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Fletcher J, O’Connor-Moneley J, Frawley D, Flanagan PR, Alaalm L, Menendez-Manjon P, Estevez SV, Hendricks S, Woodruff AL, Buscaino A, Anderson MZ, Sullivan DJ, Moran GP. Deletion of the Candida albicans TLO gene family using CRISPR-Cas9 mutagenesis allows characterisation of functional differences in α-, β- and γ- TLO gene function. PLoS Genet 2023; 19:e1011082. [PMID: 38048294 PMCID: PMC10721199 DOI: 10.1371/journal.pgen.1011082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/14/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
The Candida albicans genome contains between ten and fifteen distinct TLO genes that all encode a Med2 subunit of Mediator. In order to investigate the biological role of Med2/Tlo in C. albicans we deleted all fourteen TLO genes using CRISPR-Cas9 mutagenesis. ChIP-seq analysis showed that RNAP II localized to 55% fewer genes in the tloΔ mutant strain compared to the parent, while RNA-seq analysis showed that the tloΔ mutant exhibited differential expression of genes required for carbohydrate metabolism, stress responses, white-opaque switching and filamentous growth. Consequently, the tloΔ mutant grows poorly in glucose- and galactose-containing media, is unable to grow as true hyphae, is more sensitive to oxidative stress and is less virulent in the wax worm infection model. Reintegration of genes representative of the α-, β- and γ-TLO clades resulted in the complementation of the mutant phenotypes, but to different degrees. TLOα1 could restore phenotypes and gene expression patterns similar to wild-type and was the strongest activator of glycolytic and Tye7-regulated gene expression. In contrast, the two γ-TLO genes examined (i.e., TLOγ5 and TLOγ11) had a far lower impact on complementing phenotypic and transcriptomic changes. Uniquely, expression of TLOβ2 in the tloΔ mutant stimulated filamentous growth in YEPD medium and this phenotype was enhanced when Tloβ2 expression was increased to levels far in excess of Med3. In contrast, expression of reintegrated TLO genes in a tloΔ/med3Δ double mutant background failed to restore any of the phenotypes tested, suggesting that complementation of these Tlo-regulated processes requires a functional Mediator tail module. Together, these data confirm the importance of Med2/Tlo in a wide range of C. albicans cellular activities and demonstrate functional diversity within the gene family which may contribute to the success of this yeast as a coloniser and pathogen of humans.
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Affiliation(s)
- Jessica Fletcher
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - James O’Connor-Moneley
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Dean Frawley
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Peter R. Flanagan
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Leenah Alaalm
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | | | | | - Shane Hendricks
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Andrew L. Woodruff
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Alessia Buscaino
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Derek J. Sullivan
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Gary P. Moran
- Division of Oral Biosciences, Dublin Dental University Hospital, & University of Dublin, Trinity College Dublin, Dublin, Ireland
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Schwartz U, Komatsu T, Huber C, Lagadec F, Baumgartl C, Silberhorn E, Nuetzel M, Rayne F, Basyuk E, Bertrand E, Rehli M, Wodrich H, Laengst G. Changes in adenoviral chromatin organization precede early gene activation upon infection. EMBO J 2023; 42:e114162. [PMID: 37641864 PMCID: PMC10548178 DOI: 10.15252/embj.2023114162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unclear. Here, we combined RNA-seq, MNase-seq, ChIP-seq, and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the adenoviral genome is arranged in precisely positioned nucleoprotein particles with nucleosome-like characteristics, that we term adenosomes. We identified 238 adenosomes that are positioned by a DNA sequence code and protect about 60-70 bp of DNA. The incoming adenoviral genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replaces pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites and precedes transcriptional activation. Based on our results, we propose a central role for the viral pVII nucleoprotein architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.
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Affiliation(s)
- Uwe Schwartz
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
| | - Tetsuro Komatsu
- Laboratory of Epigenetics and Metabolism, Institute for Molecular and Cellular RegulationGunma UniversityGunmaJapan
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Claudia Huber
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
| | - Floriane Lagadec
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB)Georg‐August‐University GöttingenGöttingenGermany
| | | | | | - Margit Nuetzel
- Department of Internal Medicine IIIUniversity Hospital RegensburgRegensburgGermany
| | - Fabienne Rayne
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Eugenia Basyuk
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Edouard Bertrand
- CNRS UMR 5355Institut de Généthique Moléculaire de MontpellierMontpellierFrance
| | - Michael Rehli
- Department of Internal Medicine IIIUniversity Hospital RegensburgRegensburgGermany
- Leibniz Institute for ImmunotherapyRegensburgGermany
- University Hospital RegensburgRegensburgGermany
| | - Harald Wodrich
- CNRS UMR 5234, Microbiologie Fondamentale et PathogénicitéUniversité de BordeauxBordeauxFrance
| | - Gernot Laengst
- Biochemie Zentrum RegensburgUniversity of RegensburgRegensburgGermany
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3
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Ofer S, Blombach F, Erkelens AM, Barker D, Soloviev Z, Schwab S, Smollett K, Matelska D, Fouqueau T, van der Vis N, Kent NA, Thalassinos K, Dame RT, Werner F. DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. Commun Biol 2023; 6:968. [PMID: 37740023 PMCID: PMC10516927 DOI: 10.1038/s42003-023-05348-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into 'hypernucleosome' particles of varying sizes with each dimer wrapping 30 bp of DNA. These are composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. Here, we characterise the structure and function of the histone paralogue MJ1647 from Methanocaldococcus jannaschii that has a unique C-terminal extension enabling homotetramerisation. The 1.9 Å X-ray structure of a dimeric MJ1647 species, structural modelling of the tetramer, and site-directed mutagenesis reveal that the C-terminal tetramerization module consists of two alpha helices in a handshake arrangement. Unlike canonical histones, MJ1647 tetramers can bridge two DNA molecules in vitro. Using single-molecule tethered particle motion and DNA binding assays, we show that MJ1647 tetramers bind ~60 bp DNA and compact DNA in a highly cooperative manner. We furthermore show that MJ1647 effectively competes with the transcription machinery to block access to the promoter in vitro. To the best of our knowledge, MJ1647 is the first histone shown to have DNA bridging properties, which has important implications for genome structure and gene expression in archaea.
