1
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Doughty BR, Hinks MM, Schaepe JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L, Greenleaf WJ. Single-molecule chromatin configurations link transcription factor binding to expression in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578660. [PMID: 38352517 PMCID: PMC10862896 DOI: 10.1101/2024.02.02.578660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF's capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.
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Affiliation(s)
| | - Michaela M Hinks
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Georgi K Marinov
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Abby R Thurm
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | | | - Benjamin E Parks
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Yingxuan Tan
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Danilo Dubocanin
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Lacramioara Bintu
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - William J Greenleaf
- Genetics Department, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94205, USA
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2
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Thakur A, Park K, Cullum R, Fuglerud BM, Khoshnoodi M, Drissler S, Stephan TL, Lotto J, Kim D, Gonzalez FJ, Hoodless PA. HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements. Commun Biol 2024; 7:144. [PMID: 38297077 PMCID: PMC10830483 DOI: 10.1038/s42003-024-05835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Hepatocyte nuclear factor 4A (HNF4A/NR2a1), a transcriptional regulator of hepatocyte identity, controls genes that are crucial for liver functions, primarily through binding to enhancers. In mammalian cells, active and primed enhancers are marked by monomethylation of histone 3 (H3) at lysine 4 (K4) (H3K4me1) in a cell type-specific manner. How this modification is established and maintained at enhancers in connection with transcription factors (TFs) remains unknown. Using analysis of genome-wide histone modifications, TF binding, chromatin accessibility and gene expression, we show that HNF4A is essential for an active chromatin state. Using HNF4A loss and gain of function experiments in vivo and in cell lines in vitro, we show that HNF4A affects H3K4me1, H3K27ac and chromatin accessibility, highlighting its contribution to the establishment and maintenance of a transcriptionally permissive epigenetic state. Mechanistically, HNF4A interacts with the mixed-lineage leukaemia 4 (MLL4) complex facilitating recruitment to HNF4A-bound regions. Our findings indicate that HNF4A enriches H3K4me1, H3K27ac and establishes chromatin opening at transcriptional regulatory regions.
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Affiliation(s)
- Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Kwangjin Park
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Donghwan Kim
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Frank J Gonzalez
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, V6T 1Z4, Canada.
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3
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McDonald B, Chick BY, Hargreaves DC, Kaech SM. Early Chromatin Remodeling Events in Acutely Stimulated CD8 + T Cells. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:467-473. [PMID: 38161581 PMCID: PMC10751865 DOI: 10.59249/axgu7370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
T cells undergo extensive chromatin remodeling over several days following stimulation through the T cell receptor. However, the kinetics and gene loci targeted by early remodeling events within the first 24 hours of T cell priming to orchestrate effector differentiation have not been well described. We identified that chromatin accessibility is rapidly and extensively remodeled within 1 hour of stimulation of naïve CD8+ T cells, leading to increased global chromatin accessibility at many effector T cell-associated genes that are enriched for AP-1, early growth response (EGR), and nuclear factor of activated T cells (NFAT) binding sites, but this short duration of stimulation is insufficient for commitment to clonal expansion in vivo. Sustained 24-hour stimulation led to further chromatin remodeling and was sufficient to enable clonal expansion. These data suggest that the duration of antigen receptor signaling is intimately coupled to chromatin remodeling and activation of genes involved in effector cell differentiation and highlight a potential mechanism that helps CD8+ T cells discriminate between foreign- and self-antigens.
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Affiliation(s)
- Bryan McDonald
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of
California San Diego, La Jolla, CA, USA
| | - Brent Y. Chick
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of
California at San Diego, La Jolla, California, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
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4
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Reddy D, Bhattacharya S, Workman JL. (mis)-Targeting of SWI/SNF complex(es) in cancer. Cancer Metastasis Rev 2023; 42:455-470. [PMID: 37093326 PMCID: PMC10349013 DOI: 10.1007/s10555-023-10102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF (also called BAF) is critical for the regulation of gene expression. During the evolution from yeast to mammals, the BAF complex has evolved an enormous complexity that contains a high number of subunits encoded by various genes. Emerging studies highlight the frequent involvement of altered mammalian SWI/SNF chromatin-remodeling complexes in human cancers. Here, we discuss the recent advances in determining the structure of SWI/SNF complexes, highlight the mechanisms by which mutations affecting these complexes promote cancer, and describe the promising emerging opportunities for targeted therapies.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
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5
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Singh A, Modak SB, Chaturvedi MM, Purohit JS. SWI/SNF Chromatin Remodelers: Structural, Functional and Mechanistic Implications. Cell Biochem Biophys 2023:10.1007/s12013-023-01140-5. [PMID: 37119511 DOI: 10.1007/s12013-023-01140-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
The nuclear events of a eukaryotic cell, such as replication, transcription, recombination and repair etc. require the transition of the compactly arranged chromatin into an uncompacted state and vice-versa. This is mediated by post-translational modification of the histones, exchange of histone variants and ATP-dependent chromatin remodeling. The SWI/SNF chromatin remodeling complexes are one of the most well characterized families of chromatin remodelers. In addition to their role in modulating chromatin, they have also been assigned roles in cancer and health-related anomalies such as developmental, neurocognitive, and intellectual disabilities. Owing to their vital cellular and medical connotations, developing an understanding of the structural and functional aspects of the complex becomes imperative. However, due to the intricate nature of higher-order chromatin as well as compositional heterogeneity of the SWI/SNF complex, intra-species isoforms and inter-species homologs, this often becomes challenging. To this end, the present review attempts to present an amalgamated perspective on the discovery, structure, function, and regulation of the SWI/SNF complex.
