1
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Koshy A, Mathieux E, Stüder F, Bramoulle A, Lieb M, Colombo BM, Gronemeyer H, Mendoza-Parra MA. Synergistic activation of RARβ and RARγ nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARα-controlled programs. Life Sci Alliance 2023; 6:6/2/e202201627. [PMID: 36446525 PMCID: PMC9711859 DOI: 10.26508/lsa.202201627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
How cells respond to different external cues to develop along defined cell lineages to form complex tissues is a major question in systems biology. Here, we investigated the potential of retinoic acid receptor (RAR)-selective synthetic agonists to activate the gene regulatory programs driving cell specialization during nervous tissue formation from embryonic carcinoma (P19) and mouse embryonic (E14) stem cells. Specifically, we found that the synergistic activation of the RARβ and RARγ by selective ligands (BMS641 or BMS961) induces cell maturation to specialized neuronal subtypes, and to astrocytes and oligodendrocyte precursors. Using RAR isotype knockout lines exposed to RAR-specific agonists, interrogated by global transcriptome landscaping and in silico modeling of transcription regulatory signal propagation, revealed major RARα-driven gene programs essential for optimal neuronal cell specialization and hijacked by the synergistic activation of the RARβ and RARγ receptors. Overall, this study provides a systems biology view of the gene programs accounting for the previously observed redundancy between RARs, paving the way toward their potential use for directing cell specialization during nervous tissue formation.
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Affiliation(s)
- Aysis Koshy
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Elodie Mathieux
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - François Stüder
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Aude Bramoulle
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Michele Lieb
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Bruno Maria Colombo
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
| | - Hinrich Gronemeyer
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Marco Antonio Mendoza-Parra
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Évry, France
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2
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Ábrahám A, Villányi Z, Zsindely N, Nagy G, Szabó Á, Bodai L, Henn L, Boros IM. Despite its sequence identity with canonical H4, Drosophila H4r product is enriched at specific chromatin regions. Sci Rep 2022; 12:5007. [PMID: 35322122 PMCID: PMC8943024 DOI: 10.1038/s41598-022-09026-x] [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: 10/04/2021] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
Histone variants are different from their canonical counterparts in structure and are encoded by solitary genes with unique regulation to fulfill tissue or differentiation specific functions. A single H4 variant gene (His4r or H4r) that is located outside of the histone cluster and gives rise to a polyA tailed messenger RNA via replication-independent expression is preserved in Drosophila strains despite that its protein product is identical with canonical H4. In order to reveal information on the possible role of this alternative H4 we epitope tagged endogenous H4r and studied its spatial and temporal expression, and revealed its genome-wide localization to chromatin at the nucleosomal level. RNA and immunohistochemistry analysis of H4r expressed under its cognate regulation indicate expression of the gene throughout zygotic and larval development and presence of the protein product is evident already in the pronuclei of fertilized eggs. In the developing nervous system a slight disequibrium in H4r distribution is observable, cholinergic neurons are the most abundant among H4r-expressing cells. ChIP-seq experiments revealed H4r association with regulatory regions of genes involved in cellular stress response. The data presented here indicate that H4r has a variant histone function.
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Affiliation(s)
- Andrea Ábrahám
- Institute of Biochemistry, Biological Research Centre of Szeged, Szeged, 6726, Hungary.,Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary.,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Nóra Zsindely
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - Áron Szabó
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary.,Institute of Genetics, Biological Research Centre of Szeged, Szeged, 6726, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary
| | - László Henn
- Institute of Biochemistry, Biological Research Centre of Szeged, Szeged, 6726, Hungary.,Institute of Genetics, Biological Research Centre of Szeged, Szeged, 6726, Hungary
| | - Imre M Boros
- Institute of Biochemistry, Biological Research Centre of Szeged, Szeged, 6726, Hungary. .,Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6726, Hungary.