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Affiliation(s)
- Sapir Ofer
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Fabian Blombach
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Declan Barker
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Zoja Soloviev
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Katherine Smollett
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Dorota Matelska
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Thomas Fouqueau
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Nico van der Vis
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Nicholas A Kent
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Konstantinos Thalassinos
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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4
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Sakamoto M, Abe S, Miki Y, Miyanari Y, Sasaki H, Ishiuchi T. Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development. Genes Dev 2023; 37:590-604. [PMID: 37532472 PMCID: PMC10499016 DOI: 10.1101/gad.350376.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Down-regulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting a possible link between the chromatin assembly pathway and fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger-containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements through identifying YY1-binding sites in eight-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the eight-cell and morula stages, and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.
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Affiliation(s)
- Mizuki Sakamoto
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuka Miki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yusuke Miyanari
- NanoLSI, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Ishiuchi
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan;
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5
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Pinto PB, Domsch K, Lohmann I. Hox function and specificity – A tissue centric view. Semin Cell Dev Biol 2022:S1084-9521(22)00353-6. [PMID: 36517344 DOI: 10.1016/j.semcdb.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Since their discovery, the Hox genes, with their incredible power to reprogram the identity of complete body regions, a phenomenon called homeosis, have captured the fascination of many biologists. Recent research has provided new insights into the function of Hox proteins in different germ layers and the mechanisms they employ to control tissue morphogenesis. We focus in this review on the ectoderm and mesoderm to highlight new findings and discuss them with regards to established concepts of Hox target gene regulation. Furthermore, we highlight the molecular mechanisms involved the transcriptional repression of specific groups of Hox target genes, and summarize the role of Hox mediated gene silencing in tissue development. Finally, we reflect on recent findings identifying a large number of tissue-specific Hox interactor partners, which open up new avenues and directions towards a better understanding of Hox function and specificity in different tissues.
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6
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Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022; 31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Technological progress over the past 15 years has fueled an explosion in genome-wide chromatin profiling tools that take advantage of low-cost short-read sequencing technologies to map particular chromatin features. Here, we survey the recent development of epigenomic tools that provide precise positions of chromatin proteins genome-wide in intact cells or nuclei. Some profiling tools are based on tethering Micrococcal Nuclease to chromatin proteins of interest in situ, whereas others similarly tether Tn5 transposase to integrate DNA sequencing adapters (tagmentation) and so eliminate the need for library preparation. These in situ cleavage and tagmentation tools have gained in popularity over the past few years, with many protocol enhancements and adaptations for single-cell and spatial chromatin profiling. The application of experimental and computational tools to address problems in gene regulation, eukaryotic development, and human disease are helping to define the emerging field of chromatin structural epigenomics.
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Kami Ahmad
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
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7
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Zhang Z, Lin L, Chen H, Ye W, Dong S, Zheng X, Wang Y. ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in the Phytophthora sojae Genome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:301-310. [PMID: 35037783 DOI: 10.1094/mpmi-11-21-0291-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleosome-free open chromatin often harbors transcription factor (TF)-binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene-promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidate cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Long Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
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8
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Janssens DH, Otto DJ, Meers MP, Setty M, Ahmad K, Henikoff S. CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells. Genome Biol 2022; 23:81. [PMID: 35300717 PMCID: PMC8928696 DOI: 10.1186/s13059-022-02642-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022] Open
Abstract
Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protocol using a mixture of an antibody to the initiation form of RNA polymerase II (Pol2 Serine-5 phosphate) and an antibody to repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution to produce high-resolution maps of both the active and repressive regulomes in single cells. The ability to seamlessly map active promoters, enhancers, and repressive regulatory elements using a single workflow provides a complete regulome profiling strategy suitable for high-throughput single-cell platforms.
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Affiliation(s)
- Derek H. Janssens
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Dominik J. Otto
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.270240.30000 0001 2180 1622Translational Data Science IRC, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Michael P. Meers
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Manu Setty
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.270240.30000 0001 2180 1622Translational Data Science IRC, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Kami Ahmad
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Steven Henikoff
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA
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9
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Li Y, Hartemink AJ, MacAlpine DM. Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins. Genes (Basel) 2021; 12:genes12121998. [PMID: 34946946 PMCID: PMC8701747 DOI: 10.3390/genes12121998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/20/2023] Open
Abstract
Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle–dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors, and replication proteins through consecutive cell cycles in Saccharomyces cerevisiae. During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45–Mcm2-7–GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell-cycle–regulated chromatin dynamics and how they relate to the regulation of origin activity.
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Affiliation(s)
- Yulong Li
- Department of Computer Science, Duke University, Durham, NC 27708, USA;
| | - Alexander J. Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA;
- Correspondence: (A.J.H.); (D.M.M.)
| | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Correspondence: (A.J.H.); (D.M.M.)
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10
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Savadel SD, Hartwig T, Turpin ZM, Vera DL, Lung PY, Sui X, Blank M, Frommer WB, Dennis JH, Zhang J, Bass HW. The native cistrome and sequence motif families of the maize ear. PLoS Genet 2021; 17:e1009689. [PMID: 34383745 PMCID: PMC8360572 DOI: 10.1371/journal.pgen.1009689] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/30/2021] [Indexed: 01/22/2023] Open
Abstract
Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas. Understanding gene regulation remains a central goal of modern biology. Delineating the full set of regulatory DNA elements that orchestrate this regulation requires information at two scales; the broad landscape of accessible chromatin, and the site-specific binding of transcription factors (TFs) at discrete cis-regulatory DNA elements. Here we describe a single assay that uses micrococcal nuclease (MNase) as a structural probe to simultaneously reveal regions of accessible chromatin in addition to high-resolution footprints with signatures of TF-occupied cis-elements. We have used maize developing ear tissue as proof of concept, showing the method detects known TF-binding sites. This genome-wide assay not only defines chromatin landscapes, but crucially enables global discovery and mapping of sequence motifs underlying small footprints of ~30 bp to produce an atlas of candidate TF occupancy.