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Affiliation(s)
- Abhilasha Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Madan M Chaturvedi
- Department of Zoology, University of Delhi, Delhi, 110007, India
- SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India
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6
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Schofield JA, Hahn S. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. Cell Rep 2023; 42:112387. [PMID: 37058407 PMCID: PMC10567116 DOI: 10.1016/j.celrep.2023.112387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Three classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA, and Mediator (MED) Tail, but whether this dependence is determined by the core promoter, upstream activating sequences (UASs), or other gene features is unclear. Also unclear is whether UASs can broadly activate transcription from the different promoter classes. Here, we measure transcription and cofactor specificity for thousands of UAS-core promoter combinations and find that most UASs broadly activate promoters regardless of regulatory class, while few display strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. We find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and core promoter, while dependence on TFIID localizes to only the promoter. Finally, our results suggest the role of TATA and TATA-like promoter sequences in MED Tail function.
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Affiliation(s)
- Jeremy A Schofield
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA.
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7
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Nikolov VN, Malavia D, Kubota T. SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes. Nat Commun 2022; 13:1968. [PMID: 35413952 PMCID: PMC9005695 DOI: 10.1038/s41467-022-29591-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
The Pleiotropic Drug Resistance (PDR) network is central to the drug response in fungi, and its overactivation is associated with drug resistance. However, gene regulation of the PDR network is not well understood. Here, we show that the histone chaperone Rtt106 and the chromatin remodeller SWI/SNF control expression of the PDR network genes and confer drug resistance. In Saccharomyces cerevisiae, Rtt106 specifically localises to PDR network gene promoters dependent on transcription factor Pdr3, but not Pdr1, and is essential for Pdr3-mediated basal expression of the PDR network genes, while SWI/SNF is essential for both basal and drug-induced expression. Also in the pathogenic fungus Candida glabrata, Rtt106 and SWI/SNF regulate drug-induced PDR gene expression. Consistently, loss of Rtt106 or SWI/SNF sensitises drug-resistant S. cerevisiae mutants and C. glabrata to antifungal drugs. Since they cooperatively drive PDR network gene expression, Rtt106 and SWI/SNF represent potential therapeutic targets to combat antifungal resistance.
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Affiliation(s)
- Vladislav N Nikolov
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Dhara Malavia
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Centre for Medical Mycology, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Takashi Kubota
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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8
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Abstract
Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hinrich Boeger
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California;
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9
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Gutierrez JI, Brittingham GP, Karadeniz YB, Tran KD, Dutta A, Holehouse AS, Peterson CL, Holt LJ. SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence. eLife 2022; 11:70344. [PMID: 35129437 PMCID: PMC8890752 DOI: 10.7554/elife.70344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.
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Affiliation(s)
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, United States
| | - Yonca B Karadeniz
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Kathleen D Tran
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, United States
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10
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Sanz AB, García R, Pavón-Vergés M, Rodríguez-Peña JM, Arroyo J. Control of Gene Expression via the Yeast CWI Pathway. Int J Mol Sci 2022; 23:ijms23031791. [PMID: 35163713 PMCID: PMC8836261 DOI: 10.3390/ijms23031791] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/18/2022] Open
Abstract
Living cells exposed to stressful environmental situations can elicit cellular responses that guarantee maximal cell survival. Most of these responses are mediated by mitogen-activated protein kinase (MAPK) cascades, which are highly conserved from yeast to humans. Cell wall damage conditions in the yeast Saccharomyces cerevisiae elicit rescue mechanisms mainly associated with reprogramming specific transcriptional responses via the cell wall integrity (CWI) pathway. Regulation of gene expression by this pathway is coordinated by the MAPK Slt2/Mpk1, mainly via Rlm1 and, to a lesser extent, through SBF (Swi4/Swi6) transcription factors. In this review, we summarize the molecular mechanisms controlling gene expression upon cell wall stress and the role of chromatin structure in these processes. Some of these mechanisms are also discussed in the context of other stresses governed by different yeast MAPK pathways. Slt2 regulates both transcriptional initiation and elongation by interacting with chromatin at the promoter and coding regions of CWI-responsive genes but using different mechanisms for Rlm1- and SBF-dependent genes. Since MAPK pathways are very well conserved in eukaryotic cells and are essential for controlling cellular physiology, improving our knowledge regarding how they regulate gene expression could impact the future identification of novel targets for therapeutic intervention.
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11
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Jian Y, Shim WB, Ma Z. Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions. STRESS BIOLOGY 2021; 1:18. [PMID: 37676626 PMCID: PMC10442046 DOI: 10.1007/s44154-021-00019-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events. Studies in animals, plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses. In this review, we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription, mRNA splicing, and DNA damage response. Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis. Finally, the potentials in exploiting chromatin remodeling for management of crop disease are presented.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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12
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No Need to Stick Together to Be Connected: Multiple Types of Enhancers' Networking. Cancers (Basel) 2021; 13:cancers13205201. [PMID: 34680347 PMCID: PMC8533737 DOI: 10.3390/cancers13205201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Transcription regulation programs require the functional interaction of distal and proximal regulatory regions, interacting by specific 3D chromatin configurations. Enhancers are cis-acting regulatory elements able to promote gene expression regardless their orientation and distance from the transcription starting site. Their systematic mapping by genome-wide chromatin profiling and chromosome conformation analysis, combined with the development of gene-editing approaches to modulate their function, revealed that many enhancers work together to fine-tune the expression of their target genes. This review aim to describe the functions of different types of enhancers and the modalities of enhancers’ interaction, focusing on their role in the regulation of complex biological processes like cancer development. Abstract The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.
