification of gene expression changes in embryos using low-input mRNA-seq
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Vanessa Dumeaux
- PERFORM Center, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada.,Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada
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Xu W, Ye Y, Sharrocks AD, Zhang W, Chen X. Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation. STAR Protoc 2020; 1:100187. [PMID: 33377081 PMCID: PMC7757419 DOI: 10.1016/j.xpro.2020.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data. For complete details on the use and execution of this protocol, please refer to Schmidl et al. (2015). For example data produced by this protocol, please refer to Henriksson et al. (2019) and Zhang et al. (2019). Preparation of a transposase-assisted ChIP-seq library A simpler and cheaper approach than traditional ChIP-seq A sensitive and reliable method for transcription factors and histone modifications
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Affiliation(s)
- Wei Xu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ying Ye
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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20
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Coutte L, Antoine R, Slupek S, Solans L, Derop J, Bonnefond A, Hot D, Locht C. Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis. mSystems 2020; 5:e00208-20. [PMID: 32430408 DOI: 10.1128/mSystems.00208-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology. Bordetella pertussis regulates the production of its virulence factors by the two-component system BvgAS. In the virulence phase, BvgS phosphorylates BvgA, which then activates the transcription of virulence-activated genes (vags). In the avirulence phase, such as during growth in the presence of MgSO4, BvgA is not phosphorylated and the vags are not expressed. Instead, a set of virulence-repressed genes (vrgs) is expressed. Here, we performed transcriptome sequencing (RNAseq) analyses on B. pertussis cultivated with or without MgSO4 and on a BvgA-deficient Tohama I derivative. We observed that 146 genes were less expressed under modulating conditions or in the BvgA-deficient strain than under the nonmodulating condition, while 130 genes were more expressed. Some of the genes code for proteins with regulatory functions, suggesting a BvgA/S regulation cascade. To determine which genes are directly regulated by BvgA, we performed chromatin immunoprecipitation sequencing (ChIPseq) analyses. We identified 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Among the former, 32 are in BvgA-regulated putative promoter regions. Some vags, such as dnt and fhaL, contain no BvgA-binding site, suggesting indirect BvgA regulation. Unexpectedly, BvgA also bound to some vrg putative promoter regions. Together, these observations indicate an unrecognized complexity of BvgA/S biology. IMPORTANCEBordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology.
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21
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Zhang Y, Song X, Herrup K. Context-Dependent Functions of E2F1: Cell Cycle, Cell Death, and DNA Damage Repair in Cortical Neurons. Mol Neurobiol 2020; 57:2377-2390. [PMID: 32062842 DOI: 10.1007/s12035-020-01887-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/29/2020] [Indexed: 01/17/2023]
Abstract
DNA damage has been reported to induce cell cycle-related neuronal death. This is significant as aberrant cell cycle re-entry of mature, post-mitotic neurons contributes to neurodegeneration. In this study, we investigate how DNA damage elicited by exposure to the topoisomerase I inhibitor camptothecin (CPT) leads to cycle-related death of cultured cortical neurons and examine the function of E2F1 in this process. CPT treatment induced cell cycle initiation of cortical neurons and elevated the expression of certain cell cycle components (e.g., cyclin D1, CDK4, E2F1) but failed to drive S phase entry or DNA synthesis. The arrest in the cell cycle is explained by the elevated expression of the CDK inhibitor p21Cip1. Though its level was increased after CPT treatment, E2F1 did not drive treated neurons into the G1-S phase transition. E2F1 overexpression led to cell cycle activation and acute neuronal apoptosis without detectable entry of the neurons into S phase. ChIPseq analysis demonstrated that E2F1 predominantly occupies positions on or near the promoters of cell cycle related genes. Instead, in CPT-treated neurons, E2F1 preferentially regulated DNA repair related genes. Our study reveals that the functions of E2F1 in postmitotic neurons are context-dependent and offers novel insights into the role of E2F1 in DNA damage induced cycle-related neuronal death.