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Affiliation(s)
- Savannah D. Savadel
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Thomas Hartwig
- Institute for Molecular Physiologie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Independent research groups, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Zachary M. Turpin
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Daniel L. Vera
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Xin Sui
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Max Blank
- Institute for Molecular Physiologie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Independent research groups, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Wolf B. Frommer
- Institute for Molecular Physiologie, Heinrich-Heine-Universität, Düsseldorf, Germany
- Independent research groups, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonathan H. Dennis
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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11
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Misova I, Pitelova A, Budis J, Gazdarica J, Sedlackova T, Jordakova A, Benko Z, Smondrkova M, Mayerova N, Pichlerova K, Strieskova L, Prevorovsky M, Gregan J, Cipak L, Szemes T, Polakova SB. Repression of a large number of genes requires interplay between homologous recombination and HIRA. Nucleic Acids Res 2021; 49:1914-1934. [PMID: 33511417 PMCID: PMC7913671 DOI: 10.1093/nar/gkab027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
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Affiliation(s)
- Ivana Misova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Anna Jordakova
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Zsigmond Benko
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, H-4010 Debrecen, Hungary
| | - Maria Smondrkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Karoline Pichlerova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Lucia Strieskova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Martin Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
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12
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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13
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Wen Z, Zhang L, Ruan H, Li G. Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells. Nucleic Acids Res 2020; 48:5939-5952. [PMID: 32392318 PMCID: PMC7293034 DOI: 10.1093/nar/gkaa360] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/27/2020] [Accepted: 04/29/2020] [Indexed: 01/28/2023] Open
Abstract
Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z nucleosomes are more enriched with unwrapping states compared with canonical nucleosomes. Interestingly, +1 H2A.Z nucleosomes with 30–80 bp DNA is correlated with less active genes compared with +1 H2A.Z nucleosomes with 120–140 bp DNA. We confirmed the unwrapping of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z and H2A after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in decreased unwrapping of H3.3 nucleosomes and increased CTCF binding. Taken together, through MNase-X-ChIP-seq, we showed that histone variant H2A.Z regulates nucleosome unwrapping in vivo and that its function in regulating transcription or CTCF binding is correlated with unwrapping states of H2A.Z nucleosomes.
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Affiliation(s)
- Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Zuo Z, Jin Y, Zhang W, Lu Y, Li B, Qu K. ATAC-pipe: general analysis of genome-wide chromatin accessibility. Brief Bioinform 2020; 20:1934-1943. [PMID: 29982337 DOI: 10.1093/bib/bby056] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/16/2018] [Indexed: 01/17/2023] Open
Abstract
Assay of Transposase-Accessible Chromatin by deep sequencing (ATAC-seq) has been widely used to profile the chromatin accessibility genome-wide. For the absence of an integrated scheme for deep data mining of specific biological issues, here we present ATAC-pipe, an efficient pipeline for general analysis of chromatin accessibility data obtained from ATAC-seq experiments. ATAC-pipe captures information includes not only the quality of original data and genome-wide chromatin accessibility but also signatures of significant differential peaks, transcription factor (TF) occupancy and nucleosome positions around regulatory sites. In addition, ATAC-pipe automatically converts statistic results into intuitive plots at publication quality, such as the read length distribution, heatmaps of sample clustering and cell-type-specific regulatory elements, enriched TF occupancy with motifs footprints and TF-driven regulatory networks. ATAC-pipe provides convenient workflow for researchers to study chromatin accessibility and gene regulation. Availability https://github.com/QuKunLab/ATAC-pipe.
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Affiliation(s)
- Zuqi Zuo
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yonghao Jin
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Wen Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yichen Lu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bin Li
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kun Qu
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
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15
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Nordström KJV, Schmidt F, Gasparoni N, Salhab A, Gasparoni G, Kattler K, Müller F, Ebert P, Costa IG, Pfeifer N, Lengauer T, Schulz MH, Walter J. Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Res 2020; 47:10580-10596. [PMID: 31584093 PMCID: PMC6847574 DOI: 10.1093/nar/gkz799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023] Open
Abstract
Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often ‘called’ by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.
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Affiliation(s)
| | - Florian Schmidt
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Nina Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Gilles Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | | | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
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16
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Beads on a string-nucleosome array arrangements and folding of the chromatin fiber. Nat Struct Mol Biol 2020; 27:109-118. [PMID: 32042149 DOI: 10.1038/s41594-019-0368-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022]
Abstract
Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes.
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17
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Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
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Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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18
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Tao X, Feng S, Zhao T, Guan X. Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag. PLANT METHODS 2020; 16:120. [PMID: 32884577 PMCID: PMC7460760 DOI: 10.1186/s13007-020-00664-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/25/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND In 2019, Kaya-Okur et al. reported on the cleavage under targets and tagmentation (CUT&Tag) technology for efficient profiling of epigenetically modified DNA fragments. It was used mainly for cultured cell lines and was especially effective for small samples and single cells. This strategy generated high-resolution and low-background-noise chromatin profiling data for epigenomic analysis. CUT&Tag is well suited to be used in plant cells, especially in tissues from which small samples are taken, such as ovules, anthers, and fibers. RESULTS Here, we present a CUT&Tag protocol step by step using plant nuclei. In this protocol, we quantified the nuclei that can be used in each CUT&Tag reaction, and compared the efficiency of CUT&Tag with chromatin immunoprecipitation with sequencing (ChIP-seq) in the leaves of cotton. A general workflow for the bioinformatic analysis of CUT&Tag is also provided. Results indicated that, compared with ChIP-seq, the CUT&Tag procedure was faster and showed a higher-resolution, lower-background signal than did ChIP. CONCLUSION A CUT&Tag protocol has been refined for plant cells using intact nuclei that have been isolated.