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13
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Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194749. [PMID: 34425241 PMCID: PMC10359485 DOI: 10.1016/j.bbagrm.2021.194749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]
Abstract
The domain of transcription regulation has been notoriously difficult to annotate in the Gene Ontology, partly because of the intricacies of gene regulation which involve molecular interactions with DNA as well as amongst protein complexes. The molecular function 'transcription coregulator activity' is a part of the biological process 'regulation of transcription, DNA-templated' that occurs in the cellular component 'chromatin'. It can mechanistically link sequence-specific DNA-binding transcription factor (dbTF) regulatory DNA target sites to coactivator and corepressor target sites through the molecular function 'cis-regulatory region sequence-specific DNA binding'. Many questions arise about transcription coregulators (coTF). Here, we asked how many unannotated, putative coregulators can be identified in protein complexes? Therefore, we mined the CORUM and hu.MAP protein complex databases with known and strongly presumed human transcription coregulators. In addition, we trawled the BioGRID and IntAct molecular interaction databases for interactors of the known 1457 human dbTFs annotated by the GREEKC and GO consortia. This yielded 1093 putative transcription factor coregulator complex subunits, of which 954 interact directly with a dbTF. This substantially expands the set of coTFs that could be annotated to 'transcription coregulator activity' and sets the stage for renewed annotation and wet-lab research efforts. To this end, we devised a prioritisation score based on existing GO annotations of already curated transcription coregulators as well as interactome representation. Since all the proteins that we mined are parts of protein complexes, we propose to concomitantly engage in annotation of the putative transcription coregulator-containing complexes in the Complex Portal database.
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14
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Kim JM, Visanpattanasin P, Jou V, Liu S, Tang X, Zheng Q, Li KY, Snedeker J, Lavis LD, Lionnet T, Wu C. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 2021; 10:e69387. [PMID: 34313223 PMCID: PMC8352589 DOI: 10.7554/elife.69387] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending 'tug-of-war' that controls a temporally shifting window of accessibility for the transcription initiation machinery.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kai Yu Li
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jonathan Snedeker
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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15
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Abstract
Substance use disorders (SUDs) are chronic brain diseases characterized by transitions from recreational to compulsive drug use and aberrant drug craving that persists for months to years after abstinence is achieved. The transition to compulsive drug use implies that plasticity is occurring, altering the physiology of the brain to precipitate addicted states. Epigenetic phenomena represent a varied orchestra of transcriptional tuning mechanisms that, in response to environmental stimuli, create and maintain gene expression-mediated physiological outcomes. Therefore, epigenetic mechanisms represent a convergent regulatory framework through which the plasticity required to achieve an addicted state can arise and then persist long after drug use has ended. In the first section, we will introduce basic concepts in epigenetics, such as chromatin architecture, histones and their posttranslational modifications, DNA methylation, noncoding RNAs, and transcription factors, along with methods for their investigation. We will then examine the implications of these mechanisms in SUDs, with a particular focus on cocaine-mediated neuroepigenetic plasticity across multiple behavioral models of addiction.
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Affiliation(s)
- Andrew F Stewart
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sasha L Fulton
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ian Maze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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16
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Davis RB, Kaur T, Moosa MM, Banerjee PR. FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion-like domains. Protein Sci 2021; 30:1454-1466. [PMID: 34018649 PMCID: PMC8197437 DOI: 10.1002/pro.4127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022]
Abstract
Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates. Nuclear FUS-DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF (mSWI/SNF) is driven by heterotypic PLD-PLD interactions between FUS-DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single-molecule correlative force-fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD-driven co-condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD-DBD domain architecture for global transcriptional reprogramming.
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Affiliation(s)
- Richoo B. Davis
- Department of PhysicsUniversity at BuffaloBuffaloNew YorkUSA
| | - Taranpreet Kaur
- Department of PhysicsUniversity at BuffaloBuffaloNew YorkUSA
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17
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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18
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Interplay of two transcription factors for recruitment of the chromatin remodeling complex modulates fungal nitrosative stress response. Nat Commun 2021; 12:2576. [PMID: 33958593 PMCID: PMC8102577 DOI: 10.1038/s41467-021-22831-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023] Open
Abstract
Nitric oxide (NO) is a diffusible signaling molecule that modulates animal and plant immune responses. In addition, reactive nitrogen species derived from NO can display antimicrobial activities by reacting with microbial cellular components, leading to nitrosative stress (NS) in pathogens. Here, we identify FgAreB as a regulator of the NS response in Fusarium graminearum, a fungal pathogen of cereal crops. FgAreB serves as a pioneer transcription factor for recruitment of the chromatin-remodeling complex SWI/SNF at the promoters of genes involved in the NS response, thus promoting their transcription. FgAreB plays important roles in fungal infection and growth. Furthermore, we show that a transcription repressor (FgIxr1) competes with the SWI/SNF complex for FgAreB binding, and negatively regulates the NS response. NS, in turn, promotes the degradation of FgIxr1, thus enhancing the recruitment of the SWI/SNF complex by FgAreB.
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19
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Fluorescence resonance energy transfer in revealing protein-protein interactions in living cells. Emerg Top Life Sci 2021; 5:49-59. [PMID: 33856021 DOI: 10.1042/etls20200337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022]
Abstract
Genes are expressed to proteins for a wide variety of fundamental biological processes at the cellular and organismal levels. However, a protein rarely functions alone, but rather acts through interactions with other proteins to maintain normal cellular and organismal functions. Therefore, it is important to analyze the protein-protein interactions to determine functional mechanisms of proteins, which can also guide to develop therapeutic targets for treatment of diseases caused by altered protein-protein interactions leading to cellular/organismal dysfunctions. There is a large number of methodologies to study protein interactions in vitro, in vivo and in silico, which led to the development of many protein interaction databases, and thus, have enriched our knowledge about protein-protein interactions and functions. However, many of these interactions were identified in vitro, but need to be verified/validated in living cells. Furthermore, it is unclear whether these interactions are direct or mediated via other proteins. Moreover, these interactions are representative of cell- and time-average, but not a single cell in real time. Therefore, it is crucial to detect direct protein-protein interactions in a single cell during biological processes in vivo, towards understanding the functional mechanisms of proteins in living cells. Importantly, a fluorescence resonance energy transfer (FRET)-based methodology has emerged as a powerful technique to decipher direct protein-protein interactions at a single cell resolution in living cells, which is briefly described in a limited available space in this mini-review.