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Affiliation(s)
- Yang Zhang
- Division of Life Science and the State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuan Song
- Division of Life Science and the State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Karl Herrup
- Division of Life Science and the State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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22
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Buchberger E, Reis M, Lu TH, Posnien N. Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. Genes (Basel) 2019; 10:E492. [PMID: 31261769 PMCID: PMC6678813 DOI: 10.3390/genes10070492] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.
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Affiliation(s)
- Elisa Buchberger
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Micael Reis
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Ting-Hsuan Lu
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
- International Max Planck Research School for Genome Science, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Nico Posnien
- University Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Dpt. of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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Nash C, Boufaied N, Mills IG, Franco OE, Hayward SW, Thomson AA. Genome-wide analysis of AR binding and comparison with transcript expression in primary human fetal prostate fibroblasts and cancer associated fibroblasts. Mol Cell Endocrinol 2018; 471:1-14. [PMID: 28483704 DOI: 10.1016/j.mce.2017.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/27/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
The androgen receptor (AR) is a transcription factor, and key regulator of prostate development and cancer, which has discrete functions in stromal versus epithelial cells. AR expressed in mesenchyme is necessary and sufficient for prostate development while loss of stromal AR is predictive of prostate cancer progression. Many studies have characterized genome-wide binding of AR in prostate tumour cells but none have used primary mesenchyme or stroma. We applied ChIPseq to identify genomic AR binding sites in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR. We identified AR binding sites that were specific to fetal prostate fibroblasts (7534), cancer fibroblasts (629), WPMY1-AR (2561) as well as those common among all (783). Primary fibroblasts had a distinct AR binding profile versus prostate cancer cell lines and tissue, and showed a localisation to gene promoter binding sites 1 kb upstream of the transcriptional start site, as well as non-classical AR binding sequence motifs. We used RNAseq to define transcribed genes associated with AR binding sites and derived cistromes for embryonic and cancer fibroblasts as well as a cistrome common to both. These were compared to several in vivo ChIPseq and transcript expression datasets; which identified subsets of AR targets that were expressed in vivo and regulated by androgens. This analysis enabled us to deconvolute stromal AR targets active in stroma within tumour samples. Taken together, our data suggest that the AR shows significantly different genomic binding site locations in primary prostate fibroblasts compared to that observed in tumour cells. Validation of our AR binding site data with transcript expression in vitro and in vivo suggests that the AR target genes we have identified in primary fibroblasts may contribute to clinically significant and biologically important AR-regulated changes in prostate tissue.
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Affiliation(s)
- Claire Nash
- Department of Surgery, Division of Urology, McGill University and the Cancer Research Program of the McGill University Health Centre Research Institute, Montreal, Quebec, H4A 3J1, Canada
| | - Nadia Boufaied
- Department of Surgery, Division of Urology, McGill University and the Cancer Research Program of the McGill University Health Centre Research Institute, Montreal, Quebec, H4A 3J1, Canada
| | - Ian G Mills
- Movember/Prostate Cancer UK Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Omar E Franco
- Department of Surgery, NorthShore University HealthSystem Research Institute, 1001 University Place, Evanston, IL 60201, USA
| | - Simon W Hayward
- Department of Surgery, NorthShore University HealthSystem Research Institute, 1001 University Place, Evanston, IL 60201, USA
| | - Axel A Thomson
- Department of Surgery, Division of Urology, McGill University and the Cancer Research Program of the McGill University Health Centre Research Institute, Montreal, Quebec, H4A 3J1, Canada.