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Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Shouli Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058 China
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19
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Krajewski WA. "Direct" and "Indirect" Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality. Bioessays 2019; 42:e1900136. [PMID: 31805213 DOI: 10.1002/bies.201900136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/17/2019] [Indexed: 12/26/2022]
Abstract
The chromatin-regulatory principles of histone post-translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone "readers," and as determinants of chromatin array compaction. Alterations of histone charges by "small" chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. These fluctuations in nucleosome wrapping can be exploited by chromatin-processing machinery. In contrast, ubiquitin and SUMO are comparable in size to histones, and it seems logical that these PTMs could conflict with canonical nucleosome organization. An experimentally testable hypothesis that by adding sterical bulk these PTMs can robustly alter nucleosome primary structure is proposed. The model presented here stresses the diversity of mechanisms by which histone PTMs regulate chromatin dynamics, primary structure and, hence, functionality.
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Affiliation(s)
- Wladyslaw A Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
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20
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Mivelaz M, Cao AM, Kubik S, Zencir S, Hovius R, Boichenko I, Stachowicz AM, Kurat CF, Shore D, Fierz B. Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor. Mol Cell 2019; 77:488-500.e9. [PMID: 31761495 PMCID: PMC7005674 DOI: 10.1016/j.molcel.2019.10.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 02/03/2023]
Abstract
Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression. The yeast transcription factor Rap1 can invade compact chromatin Rap1 directly opens chromatin structure by preventing nucleosome stacking Stable Rap1 binding requires collaboration with RSC to shift promoter nucleosomes
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Affiliation(s)
- Maxime Mivelaz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anne-Marinette Cao
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Sevil Zencir
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Ruud Hovius
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Iuliia Boichenko
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland
| | - Anna Maria Stachowicz
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Christoph F Kurat
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Station 6, 1015 Lausanne, Switzerland.
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21
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Owens N, Papadopoulou T, Festuccia N, Tachtsidi A, Gonzalez I, Dubois A, Vandormael-Pournin S, Nora EP, Bruneau BG, Cohen-Tannoudji M, Navarro P. CTCF confers local nucleosome resiliency after DNA replication and during mitosis. eLife 2019; 8:e47898. [PMID: 31599722 PMCID: PMC6844645 DOI: 10.7554/elife.47898] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. Correlative analyses suggest this is associated with fast gene reactivation following replication and mitosis. While regions bound by other TFs (Oct4/Sox2), display major rearrangement, the post-replication and mitotic nucleosome positioning activity of CTCF is not unique: Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, selected TFs such as CTCF and Esrrb act as resilient TFs governing the inheritance of nucleosome positioning at regulatory regions throughout the cell-cycle.
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Affiliation(s)
- Nick Owens
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Thaleia Papadopoulou
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Nicola Festuccia
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Alexandra Tachtsidi
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
- Sorbonne Université, Collège DoctoralParisFrance
| | - Inma Gonzalez
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Agnes Dubois
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Sandrine Vandormael-Pournin
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Elphège P Nora
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Benoit G Bruneau
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of PediatricsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michel Cohen-Tannoudji
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Pablo Navarro
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
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22
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Meers MP, Janssens DH, Henikoff S. Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded. Mol Cell 2019; 75:562-575.e5. [PMID: 31253573 PMCID: PMC6697550 DOI: 10.1016/j.molcel.2019.05.025] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
Although the in vitro structural and in vivo spatial characteristics of transcription factor (TF) binding are well defined, TF interactions with chromatin and other companion TFs during development are poorly understood. To analyze such interactions in vivo, we profiled several TFs across a time course of human embryonic stem cell differentiation and studied their interactions with nucleosomes and co-occurring TFs by enhanced chromatin occupancy (EChO), a computational strategy for classifying TF interactions with chromatin. EChO shows that multiple individual TFs can employ either direct DNA binding or "pioneer" nucleosome binding at different enhancer targets. Nucleosome binding is not exclusively confined to inaccessible chromatin but rather correlated with local binding of other TFs and degeneracy at key bases in the pioneer factor target motif responsible for direct DNA binding. Our strategy reveals a dynamic exchange of TFs at enhancers across developmental time that is aided by pioneer nucleosome binding.
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Affiliation(s)
- Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA; Howard Hughes Medical Institute, USA.
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23
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Kubik S, Bruzzone MJ, Challal D, Dreos R, Mattarocci S, Bucher P, Libri D, Shore D. Opposing chromatin remodelers control transcription initiation frequency and start site selection. Nat Struct Mol Biol 2019; 26:744-754. [PMID: 31384063 DOI: 10.1038/s41594-019-0273-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/28/2019] [Indexed: 12/31/2022]
Abstract
Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Drice Challal
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - René Dreos
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Philipp Bucher
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Domenico Libri
- Institut Jacques Monod, CNRS-Université Paris Diderot, Paris, France
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland.