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Wolff MR, Schmid A, Korber P, Gerland U. Effective dynamics of nucleosome configurations at the yeast PHO5 promoter. eLife 2021; 10:58394. [PMID: 33666171 PMCID: PMC8004102 DOI: 10.7554/elife.58394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Chromatin dynamics are mediated by remodeling enzymes and play crucial roles in gene regulation, as established in a paradigmatic model, the Saccharomyces cerevisiae PHO5 promoter. However, effective nucleosome dynamics, that is, trajectories of promoter nucleosome configurations, remain elusive. Here, we infer such dynamics from the integration of published single-molecule data capturing multi-nucleosome configurations for repressed to fully active PHO5 promoter states with other existing histone turnover and new chromatin accessibility data. We devised and systematically investigated a new class of 'regulated on-off-slide' models simulating global and local nucleosome (dis)assembly and sliding. Only seven of 68,145 models agreed well with all data. All seven models involve sliding and the known central role of the N-2 nucleosome, but regulate promoter state transitions by modulating just one assembly rather than disassembly process. This is consistent with but challenges common interpretations of previous observations at the PHO5 promoter and suggests chromatin opening by binding competition.
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Affiliation(s)
| | - Andrea Schmid
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ulrich Gerland
- Department of Physics, Technical University of Munich, Garching, Germany
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21
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What do Transcription Factors Interact With? J Mol Biol 2021; 433:166883. [PMID: 33621520 DOI: 10.1016/j.jmb.2021.166883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Although we have made significant progress, we still possess a limited understanding of how genomic and epigenomic information directs gene expression programs through sequence-specific transcription factors (TFs). Extensive research has settled on three general classes of TF targets in metazoans: promoter accessibility via chromatin regulation (e.g., SAGA), assembly of the general transcription factors on promoter DNA (e.g., TFIID), and recruitment of RNA polymerase (Pol) II (e.g., Mediator) to establish a transcription pre-initiation complex (PIC). Here we discuss TFs and their targets. We also place this in the context of our current work with Saccharomyces (yeast), where we find that promoters typically lack an architecture that supports TF function. Moreover, yeast promoters that support TF binding also display interactions with cofactors like SAGA and Mediator, but not TFIID. It is unknown to what extent all genes in metazoans require TFs and their cofactors.
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22
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Marr LT, Ocampo J, Clark DJ, Hayes JJ. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin 2021; 14:5. [PMID: 33430969 PMCID: PMC7802155 DOI: 10.1186/s13072-020-00381-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/28/2020] [Indexed: 01/09/2023] Open
Abstract
Background The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM). Results Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A–H2B dimer/H3–H4 tetramer interface, and H3 A110C, resides at the H3–H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed. Conclusions Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.
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Affiliation(s)
- Luke T Marr
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), C1428ADN, Buenos Aires, Argentina
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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Mazina MY, Vorobyeva NE. Chromatin Modifiers in Transcriptional Regulation: New Findings and Prospects. Acta Naturae 2021; 13:16-30. [PMID: 33959384 PMCID: PMC8084290 DOI: 10.32607/actanaturae.11101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/17/2020] [Indexed: 02/04/2023] Open
Abstract
Histone-modifying and remodeling complexes are considered the main coregulators that affect transcription by changing the chromatin structure. Coordinated action by these complexes is essential for the transcriptional activation of any eukaryotic gene. In this review, we discuss current trends in the study of histone modifiers and chromatin remodelers, including the functional impact of transcriptional proteins/ complexes i.e., "pioneers"; remodeling and modification of non-histone proteins by transcriptional complexes; the supplementary functions of the non-catalytic subunits of remodelers, and the participation of histone modifiers in the "pause" of RNA polymerase II. The review also includes a scheme illustrating the mechanisms of recruitment of the main classes of remodelers and chromatin modifiers to various sites in the genome and their functional activities.
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Affiliation(s)
- M. Yu. Mazina
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
| | - N. E. Vorobyeva
- Institute of Gene Biology RAS, Group of transcriptional complexes dynamics, Moscow, 119334 Russia
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24
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Molecular Regulation of Circadian Chromatin. J Mol Biol 2020; 432:3466-3482. [PMID: 31954735 DOI: 10.1016/j.jmb.2020.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Circadian rhythms are generated by transcriptional negative feedback loops and require histone modifications and chromatin remodeling to ensure appropriate timing and amplitude of clock gene expression. Circadian modifications to histones are important for transcriptional initiation and feedback inhibition serving as signaling platform for chromatin-remodeling enzymes. Current models indicate circadian-regulated facultative heterochromatin (CRFH) is a conserved mechanism at clock genes in Neurospora, Drosophila, and mice. CRFH consists of antiphasic rhythms in activating and repressive modifications generating chromatin states that cycle between transcriptionally permissive and nonpermissive. There are rhythms in histone H3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac) and histone H3 lysine 4 methylation (H3K4me) during activation; while deacetylation, histone H3 lysine 9 methylation (H3K9me) and heterochromatin protein 1 (HP1) are hallmarks of repression. ATP-dependent chromatin-remodeling enzymes control accessibility, nucleosome positioning/occupancy, and nuclear organization. In Neurospora, the rhythm in facultative heterochromatin is mediated by the frequency (frq) natural antisense transcript (NAT) qrf. While in mammals, histone deacetylases (HDACs), histone H3 lysine 9 methyltransferase (KMT1/SUV39), and components of nucleosome remodeling and deacetylase (NuRD) are part of the nuclear PERIOD complex (PER complex). Genomics efforts have found relationships among rhythmic chromatin modifications at clock-controlled genes (ccg) revealing circadian control of genome-wide chromatin states. There are also circadian clock-regulated lncRNAs with an emerging function that includes assisting in chromatin dynamics. In this review, we explore the connections between circadian clock, chromatin remodeling, lncRNAs, and CRFH and how these impact rhythmicity, amplitude, period, and phase of circadian clock genes.