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Baur J, Otto C, Steger U, Klein-Hessling S, Muhammad K, Pusch T, Murti K, Wismer R, Germer CT, Klein I, Müller N, Serfling E, Avots A. The Transcription Factor NFATc1 Supports the Rejection of Heterotopic Heart Allografts. Front Immunol 2018; 9:1338. [PMID: 29946322 PMCID: PMC6005848 DOI: 10.3389/fimmu.2018.01338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022] Open
Abstract
The immune suppressants cyclosporin A (CsA) and tacrolimus (FK506) are used worldwide in transplantation medicine to suppress graft rejection. Both CsA and FK506 inhibit the phosphatase calcineurin (CN) whose activity controls the immune receptor-mediated activation of lymphocytes. Downstream targets of CN in lymphocytes are the nuclear factors of activated T cells (NFATs). We show here that the activity of NFATc1, the most prominent NFAT factor in activated lymphocytes supports the acute rejection of heterotopic heart allografts. While ablation of NFATc1 in T cells prevented graft rejection, ectopic expression of inducible NFATc1/αA isoform led to rejection of heart allografts in recipient mice. Acceptance of transplanted hearts in mice bearing NFATc1-deficient T cells was accompanied by a reduction in number and cytotoxicity of graft infiltrating cells. In CD8+ T cells, NFATc1 controls numerous intracellular signaling pathways that lead to the metabolic switch to aerobic glycolysis and the expression of numerous lymphokines, chemokines, and their receptors, including Cxcr3 that supports the rejection of allogeneic heart transplants. These findings favors NFATc1 as a molecular target for the development of new strategies to control the cytotoxicity of T cells upon organ transplantation.
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Affiliation(s)
- Johannes Baur
- Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Christoph Otto
- Experimental Surgery, Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Ulrich Steger
- Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Stefan Klein-Hessling
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Khalid Muhammad
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Tobias Pusch
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Krisna Murti
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Rhoda Wismer
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Christoph-Thomas Germer
- Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Ingo Klein
- Transplant and Hepatobiliary Surgery, Department of General, Visceral, Vascular, and Pediatric Surgery, University Hospital of Würzburg, Würzburg, Germany
| | - Nora Müller
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Edgar Serfling
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Andris Avots
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center Mainfranken, Julius-Maximilians University of Würzburg, Würzburg, Germany
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Jain D, Nemec S, Luxey M, Gauthier Y, Bemmo A, Balsalobre A, Drouin J. Regulatory integration of Hox factor activity with T-box factors in limb development. Development 2018; 145:dev.159830. [PMID: 29490982 DOI: 10.1242/dev.159830] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/16/2018] [Indexed: 01/26/2023]
Abstract
In tetrapods, Tbx4, Tbx5 and Hox cluster genes are crucial for forelimb and hindlimb development and mutations in these genes are responsible for congenital limb defects. The molecular basis of their integrated mechanisms of action in the context of limb development remains poorly understood. We studied Tbx4 and Hoxc10 owing to their overlapping loss-of-function phenotypes and colocalized expression in mouse hindlimb buds. We report an extensive overlap between Tbx4 and Hoxc10 genome occupancy and their putative target genes. Tbx4 and Hoxc10 interact directly with each other, have the ability to bind to a previously unrecognized T-box-Hox composite DNA motif and show synergistic activity when acting on reporter genes. Pitx1, the master regulator for hindlimb specification, also shows extensive genomic colocalization with Tbx4 and Hoxc10. Genome occupancy by Tbx4 in hindlimb buds is similar to Tbx5 occupancy in forelimbs. By contrast, another Hox factor, Hoxd13, also interacts with Tbx4/Tbx5 but antagonizes Tbx4/Tbx5-dependent transcriptional activity. Collectively, the modulation of Tbx-dependent activity by Hox factors acting on common DNA targets may integrate different developmental processes for the balanced formation of proportionate limbs.
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Affiliation(s)
- Deepak Jain
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Stephen Nemec
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Amandine Bemmo
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Departement de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, QC, H3J 3J7 Canada
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26
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Nemec S, Luxey M, Jain D, Huang Sung A, Pastinen T, Drouin J. Pitx1 directly modulates the core limb development program to implement hindlimb identity. Development 2017; 144:3325-3335. [PMID: 28807899 DOI: 10.1242/dev.154864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 01/24/2023]
Abstract
Forelimbs (FLs) and hindlimbs (HLs) develop complex musculoskeletal structures that rely on the deployment of a conserved developmental program. Pitx1, a transcription factor gene with expression restricted to HL and absent from FL, plays an important role in generating HL features. The genomic mechanisms by which Pitx1 effects HL identity remain poorly understood. Here, we use expression profiling and analysis of direct Pitx1 targets to characterize the HL- and FL-restricted genetic programs in mouse and situate the Pitx1-dependent gene network within the context of limb-specific gene regulation. We show that Pitx1 is a crucial component of a narrow network of HL-restricted regulators, acting on a developmental program that is shared between FL and HL. Pitx1 targets sites that are in a similar chromatin state in FL and HL and controls expression of patterning genes as well as the chondrogenic program, consistent with impaired chondrogenesis in Pitx1-/- HL. These findings support a model in which multifactorial actions of a limited number of HL regulators redirect the generic limb development program in order to generate the unique structural features of the limb.