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24
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Abstract
Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal −1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level. SLIM-ChIP is a low-input, robust, high-resolution, automatable TF mapping protocol SLIM-ChIP is applicable to a range of TFs from yeast to mammals DNA fragments from SLIM-ChIP provide targeted footprinting at the bound site RSC-mediated Reb1-nucleosome interactions affect promoter directionality
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25
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Foss EJ, Gatbonton-Schwager T, Thiesen AH, Taylor E, Soriano R, Lao U, MacAlpine DM, Bedalov A. Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats. PLoS Genet 2019; 15:e1008138. [PMID: 31083663 PMCID: PMC6532929 DOI: 10.1371/journal.pgen.1008138] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/23/2019] [Accepted: 04/15/2019] [Indexed: 11/23/2022] Open
Abstract
Repetitive DNA sequences within eukaryotic heterochromatin are poorly transcribed and replicate late in S-phase. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). Despite the widespread association between transcription and replication timing, it remains unclear how transcription might impinge on replication, or vice versa. Here we show that, when silencing of an RNA polymerase II (RNA Pol II)-transcribed non-coding RNA at the rDNA is disrupted by SIR2 deletion, RNA polymerase pushes and thereby relocalizes replicative Mcm2-7 helicases away from their loading sites to an adjacent region with low nucleosome occupancy, and this relocalization is associated with increased rDNA origin efficiency. Our results suggest a model in which two of the major defining features of heterochromatin, transcriptional silencing and late replication, are mechanistically linked through suppression of polymerase-mediated displacement of replication initiation complexes. Eukaryotic genomes typically contain large regions of repetitive DNA, referred to as heterochromatin, that are both transcriptionally silent and late replicating. We provide a possible explanation for the association between transcriptional silencing and late replication. Budding yeast contains a histone deacetylase called SIR2 that was originally identified as a transcriptional repressor, but was later also found to ensure late replication of repetitive ribosomal DNA (rDNA) sequences. We show that the transcription that occurs in the absence of SIR2 directly displaces the helicase required for replication initiation at the rDNA. This work represents an important advance in understanding the interplay between transcription and replication at repetitive sequences by directly linking transcription with replication machinery in heterochromatin.
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Affiliation(s)
- Eric J Foss
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | | | - Adam H Thiesen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Erin Taylor
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Rafael Soriano
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Uyen Lao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, United States of America
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.,Department of Medicine, University of Washington, Seattle, WA, United States of America.,Department of Biochemistry, University of Washington, Seattle, WA, United States of America
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26
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Harwood JC, Kent NA, Allen ND, Harwood AJ. Nucleosome dynamics of human iPSC during neural differentiation. EMBO Rep 2019; 20:embr.201846960. [PMID: 31036712 PMCID: PMC6549019 DOI: 10.15252/embr.201846960] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 01/07/2023] Open
Abstract
Nucleosome positioning is important for neurodevelopment, and genes mediating chromatin remodelling are strongly associated with human neurodevelopmental disorders. To investigate changes in nucleosome positioning during neural differentiation, we generate genome‐wide nucleosome maps from an undifferentiated human‐induced pluripotent stem cell (hiPSC) line and after its differentiation to the neural progenitor cell (NPC) stage. We find that nearly 3% of nucleosomes are highly positioned in NPC, but significantly, there are eightfold fewer positioned nucleosomes in pluripotent cells, indicating increased positioning during cell differentiation. Positioned nucleosomes do not strongly correlate with active chromatin marks or gene transcription. Unexpectedly, we find a small population of nucleosomes that occupy similar positions in pluripotent and neural progenitor cells and are found at binding sites of the key gene regulators NRSF/REST and CTCF. Remarkably, the presence of these nucleosomes appears to be independent of the associated regulatory complexes. Together, these results present a scenario in human cells, where positioned nucleosomes are sparse and dynamic, but may act to alter gene expression at a distance via the structural conformation at sites of chromatin regulation.
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Affiliation(s)
- Janet C Harwood
- MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, UK
| | | | | | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, UK .,Neuroscience and Mental Health Research Institute (NMHRI), Cardiff University, Cardiff, UK
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27
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Nucleosome positioning and spacing: from genome-wide maps to single arrays. Essays Biochem 2019; 63:5-14. [PMID: 31015380 DOI: 10.1042/ebc20180058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/07/2023]
Abstract
The positioning of nucleosomes relative to DNA and their neighboring nucleosomes represents a fundamental layer of chromatin organization. Changes in nucleosome positioning and spacing affect the accessibility of DNA to regulatory factors and the formation of higher order chromatin structures. Sequencing of mononucleosomal fragments allowed mapping nucleosome positions on a genome-wide level in many organisms. This revealed that successions of evenly spaced and well-positioned nucleosomes-so called phased nucleosome arrays-occur at the 5' end of many active genes and in the vicinity of transcription factor and other protein binding sites. Phased arrays arise from the interplay of barrier elements on the DNA, which position adjacent nucleosomes, and the nucleosome spacing activity of ATP-dependent chromatin remodelers. A shortcoming of classic mononucleosomal mapping experiments is that they only reveal nucleosome spacing and array regularity at select sites in the genome with well-positioned nucleosomes. However, new technological approaches elucidate nucleosome array structure throughout the genome and with single-cell resolution. In the future, it will be interesting to see whether changes in nucleosome array regularity and spacing contribute to the formation of higher order chromatin structures and the spatial organization of the genome in vivo.
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28
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Kubik S, O'Duibhir E, de Jonge WJ, Mattarocci S, Albert B, Falcone JL, Bruzzone MJ, Holstege FCP, Shore D. Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription. Mol Cell 2019; 71:89-102.e5. [PMID: 29979971 DOI: 10.1016/j.molcel.2018.05.030] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/17/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation at eukaryotic promoters. We investigated the mechanistic links between promoter DNA sequence, nucleosome positioning, and transcription. Our results indicate that positioning of the transcription start site-associated +1 nucleosome in yeast is critical for efficient TBP binding and is driven by two key factors, the essential chromatin remodeler RSC and a small set of ubiquitous general regulatory factors (GRFs). Our findings indicate that the strength and directionality of RSC action on promoter nucleosomes depends on the arrangement and proximity of two specific DNA motifs. This, together with the effect on nucleosome position observed in double depletion experiments, suggests that, despite their widespread co-localization, RSC and GRFs predominantly act through independent signals to generate accessible chromatin. Our results provide mechanistic insight into how the promoter DNA sequence instructs trans-acting factors to control nucleosome architecture and stimulate transcription initiation.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Wim J de Jonge
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Benjamin Albert
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Jean-Luc Falcone
- Center for Advanced Modeling Sciences, Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
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29
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Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora. Genetics 2018; 211:563-578. [PMID: 30554169 DOI: 10.1534/genetics.118.301711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/11/2018] [Indexed: 01/04/2023] Open
Abstract
In the filamentous fungus Neurospora crassa, constitutive heterochromatin is marked by tri-methylation of histone H3 lysine 9 (H3K9me3) and DNA methylation. We identified mutations in the Neurospora defective in methylation-1 (dim-1) gene that cause defects in cytosine methylation and implicate a putative AAA-ATPase chromatin remodeler. Although it was well-established that chromatin remodelers can affect transcription by influencing DNA accessibility with nucleosomes, little was known about the role of remodelers on chromatin that is normally not transcribed, including regions of constitutive heterochromatin. We found that dim-1 mutants display both reduced DNA methylation in heterochromatic regions as well as increased DNA methylation and H3K9me3 in some intergenic regions associated with highly expressed genes. Deletion of dim-1 leads to atypically spaced nucleosomes throughout the genome and numerous changes in gene expression. DIM-1 localizes to both heterochromatin and intergenic regions that become hyper-methylated in dim-1 strains. Our findings indicate that DIM-1 normally positions nucleosomes in both heterochromatin and euchromatin and that the standard arrangement and density of nucleosomes is required for the proper function of heterochromatin machinery.