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25
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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26
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Cao Y, Zheng F, Zhang W, Meng X, Liu W. Trichoderma reesei XYR1 recruits SWI/SNF to facilitate cellulase gene expression. Mol Microbiol 2019; 112:1145-1162. [PMID: 31309604 DOI: 10.1111/mmi.14352] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Cellulase gene expression in Trichoderma reesei is highly responsive to environmental cues and is under stringent regulation by multiple transcription factors. XYR1 (Xylanase regulator 1) has been identified as the most important transcriptional activator of cellulase/hemicellulase gene expression although the precise transactivating mechanism remains largely elusive. Here we show that the activation domain of XYR1 interacts with the T. reesei homolog of the TrSNF12 subunit of SWI/SNF complex. Deletion of Trsnf12 markedly impaired the induced cellulase gene expression. Individual loss of other SWI/SNF subunits including the catalytic subunit also severely compromised cellulase gene expression and interfered with loss of histone H4 in the cbh1 and eg1 promoters upon cellulose induction. In addition, we find that the SWI/SNF occupancy on cellulase gene promoters strictly required XYR1 and TrSNF12 but TrSNF12 was dispensable for the XYR1 binding to these promoters. These data suggest a model in which XYR1 recruits SWI/SNF through direct interactions with TrSNF12 to remodel chromatin at cellulase gene promoters, thereby activating cellulase gene expression to initiate the cellulolytic response in T. reesei.
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Affiliation(s)
- Yanli Cao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
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27
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Rodrigues-Pousada C, Devaux F, Caetano SM, Pimentel C, da Silva S, Cordeiro AC, Amaral C. Yeast AP-1 like transcription factors (Yap) and stress response: a current overview. MICROBIAL CELL 2019; 6:267-285. [PMID: 31172012 PMCID: PMC6545440 DOI: 10.15698/mic2019.06.679] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Yeast adaptation to stress has been extensively studied. It involves large reprogramming of genome expression operated by many, more or less specific, transcription factors. Here, we review our current knowledge on the function of the eight Yap transcription factors (Yap1 to Yap8) in Saccharomyces cerevisiae, which were shown to be involved in various stress responses. More precisely, Yap1 is activated under oxidative stress, Yap2/Cad1 under cadmium, Yap4/Cin5 and Yap6 under osmotic shock, Yap5 under iron overload and Yap8/Arr1 by arsenic compounds. Yap3 and Yap7 seem to be involved in hydroquinone and nitrosative stresses, respectively. The data presented in this article illustrate how much knowledge on the function of these Yap transcription factors is advanced. The evolution of the Yap family and its roles in various pathogenic and non-pathogenic fungal species is discussed in the last section.
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Affiliation(s)
- Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Soraia M Caetano
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Sofia da Silva
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Ana Carolina Cordeiro
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
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Yu X, Meng X, Liu Y, Li N, Zhang A, Wang TJ, Jiang L, Pang J, Zhao X, Qi X, Zhang M, Wang S, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize. PLANT MOLECULAR BIOLOGY 2018; 97:451-465. [PMID: 29956114 DOI: 10.1007/s11103-018-0751-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/18/2018] [Indexed: 05/16/2023]
Abstract
The maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Drought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the model plant Arabidopsis thaliana suggests that core components of SWI/SNF chromatin remodeling complexes play essential roles in abiotic stress responses. However, how maize SWI/SNF chromatin remodeling complexes function in osmotic and drought stress responses remains unknown. Here we show that ZmCHB101, a homolog of A. thaliana SWI3D in maize, plays essential roles in osmotic and dehydration stress responses. ZmCHB101-RNA interference (RNAi) transgenic plants displayed osmotic, salt and drought stress-sensitive phenotypes. Genome-wide RNA-sequencing analysis revealed that ZmCHB101 impacts the transcriptional expression landscape of osmotic stress-responsive genes. Intriguingly, ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Furthermore, we identified that ZmCHB101 associates with RNA polymerase II (RNAPII) in vivo and is a prerequisite for the proper occupancy of RNAPII on the proximal regions of transcription start sites of stress-response genes. Taken together, our findings suggest that ZmCHB101 affects gene expression by remodeling chromatin states and controls RNAPII occupancies in maize under osmotic stress.
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Affiliation(s)
- Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
- Department of Bioengineering, Jilin Agricultural Science and Technology College, Jilin, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Xinxin Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Meishan Zhang
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
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KLU suppresses megasporocyte cell fate through SWR1-mediated activation of WRKY28 expression in Arabidopsis. Proc Natl Acad Sci U S A 2017; 115:E526-E535. [PMID: 29288215 DOI: 10.1073/pnas.1716054115] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Germ-line specification is essential for sexual reproduction. In the ovules of most flowering plants, only a single hypodermal cell enlarges and differentiates into a megaspore mother cell (MMC), the founder cell of the female germ-line lineage. The molecular mechanisms restricting MMC specification to a single cell remain elusive. We show that the Arabidopsis transcription factor WRKY28 is exclusively expressed in hypodermal somatic cells surrounding the MMC and is required to repress these cells from acquiring MMC-like cell identity. In this process, the SWR1 chromatin remodeling complex mediates the incorporation of the histone variant H2A.Z at the WRKY28 locus. Moreover, the cytochrome P450 gene KLU, expressed in inner integument primordia, non-cell-autonomously promotes WRKY28 expression through H2A.Z deposition at WRKY28. Taken together, our findings show how somatic cells in ovule primordia cooperatively use chromatin remodeling to restrict germ-line cell specification to a single cell.
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Dai X, Bai Y, Zhao L, Dou X, Liu Y, Wang L, Li Y, Li W, Hui Y, Huang X, Wang Z, Qin Y. H2A.Z Represses Gene Expression by Modulating Promoter Nucleosome Structure and Enhancer Histone Modifications in Arabidopsis. MOLECULAR PLANT 2017; 10:1274-1292. [PMID: 28951178 DOI: 10.1016/j.molp.2017.09.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 05/19/2023]
Abstract
Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at +1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed +1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcriptional control.
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Affiliation(s)
- Xiaozhuan Dai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youhuang Bai
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lihua Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xianying Dou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanhui Liu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lulu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanan Hui
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Ocean Science, Minjiang University, Fuzhou 350108, China.