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3
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [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: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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4
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Aubert A, Stüder F, Colombo BM, Mendoza-Parra MA. A Core Transcription Regulatory Circuitry Defining Microglia Cell Identity Inferred from the Reanalysis of Multiple Human Microglia Differentiation Protocols. Brain Sci 2021; 11:brainsci11101338. [PMID: 34679401 PMCID: PMC8533937 DOI: 10.3390/brainsci11101338] [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: 09/13/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022] Open
Abstract
Microglia, the immune cells in the brain involved in both homeostasis and injury/infection control, play a predominant role in neurodegenerative diseases. In vivo studies on microglia are limited due to the requirement of surgical intervention, which can lead to the destruction of the tissues. Over the last few years, multiple protocols-presenting a variety of strategies-have described microglia differentiation issued from human pluripotent stem cells. Herein, we have reanalyzed the transcriptomes released on six different microglia differentiation protocols and revealed a consensus core of master transcription regulatory circuitry defining microglia identity. Furthermore, we have discussed the major divergencies among the studied protocols and have provided suggestions to further enhance microglia differentiation assays.
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Basova L, Lindsey A, McGovern AM, Ellis RJ, Marcondes MCG. Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis. Viruses 2021; 13:544. [PMID: 33805201 PMCID: PMC8064323 DOI: 10.3390/v13040544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
Human postmortem specimens are extremely valuable resources for investigating translational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic signatures would be more stable than RNA for assessing global changes associated with outcomes of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was abundant and stable up to the 72 h postmortem. We tested our ability to use HeK4me3 in human prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not (Meth +/-) which exhibited poor RNA quality and were not suitable for transcriptional profiling. Systems strategies that are typically used in transcriptional metadata were applied to H3K4me3 peaks revealing consistent genomic activity differences in regions where addiction and neuronal synapses pathway genes are represented, including genes of the dopaminergic system, as well as inflammatory pathways. The resulting comparisons mirrored previously observed effects of Meth on suppressing gene expression and provided insights on neurological processes affected by Meth. The results suggested that H3K4me3 detection in chromatin may reflect transcriptional patterns, thus providing opportunities for analysis of larger numbers of specimens from cases with substance use and neurological deficits. In conclusion, the detection of H3K4me3 in isolated chromatin can be an alternative to transcriptome strategies to increase the power of association using specimens with long postmortem intervals and low RNA quality.
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Affiliation(s)
- Liana Basova
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Alexander Lindsey
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Anne Marie McGovern
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA; (L.B.); (A.L.); (A.M.M.)
| | - Ronald J. Ellis
- Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA;
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Variant Calling in Next Generation Sequencing Data. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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7
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Chèneby J, Ménétrier Z, Mestdagh M, Rosnet T, Douida A, Rhalloussi W, Bergon A, Lopez F, Ballester B. ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. Nucleic Acids Res 2020; 48:D180-D188. [PMID: 31665499 PMCID: PMC7145625 DOI: 10.1093/nar/gkz945] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023] Open
Abstract
ReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators from DNA-binding experiments in Human and Arabidopsis (Arabidopsis thaliana). In this 2020 update of ReMap we have collected, analyzed and retained after quality control 2764 new human ChIP-seq and 208 ChIP-exo datasets available from public sources. The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks. This ReMap update comes with two unique Arabidopsis regulatory catalogs. First, a catalog of 372 Arabidopsis TRs across 2.6M peaks as a result of the integration of 509 ChIP-seq and DAP-seq datasets. Second, a catalog of 33 histone modifications and variants across 4.5M peaks from the integration of 286 ChIP-seq datasets. All catalogs are made available through track hubs at Ensembl and UCSC Genome Browsers. Additionally, this update comes with a new web framework providing an interactive user-interface, including improved search features. Finally, full programmatically access to the underlying data is available using a RESTful API together with a new R Shiny interface for a TRs binding enrichment analysis tool.