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30
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van Eijk P, Nandi SP, Yu S, Bennett M, Leadbitter M, Teng Y, Reed SH. Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure. Genome Res 2018; 29:74-84. [PMID: 30552104 PMCID: PMC6314166 DOI: 10.1101/gr.237198.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/07/2018] [Indexed: 11/24/2022]
Abstract
Repair of UV-induced DNA damage requires chromatin remodeling. How repair is initiated in chromatin remains largely unknown. We recently demonstrated that global genome–nucleotide excision repair (GG-NER) in chromatin is organized into domains in relation to open reading frames. Here, we define these domains, identifying the genomic locations from which repair is initiated. By examining DNA damage–induced changes in the linear structure of nucleosomes at these sites, we demonstrate how chromatin remodeling is initiated during GG-NER. In undamaged cells, we show that the GG-NER complex occupies chromatin, establishing the nucleosome structure at these genomic locations, which we refer to as GG-NER complex binding sites (GCBSs). We demonstrate that these sites are frequently located at genomic boundaries that delineate chromosomally interacting domains (CIDs). These boundaries define domains of higher-order nucleosome–nucleosome interaction. We demonstrate that initiation of GG-NER in chromatin is accompanied by the disruption of dynamic nucleosomes that flank GCBSs by the GG-NER complex.
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Affiliation(s)
- Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shuvro Prokash Nandi
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Shirong Yu
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Mark Bennett
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Matthew Leadbitter
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Yumin Teng
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
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31
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Tetratricopeptide repeat domain 7A is a nuclear factor that modulates transcription and chromatin structure. Cell Discov 2018; 4:61. [PMID: 30455981 PMCID: PMC6232119 DOI: 10.1038/s41421-018-0061-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 02/04/2023] Open
Abstract
A loss-of-function mutation in tetratricopeptide repeat domain 7A (TTC7A) is a recently identified cause of human intestinal and immune disorders. However, clues to related underlying molecular dysfunctions remain elusive. It is now shown based on the study of TTC7A-deficient and wild-type cells that TTC7A is an essential nuclear protein. It binds to chromatin, preferentially at actively transcribed regions. Its depletion results in broad range of epigenomic changes at proximal and distal transcriptional regulatory elements and in altered control of the transcriptional program. Loss of WT_TTC7A induces general decrease in chromatin compaction, unbalanced cellular distribution of histones, higher nucleosome accessibility to nuclease digestion along with genome instability, and reduced cell viability. Our observations characterize for the first time unreported functions for TTC7A in the nucleus that exert a critical role in chromatin organization and gene regulation to safeguard healthy immune and intestinal status.
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32
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Krajewski WA. Effects of DNA Superhelical Stress on the Stability of H2B-Ubiquitylated Nucleosomes. J Mol Biol 2018; 430:5002-5014. [PMID: 30267746 DOI: 10.1016/j.jmb.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/27/2018] [Accepted: 09/21/2018] [Indexed: 01/31/2023]
Abstract
On the nucleosome level, histone posttranslational modifications function mainly as the regulatory signals; in addition, some posttranslational modifications can enhance nucleosome stochastic folding, which is restricted in "canonic" nucleosomes. Recently, it has been shown in vitro that symmetric or asymmetric nucleosome ubiquitylation at H2BK34 (and H2BK120, to a lesser extent) can destabilize one of the nucleosomal H2A-H2B dimers and promote nucleosome conversion to a hexasome particle [Krajewski et al. (2018). Nucleic Acids Res., 46, 7631-7642]. Such lability of H2Bub nucleosomes raises a question of whether they could accommodate transient changes in DNA torsional tensions, which are generated by virtually any process that manipulates DNA strands. Using positively or negatively supercoiled DNA minicircles and homogeneously-modified H2Bub histones, we have found that DNA topology could strongly and selectively affect nucleosome stability depending on its ubiquitylation state (here the term "nucleosome stability" means the nucleosome property to maintain its structural integrity and dynamics characteristic to "canonic" nucleosomes). The results point to a role for H2B ubiquitylation in amplifying or mitigating the effects of a DNA torque on the nucleosome stability and dynamics.
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Affiliation(s)
- Wladyslaw A Krajewski
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow 119334, Russia.