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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31
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García A, González S, Antequera F. Nucleosomal organization and DNA base composition patterns. Nucleus 2017. [PMID: 28635365 PMCID: PMC5703254 DOI: 10.1080/19491034.2017.1337611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleosomes are the basic units of chromatin. They compact the genome inside the nucleus and regulate the access of proteins to DNA. In the yeast genome, most nucleosomes occupy well-defined positions, which are maintained under many different physiological situations and genetic backgrounds. Although several short sequence elements have been described that favor or reduce the affinity between histones and DNA, the extent to which the DNA sequence affects nucleosome positioning in the genomic context remains unclear. Recent analyses indicate that the base composition pattern of mononucleosomal DNA differs among species, and that the same sequence elements have a different impact on nucleosome positioning in different genomes despite the high level of phylogenetic conservation of histones. These studies have also shown that the DNA sequence contributes to nucleosome positioning to the point that it is possible to design synthetic DNA molecules capable of generating regular and species-specific nucleosomal patterns in vivo.
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Affiliation(s)
- Alicia García
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
| | - Sara González
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
| | - Francisco Antequera
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
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32
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Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 2017; 18:407-422. [PMID: 28512350 DOI: 10.1038/nrm.2017.26] [Citation(s) in RCA: 674] [Impact Index Per Article: 96.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Burrowes SG, Salem NA, Tseng AM, Balaraman S, Pinson MR, Garcia C, Miranda RC. The BAF (BRG1/BRM-Associated Factor) chromatin-remodeling complex exhibits ethanol sensitivity in fetal neural progenitor cells and regulates transcription at the miR-9-2 encoding gene locus. Alcohol 2017; 60:149-158. [PMID: 28438527 DOI: 10.1016/j.alcohol.2017.01.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/15/2016] [Accepted: 01/03/2017] [Indexed: 12/25/2022]
Abstract
Fetal alcohol spectrum disorders are a leading cause of intellectual disability worldwide. Previous studies have shown that developmental ethanol exposure results in loss of microRNAs (miRNAs), including miR-9, and loss of these miRNAs, in turn, mediates some of ethanol's teratogenic effects in the developing brain. We previously found that ethanol increased methylation at the miR-9-2 encoding gene locus in mouse fetal neural stem cells (NSC), advancing a mechanism for epigenetic silencing of this locus and consequently, miR-9 loss in NSCs. Therefore, we assessed the role of the BAF (BRG1/BRM-Associated Factor) complex, which disassembles nucleosomes to facilitate access to chromatin, as an epigenetic mediator of ethanol's effects on miR-9. Chromatin immunoprecipitation and DNAse I-hypersensitivity analyses showed that the BAF complex was associated with both transcriptionally accessible and heterochromatic regions of the miR-9-2 locus, and that disintegration of the BAF complex by combined knockdown of BAF170 and BAF155 resulted in a significant decrease in miR-9. We hypothesized that ethanol exposure would result in loss of BAF-complex function at the miR-9-2 locus. However, ethanol exposure significantly increased mRNA transcripts for maturation-associated BAF-complex members BAF170, SS18, ARID2, BAF60a, BRM/BAF190b, and BAF53b. Ethanol also significantly increased BAF-complex binding within an intron containing a CpG island and in the terminal exon encoding precursor (pre)-miR-9-2. These data suggest that the BAF complex may adaptively respond to ethanol exposure to protect against a complete loss of miR-9-2 in fetal NSCs. Chromatin remodeling factors may adapt to the presence of a teratogen, to maintain transcription of critical miRNA regulatory pathways.
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Mediator, SWI/SNF and SAGA complexes regulate Yap8-dependent transcriptional activation of ACR2 in response to arsenate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:472-481. [DOI: 10.1016/j.bbagrm.2017.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/12/2023]
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Hepp MI, Smolle M, Gidi C, Amigo R, Valenzuela N, Arriagada A, Maureira A, Gogol MM, Torrejón M, Workman JL, Gutiérrez JL. Role of Nhp6 and Hmo1 in SWI/SNF occupancy and nucleosome landscape at gene regulatory regions. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:316-326. [PMID: 28089519 PMCID: PMC5913752 DOI: 10.1016/j.bbagrm.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/05/2017] [Accepted: 01/07/2017] [Indexed: 10/20/2022]
Abstract
Diverse chromatin modifiers are involved in regulation of gene expression at the level of transcriptional regulation. Among these modifiers are ATP-dependent chromatin remodelers, where the SWI/SNF complex is the founding member. It has been observed that High Mobility Group (HMG) proteins can influence the activity of a number of these chromatin remodelers. In this context, we have previously demonstrated that the yeast HMG proteins Nhp6 and Hmo1 can stimulate SWI/SNF activity. Here, we studied the genome-wide binding patterns of Nhp6, Hmo1 and the SWI/SNF complex, finding that most of gene promoters presenting high occupancy of this complex also display high enrichment of these HMG proteins. Using deletion mutant strains we demonstrate that binding of SWI/SNF is significantly reduced at numerous genomic locations by deletion of NHP6 and/or deletion of HMO1. Moreover, alterations in the nucleosome landscape take place at gene promoters undergoing reduced SWI/SNF binding. Additional analyses show that these effects also correlate with alterations in transcriptional activity. Our results suggest that, besides the ability to stimulate SWI/SNF activity, these HMG proteins are able to assist the loading of this complex onto gene regulatory regions.
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Affiliation(s)
- Matias I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Michaela Smolle
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Cristian Gidi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Roberto Amigo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Nicole Valenzuela
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Axel Arriagada
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Alejandro Maureira
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Marcela Torrejón
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile.