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Affiliation(s)
- Stephen Nemec
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Deepak Jain
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Aurélie Huang Sung
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1 Canada
| | - Jacques Drouin
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
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Abstract
The canonical pathway of thyroid hormone signaling involves its binding to nuclear receptors (TRs) acting directly on the transcription of a number of genes. Recent genome-wide studies revealed that chromatin occupancy by TR is not sufficient for transactivation of gene expression. Reciprocally, in some cases, DNA binding by TR may not be required for cellular response. This leaves many new questions to be addressed in future research.
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Affiliation(s)
- Frédéric Flamant
- École Normale Supérieure de Lyon, CNRS, INRA, Institut de Génomique Fonctionnelle de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- *Correspondence: Frédéric Flamant,
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Merhej J, Frigo A, Le Crom S, Camadro JM, Devaux F, Lelandais G. bPeaks: a bioinformatics tool to detect transcription factor binding sites from ChIPseq data in yeasts and other organisms with small genomes. Yeast 2014; 31:375-91. [PMID: 25041923 DOI: 10.1002/yea.3031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 01/04/2023] Open
Abstract
Peak calling is a critical step in ChIPseq data analysis. Choosing the correct algorithm as well as optimized parameters for a specific biological system is an essential task. In this article, we present an original peak-calling method (bPeaks) specifically designed to detect transcription factor (TF) binding sites in small eukaryotic genomes, such as in yeasts. As TF interactions with DNA are strong and generate high binding signals, bPeaks uses simple parameters to compare the sequences (reads) obtained from the immunoprecipitation (IP) with those from the control DNA (input). Because yeasts have small genomes (<20 Mb), our program has the advantage of using ChIPseq information at the single nucleotide level and can explore, in a reasonable computational time, results obtained with different sets of parameter values. Graphical outputs and text files are provided to rapidly assess the relevance of the detected peaks. Taking advantage of the simple promoter structure in yeasts, additional functions were implemented in bPeaks to automatically assign the peaks to promoter regions and retrieve peak coordinates on the DNA sequence for further predictions of regulatory motifs, enriched in the list of peaks. Applications of the bPeaks program to three different ChIPseq datasets from Saccharomyces cerevisiae, Candida albicans and Candida glabrata are presented. Each time, bPeaks allowed us to correctly predict the DNA binding sequence of the studied TF and provided relevant lists of peaks. The bioinformatics tool bPeaks is freely distributed to academic users. Supplementary data, together with detailed tutorials, are available online: http://bpeaks.gene-networks.net.
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Affiliation(s)
- Jawad Merhej
- Sorbonne Universités, UPMC University of Paris 06, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France; CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
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29
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Abstract
ChIP-sequencing is a method of choice to localize the positions of protein binding sites on DNA on a whole genomic scale. The deciphering of the sequencing data produced by this novel technique is challenging and it is achieved by their rigorous interpretation using dedicated tools and adapted visualization programs. Here, we present a bioinformatics tool (D-peaks) that adds several possibilities (including, user-friendliness, high-quality, relative position with respect to the genomic features) to the well-known visualization browsers or databases already existing. D-peaks is directly available through its web interface http://rsat.ulb.ac.be/dpeaks/ as well as a command line tool.
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Affiliation(s)
- Sylvain Brohée
- Machine Learning Group, Computer Science Department, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium.
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