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33
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Xu Y, Lee JH, Li Z, Wang L, Ordog T, Bailey RC. A droplet microfluidic platform for efficient enzymatic chromatin digestion enables robust determination of nucleosome positioning. LAB ON A CHIP 2018; 18:2583-2592. [PMID: 30046796 PMCID: PMC6103843 DOI: 10.1039/c8lc00599k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The first step in chromatin-based epigenetic assays involves the fragmentation of chromatin to facilitate precise genomic localization of the associated DNA. Here, we report the development of a droplet microfluidic device that can rapidly and efficiently digest chromatin into single nucleosomes starting from whole-cell input material offering simplified and automated processing compared to conventional manual preparation. We demonstrate the digestion of chromatin from 2500-125 000 Jurkat cells using micrococcal nuclease for enzymatic processing. We show that the yield of mononucleosomal DNA can be optimized by controlling enzyme concentration and incubation time, with resulting mononucleosome yields exceeding 80%. Bioinformatic analysis of sequenced mononucleosomal DNA (MNase-seq) indicated a high degree of reproducibility and concordance (97-99%) compared with conventionally processed preparations. Our results demonstrate the feasibility of robust and automated nucleosome preparation using a droplet microfluidic platform for nucleosome positioning and downstream epigenomic assays.
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Affiliation(s)
- Yi Xu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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34
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Baldi S, Krebs S, Blum H, Becker PB. Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing. Nat Struct Mol Biol 2018; 25:894-901. [DOI: 10.1038/s41594-018-0110-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022]
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35
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Umeyama T, Ito T. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. Cell Rep 2018; 21:289-300. [PMID: 28978481 DOI: 10.1016/j.celrep.2017.09.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/31/2017] [Accepted: 09/08/2017] [Indexed: 01/05/2023] Open
Abstract
Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions.
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Affiliation(s)
- Taichi Umeyama
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan; Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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36
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Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc 2018; 13:1006-1019. [PMID: 29651053 DOI: 10.1038/nprot.2018.015] [Citation(s) in RCA: 456] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely used chromatin immunoprecipitation (ChIP) protocols in resolution, signal-to-noise ratio and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and has been used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here, we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data when starting with only 100 cells for a histone modification and 1,000 cells for a transcription factor. From cells to purified DNA, CUT&RUN requires less than a day at the laboratory bench and requires no specialized skills.
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Affiliation(s)
- Peter J Skene
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Jorja G Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Howard Hughes Medical Institute, Seattle, Washington, USA
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37
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Druliner BR, Vera D, Johnson R, Ruan X, Apone LM, Dimalanta ET, Stewart FJ, Boardman L, Dennis JH. Comprehensive nucleosome mapping of the human genome in cancer progression. Oncotarget 2017; 7:13429-45. [PMID: 26735342 PMCID: PMC4924652 DOI: 10.18632/oncotarget.6811] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022] Open
Abstract
Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.
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Affiliation(s)
- Brooke R Druliner
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Daniel Vera
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.,The Center for Genomics and Personalized Medicine, The Florida State University, Tallahassee, Florida, United States of America
| | - Ruth Johnson
- Department of Laboratory Medicine and Experimental Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xiaoyang Ruan
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Lynn M Apone
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Eileen T Dimalanta
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Fiona J Stewart
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.,The Center for Genomics and Personalized Medicine, The Florida State University, Tallahassee, Florida, United States of America.,Institute of Molecular Biophysics, The Florida State University, Tallahassee, Florida, United States of America
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38
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Kubik S, Bruzzone MJ, Albert B, Shore D. A Reply to "MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers," by Chereji et al. Mol Cell 2017; 65:578-580. [PMID: 28157510 DOI: 10.1016/j.molcel.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 11/25/2022]
Abstract
In this issue of Molecular Cell, Chereji et al. (2017) present new data on MNase-sensitive particles previously identified upstream of transcription start sites at many promoters in budding yeast, and they argue, based upon negative histone-ChIP results, that they are non-nucleosomal signals generated by transcription factors (TFs). We show instead, based upon functional experiments where the relevant TFs are rapidly depleted, that this explanation does not hold, and we argue instead that histone ChIP and chemical cleavage assays have a limited capacity to capture these highly dynamic, MNase-sensitive "fragile" nucleosomes.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, Geneva 4, CH-1211 Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, Geneva 4, CH-1211 Switzerland
| | - Benjamin Albert
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, Geneva 4, CH-1211 Switzerland
| | - David Shore
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, Geneva 4, CH-1211 Switzerland.
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39
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Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet 2017; 13:e1006988. [PMID: 28902852 PMCID: PMC5597176 DOI: 10.1371/journal.pgen.1006988] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start site (TSS) of active genes. We investigated the response of the chromatin landscape to changes in environmental conditions using light and dark growth, given the large transcriptional changes resulting from this simple alteration. The resulting shifts in the suites of expressed and repressed genes show little correspondence to changes in nucleosome positioning, but led to significant alterations in the profile of subNSPs upstream of TSS both globally and locally. We examined previously mapped positions for the TFs PIF3, PIF4 and CCA1, which regulate light responses, and found that changes in subNSPs co-localized with these binding sites. This small particle structure is detected only under low levels of MNase digestion and is lost on more complete digestion of chromatin to nucleosomes. We conclude that wide-spectrum analysis of the Arabidopsis genome by differential MNase digestion allows detection of sensitive features hereto obscured, and the comparisons between genome-wide subNSP profiles reveals dynamic changes in their distribution, particularly at distinct genomic locations (i.e. 5'UTRs). The method here employed allows insight into the complex influence of genetic and extrinsic factors in modifying the sub-nucleosomal landscape in association with transcriptional changes.
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Affiliation(s)
- Daniel Antony Pass
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Angela Marchbank
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Margaret R. Crawford
- Genome Centre, University of Sussex, Sussex House, Falmer, Brighton, United Kingdom
| | - Konrad Paszkiewicz
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Nicholas A. Kent
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
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40
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Chen J, Li E, Zhang X, Dong X, Lei L, Song W, Zhao H, Lai J. Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize. MOLECULAR PLANT 2017; 10:962-974. [PMID: 28487258 DOI: 10.1016/j.molp.2017.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/16/2023]
Abstract
Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites (+1 nucleosome) and upstream of transcriptional termination sites (-1 nucleosome). Intrinsically DNA-encoded nucleosome organization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5' and 3' nucleosome-depleted regions as well as further +1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - En Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China.