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Dréos R, Ambrosini G, Groux R, Périer RC, Bucher P. MGA repository: a curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res 2019; 46:D175-D180. [PMID: 29069466 PMCID: PMC5753388 DOI: 10.1093/nar/gkx995] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/20/2017] [Indexed: 01/09/2023] Open
Abstract
The Mass Genome Annotation (MGA) repository is a resource designed to store published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) in a completely standardised format. Each sample has undergone local processing in order the meet the strict MGA format requirements. The original data source, the reformatting procedure and the biological characteristics of the samples are described in an accompanying documentation file manually edited by data curators. 10 model organisms are currently represented: Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Apis mellifera, Caenorhabditis elegans, Arabidopsis thaliana, Zea mays, Saccharomyces cerevisiae and Schizosaccharomyces pombe. As of today, the resource contains over 24 000 samples. In conjunction with other tools developed by our group (the ChIP-Seq and SSA servers), it allows users to carry out a great variety of analysis task with MGA samples, such as making aggregation plots and heat maps for selected genomic regions, finding peak regions, generating custom tracks for visualizing genomic features in a UCSC genome browser window, or downloading chromatin data in a table format suitable for local processing with more advanced statistical analysis software such as R. Home page: http://ccg.vital-it.ch/mga/.
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Affiliation(s)
- René Dréos
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Giovanna Ambrosini
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Romain Groux
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | | | - Philipp Bucher
- Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
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9
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Devailly G, Joshi A. Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. BMC Bioinformatics 2018; 19:409. [PMID: 30453943 PMCID: PMC6245581 DOI: 10.1186/s12859-018-2377-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Transcription regulation is a major controller of gene expression dynamics during development and disease, where transcription factors (TFs) modulate expression of genes through direct or indirect DNA interaction. ChIP sequencing has become the most widely used technique to get a genome wide view of TF occupancy in a cell type of interest, mainly due to established standard protocols and a rapid decrease in the cost of sequencing. The number of available ChIP sequencing data sets in public domain is therefore ever increasing, including data generated by individual labs together with consortia such as the ENCODE project. Results A total of 1735 ChIP-sequencing datasets in mouse and human cell types and tissues were used to perform bioinformatic analyses to unravel diverse features of transcription control. 1- We used the Heat*seq webtool to investigate global relations across the ChIP-seq samples. 2- We demonstrated that factors have a specific genomic location preferences that are, for most factors, conserved across species. 3- Promoter proximal binding of factors was more conserved across cell types while the distal binding sites are more cell type specific. 4- We identified combinations of factors preferentially acting together in a cellular context. 5- Finally, by integrating the data with disease-associated gene loci from GWAS studies, we highlight the value of this data to associate novel regulators to disease. Conclusion In summary, we demonstrate how ChIP sequencing data integration and analysis is powerful to get new insights into mammalian transcription control and demonstrate the utility of various bioinformatic tools to generate novel testable hypothesis using this public resource.
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Affiliation(s)
- Guillaume Devailly
- Division of Developmental Biology, the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Anagha Joshi
- Division of Developmental Biology, the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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10
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Guertin MJ, Cullen AE, Markowetz F, Holding AN. Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq. Nucleic Acids Res 2018; 46:e75. [PMID: 29672735 PMCID: PMC6093181 DOI: 10.1093/nar/gky252] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 03/15/2018] [Accepted: 03/28/2018] [Indexed: 11/17/2022] Open
Abstract
A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery. We present a novel normalization strategy utilizing an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalization. We compare our approach to normalization by total read depth and two alternative methods that utilize external experimental controls to study TF binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in patient-derived xenographs. This is supported by an adaptable pipeline to normalize and quantify differential TF binding genome-wide and generate metrics for differential binding at individual sites.
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Affiliation(s)
- Michael J Guertin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Amy E Cullen
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
| | - Andrew N Holding
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0RE, UK
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Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B. ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Res 2018; 46:D267-D275. [PMID: 29126285 PMCID: PMC5753247 DOI: 10.1093/nar/gkx1092] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/22/2022] Open
Abstract
With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human.
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Affiliation(s)
- Jeanne Chèneby
- INSERM, UMR1090 TAGC, Marseille F-13288, France
- Aix-Marseille Université, UMR1090 TAGC, Marseille F-13288, France
| | - Marius Gheorghe
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Marie Artufel
- INSERM, UMR1090 TAGC, Marseille F-13288, France
- Aix-Marseille Université, UMR1090 TAGC, Marseille F-13288, France
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Benoit Ballester
- INSERM, UMR1090 TAGC, Marseille F-13288, France
- Aix-Marseille Université, UMR1090 TAGC, Marseille F-13288, France
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