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36
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Kwok RS, Lam VH, Chiu JC. Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila. Fly (Austin) 2016; 9:145-54. [PMID: 26926115 PMCID: PMC4862430 DOI: 10.1080/19336934.2016.1143993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian clocks enable organisms to anticipate daily changes in the environment and coordinate temporal rhythms in physiology and behavior with the 24-h day-night cycle. The robust cycling of circadian gene expression is critical for proper timekeeping, and is regulated by transcription factor binding, RNA polymerase II (RNAPII) recruitment and elongation, and post-transcriptional mechanisms. Recently, it has become clear that dynamic alterations in chromatin landscape at the level of histone posttranslational modification and nucleosome density facilitate rhythms in transcription factor recruitment and RNAPII activity, and are essential for progression through activating and repressive phases of circadian transcription. Here, we discuss the characterization of the BRAHMA (BRM) chromatin-remodeling protein in Drosophila in the context of circadian clock regulation. By dissecting its catalytic vs. non-catalytic activities, we propose a model in which the non-catalytic activity of BRM functions to recruit repressive factors to limit the transcriptional output of CLOCK (CLK) during the active phase of circadian transcription, while the primary function of the ATP-dependent catalytic activity is to tune and prevent over-recruitment of negative regulators by increasing nucleosome density. Finally, we divulge ongoing efforts and investigative directions toward a deeper mechanistic understanding of transcriptional regulation of circadian gene expression at the chromatin level.
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Affiliation(s)
- Rosanna S Kwok
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Vu H Lam
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
| | - Joanna C Chiu
- a Department of Entomology and Nematology ; University of California Davis ; Davis , CA 95616 , USA
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37
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Bowman GD, McKnight JN. Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome. Bioessays 2016; 39:1-8. [PMID: 27862071 DOI: 10.1002/bies.201600183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Eukaryotic genomes are functionally organized into chromatin, a compact packaging of nucleoproteins with the basic repeating unit known as the nucleosome. A major focus for the chromatin field has been understanding what rules govern nucleosome positioning throughout the genome, and here we review recent findings using a novel, sequence-targeted remodeling enzyme. Nucleosomes are often packed into evenly spaced arrays that are reproducibly positioned, but how such organization is established and maintained through dramatic events such as DNA replication is poorly understood. We hypothesize that a major fraction of positioned nucleosomes arises from sequence-specific targeting of chromatin remodelers to generate "founding" nucleosomes, providing reproducible, predictable, and condition-specific nucleation sites against which neighboring nucleosomes are packed into evenly spaced arrays.
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Affiliation(s)
- Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
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38
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González S, García A, Vázquez E, Serrano R, Sánchez M, Quintales L, Antequera F. Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome. Genome Res 2016; 26:1532-1543. [PMID: 27662899 PMCID: PMC5088595 DOI: 10.1101/gr.207241.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and nontranscribed regions, suggesting the existence of sequence elements that contribute to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and noncoding DNA molecules capable of directing their own nucleosomal organization.
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Affiliation(s)
- Sara González
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alicia García
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Enrique Vázquez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Rebeca Serrano
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Luis Quintales
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain.,Departamento de Informática y Automática, Universidad de Salamanca/Facultad de Ciencias, 37007 Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
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39
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Mazina MY, Vorobyeva NE. The role of ATP-dependent chromatin remodeling complexes in regulation of genetic processes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416050082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Nocetti N, Whitehouse I. Nucleosome repositioning underlies dynamic gene expression. Genes Dev 2016; 30:660-72. [PMID: 26966245 PMCID: PMC4803052 DOI: 10.1101/gad.274910.115] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/09/2016] [Indexed: 11/25/2022]
Abstract
Nocetti and Whitehouse report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. Nucleosome repositioning at gene promoters is a fundamental aspect of the regulation of gene expression. However, the extent to which nucleosome repositioning is used within eukaryotic genomes is poorly understood. Here we report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. We present evidence of extensive nucleosome repositioning at thousands of gene promoters as genes are activated and repressed. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. The extent of nucleosome shifting is closely related to the dynamic range of gene transcription and generally related to DNA sequence properties and use of the coactivators TFIID or SAGA. However, dynamic gene expression is not limited to SAGA-regulated promoters and is an inherent feature of most genes. While nucleosome repositioning occurs pervasively, we found that a class of genes required for growth experience acute nucleosome shifting as cells enter the cell cycle. Significantly, our data identify that the ATP-dependent chromatin-remodeling enzyme Snf2 plays a fundamental role in nucleosome repositioning and the expression of growth genes. We also reveal that nucleosome organization changes extensively in concert with phases of the cell cycle, with large, regularly spaced nucleosome arrays being established in mitosis. Collectively, our data and analysis provide a framework for understanding nucleosome dynamics in relation to fundamental DNA-dependent transactions.
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Affiliation(s)
- Nicolas Nocetti
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; BCMB Graduate Program, Weill Cornell Medical College, New York, New York 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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41
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Krasnov AN, Mazina MY, Nikolenko JV, Vorobyeva NE. On the way of revealing coactivator complexes cross-talk during transcriptional activation. Cell Biosci 2016; 6:15. [PMID: 26913181 PMCID: PMC4765067 DOI: 10.1186/s13578-016-0081-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/09/2016] [Indexed: 08/07/2023] Open
Abstract
Transcriptional activation is a complex, multistage process implemented by hundreds of proteins. Many transcriptional proteins are organized into coactivator complexes, which participate in transcription regulation at numerous genes and are a driver of this process. The molecular action mechanisms of coactivator complexes remain largely understudied. Relevant publications usually deal with the involvement of these complexes in the entire process of transcription, and only a few studies are aimed to elucidate their functions at its particular stages. This review summarizes available information on the participation of key coactivator complexes in transcriptional activation. The timing of coactivator complex binding/removal has been used for restructuring previously described information about the transcriptional process. Several major stages of transcriptional activation have been distinguished based on the presence of covalent histone modifications and general transcriptional factors, and the recruitment and/or removal phases have been determined for each coactivator included in analysis. Recruitment of Mediator, SWItch/Sucrose Non-Fermentable and NUcleosome Remodeling Factor complexes during transcription activation has been investigated thoroughly; CHD and INOsitol auxotrophy 80 families are less well studied. In most cases, the molecular mechanisms responsible for the removal of certain coactivator complexes after the termination of their functions at the promoters are still not understood. On the basis of the summarized information, we propose a scheme that illustrates the involvement of coactivator complexes in different stages of the transcription activation process. This scheme may help to gain a deeper insight into the molecular mechanism of functioning of coactivator complexes, find novel participants of the process, and reveal novel structural or functional connections between different coactivators.