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41
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Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017; 39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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42
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Platt JL, Kent NA, Kimmel AR, Harwood AJ. Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium. Genome Res 2017; 27:591-600. [PMID: 28330902 PMCID: PMC5378177 DOI: 10.1101/gr.216309.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/27/2017] [Indexed: 01/14/2023]
Abstract
Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.
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Affiliation(s)
- James L Platt
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas A Kent
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
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43
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Rychkov GN, Ilatovskiy AV, Nazarov IB, Shvetsov AV, Lebedev DV, Konev AY, Isaev-Ivanov VV, Onufriev AV. Partially Assembled Nucleosome Structures at Atomic Detail. Biophys J 2016; 112:460-472. [PMID: 28038734 DOI: 10.1016/j.bpj.2016.10.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/06/2016] [Accepted: 10/28/2016] [Indexed: 11/29/2022] Open
Abstract
The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.
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Affiliation(s)
- Georgy N Rychkov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Igor B Nazarov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey V Shvetsov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia; Institute of Applied Mathematics and Mechanics, NRU Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Dmitry V Lebedev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexander Y Konev
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Vladimir V Isaev-Ivanov
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Orlova Roscha, Gatchina, Leningrad District, Russia
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Tech, Blacksburg, Virginia.
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44
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Sexton BS, Druliner BR, Vera DL, Avey D, Zhu F, Dennis JH. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response. Oncotarget 2016; 7:6460-75. [PMID: 26771136 PMCID: PMC4872727 DOI: 10.18632/oncotarget.6841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022] Open
Abstract
Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response.
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Affiliation(s)
- Brittany S Sexton
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Brooke R Druliner
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA.,Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel L Vera
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA.,The Center for Genomics and Personalized Medicine The Florida State University, Tallahassee, Florida, USA
| | - Denis Avey
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Fanxiu Zhu
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Jonathan H Dennis
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
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45
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de Jonge WJ, O'Duibhir E, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Kemmeren P, Holstege FC. Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters. EMBO J 2016; 36:274-290. [PMID: 27979920 PMCID: PMC5286361 DOI: 10.15252/embj.201695621] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/18/2016] [Accepted: 11/01/2016] [Indexed: 11/28/2022] Open
Abstract
An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA‐dominated/TATA‐box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA‐like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA‐box promoters are more dynamic because TATA‐binding protein recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA‐box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.
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Affiliation(s)
- Wim J de Jonge
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Eoghan O'Duibhir
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marian Ja Groot Koerkamp
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Frank Cp Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands .,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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46
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Xiong J, Gao S, Dui W, Yang W, Chen X, Taverna SD, Pearlman RE, Ashlock W, Miao W, Liu Y. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin. Nucleic Acids Res 2016; 44:10091-10105. [PMID: 27488188 PMCID: PMC5137421 DOI: 10.1093/nar/gkw684] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 02/06/2023] Open
Abstract
The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.
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Affiliation(s)
- Jie Xiong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,These authors contributed equally to this work as first authors
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China,These authors contributed equally to this work as first authors
| | - Wen Dui
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wentao Yang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences and The Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ronald E. Pearlman
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wendy Ashlock
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,Correspondence may also be addressed to Wei Miao.
| | - Yifan Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA,To whom correspondence should be addressed. Tel: +1 734 6154239;
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47
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Cam HP, Whitehall S. Micrococcal Nuclease Digestion of Schizosaccharomyces pombe Chromatin. Cold Spring Harb Protoc 2016; 2016:2016/11/pdb.prot091538. [PMID: 27803256 DOI: 10.1101/pdb.prot091538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Digestion of chromatin with micrococcal nuclease (MNase) is widely used to probe nucleosome organization. Analysis of MNase digests by end-labeling techniques or overlapping quantitative polymerase chain reaction (qPCR) can be used to map locus-specific nucleosome positions. Furthermore, the application of genomic technologies can provide genome-wide views of nucleosome position and occupancy. This protocol provides a basic method for MNase digestion of Schizosaccharomyces pombe chromatin and depends on the production of permeabilized spheroplasts.
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Affiliation(s)
- Hugh P Cam
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467
| | - Simon Whitehall
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle NE2 4HH, United Kingdom
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48
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Abstract
Eukaryotic genomes are packaged into an extensively folded state known as chromatin. Analysis of the structure of eukaryotic chromosomes has been revolutionized by development of a suite of genome-wide measurement technologies, collectively termed “epigenomics.” We review major advances in epigenomic analysis of eukaryotic genomes, covering aspects of genome folding at scales ranging from whole chromosome folding down to nucleotide-resolution assays that provide structural insights into protein-DNA interactions. We then briefly outline several challenges remaining and highlight new developments such as single-cell epigenomic assays that will help provide us with a high-resolution structural understanding of eukaryotic genomes.
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Affiliation(s)
- Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University, Jerusalem 9190401, Israel
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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49
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Krajewski WA. On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function. Biochem Biophys Rep 2016; 5:492-501. [PMID: 28955857 PMCID: PMC5600426 DOI: 10.1016/j.bbrep.2016.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 01/10/2023] Open
Abstract
Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is 'translated' to the particular 'activating' or 'repressing' chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content - such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products) of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a 'polymer' of individual 'canonical' nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.
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Affiliation(s)
- Wladyslaw A Krajewski
- Institute of Developmental Biology of Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334 Russia
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50
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Kubik S, Bruzzone MJ, Jacquet P, Falcone JL, Rougemont J, Shore D. Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast. Mol Cell 2016; 60:422-34. [PMID: 26545077 DOI: 10.1016/j.molcel.2015.10.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/30/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or -depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a narrower, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Philippe Jacquet
- Swiss Institute of Bioinformatics (SIB) and Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Luc Falcone
- Center for Advanced Modeling Sciences, Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland
| | - Jacques Rougemont
- Swiss Institute of Bioinformatics (SIB) and Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland.
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