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Affiliation(s)
- Aleksey N Krasnov
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Marina Yu Mazina
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Julia V Nikolenko
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Nadezhda E Vorobyeva
- Department of Transcription Regulation and Chromatin Dynamic, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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42
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Kharerin H, Bhat PJ, Marko JF, Padinhateeri R. Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression. Sci Rep 2016; 6:20319. [PMID: 26843321 PMCID: PMC4740855 DOI: 10.1038/srep20319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/30/2015] [Indexed: 12/11/2022] Open
Abstract
Studying nucleosome dynamics in promoter regions is crucial for understanding gene regulation. Nucleosomes regulate gene expression by sterically occluding transcription factors (TFs) and other non–histone proteins accessing genomic DNA. How the binding competition between nucleosomes and TFs leads to transcriptionally compatible promoter states is an open question. Here, we present a computational study of the nucleosome dynamics and organization in the promoter region of PHO5 gene in Saccharomyces cerevisiae. Introducing a model for nucleosome kinetics that takes into account ATP-dependent remodeling activity, DNA sequence effects, and kinetics of TFs (Pho4p), we compute the probability of obtaining different “promoter states” having different nucleosome configurations. Comparing our results with experimental data, we argue that the presence of local remodeling activity (LRA) as opposed to basal remodeling activity (BRA) is crucial in determining transcriptionally active promoter states. By modulating the LRA and Pho4p binding rate, we obtain different mRNA distributions—Poisson, bimodal, and long-tail. Through this work we explain many features of the PHO5 promoter such as sequence-dependent TF accessibility and the role of correlated dynamics between nucleosomes and TFs in opening/coverage of the TATA box. We also obtain possible ranges for TF binding rates and the magnitude of LRA.
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Affiliation(s)
- Hungyo Kharerin
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Paike J Bhat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - John F Marko
- Department of Physics, Department of Molecular Biosciences, Northwestern University, Evanston, IL
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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43
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Abstract
In eukaryotic cells, DNA associates with histones and exists in the form of a chromatin hierarchy. Thus, it is generally believed that many eukaryotic cellular DNA processing events such as replication, transcription, recombination and DNA repair are influenced by the packaging of DNA into chromatin. This mini-review covers the current knowledge of DNA damage and repair in chromatin based on in vitro studies. Specifically, nucleosome assembly affects DNA damage formation in both random sequences and sequences with strong nucleosome-positioning signals such as 5S rDNA. At least three systems have been used to analyze the effect of nucleosome folding on nucleotide excision repair (NER) in vitro: (a) human cell extracts that have to rely on labeling of repair synthesis to monitor DNA repair, due to very low repair efficacy; (b) Xenopus oocyte nuclear extracts, that have very robust DNA repair efficacy, have been utilized to follow direct removal of DNA damage; (c) six purified human DNA repair factors (RPA, XPA, XPC, TFIIH, XPG, and XPF-ERCC1) that have been used to reconstitute excision repair in vitro. In general, the results have shown that nucleosome folding inhibits NER and, therefore, its activity must be enhanced by chromatin remodeling factors like SWI/SNF. In addition, binding of transcription factors such as TFIIIA to the 5S rDNA promoter also modulates NER efficacy.
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Affiliation(s)
- Xiaoqi Liu
- Department of Biochemistry and Center for Cancer Research, Purdue University, 175 S. University Street, West Lafayette, IN 47907, United States.
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44
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Nucleosome avidities and transcriptional silencing in yeast. Curr Biol 2015; 25:1215-20. [PMID: 25891403 DOI: 10.1016/j.cub.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 02/02/2015] [Accepted: 03/05/2015] [Indexed: 11/22/2022]
Abstract
A classical example of "transcriptional silencing" is found in the yeast S. cerevisiae mating-type switch [1, 2]. The gene pairs a1/a2 and α1/α2, positioned at the loci HMR and HML, respectively, are silenced by Sir proteins recruited by proteins that bind sites flanking each locus. Transfer of either gene pair to the Sir-free MAT locus, or mutation of the Sirs, allows expression of those genes at levels sufficient to foster yeast mating. Here we confirm that, in the absence of Sirs, a1 and a2 at HMR are expressed at low levels [3]. This level is low because, we show, the relevant transcriptional activators, which work from regulatory sites located between the divergently transcribed genes, are weak. That property-weak activation-is a prerequisite for effective silencing upon recruitment of Sirs. We use our quantitative nucleosome occupancy assay to show that Sirs (which bind nucleosomes) increase the avidities with which those nucleosomes form at the promoters. That increase can account for at least part of the repressive effects of the Sirs and can explain why silencing is effective in countering weak activation only. We suggest that "silencing" in higher eukaryotes (e.g., by Polycomb or HP1) follows similar rules [4, 5] and note where such effects could be important.
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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Wang B, Kettenbach AN, Gerber SA, Loros JJ, Dunlap JC. Neurospora WC-1 recruits SWI/SNF to remodel frequency and initiate a circadian cycle. PLoS Genet 2014; 10:e1004599. [PMID: 25254987 PMCID: PMC4177678 DOI: 10.1371/journal.pgen.1004599] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 07/13/2014] [Indexed: 12/23/2022] Open
Abstract
In the negative feedback loop comprising the Neurospora circadian oscillator, the White Collar Complex (WCC) formed from White Collar-1 (WC-1) and White Collar-2 (WC-2) drives transcription of the circadian pacemaker gene frequency (frq). Although FRQ-dependent repression of WCC has been extensively studied, the mechanism by which the WCC initiates a circadian cycle remains elusive. Structure/function analysis of WC-1 eliminated domains previously thought to transactivate frq expression but instead identified amino acids 100–200 as essential for frq circadian expression. A proteomics-based search for coactivators with WCC uncovered the SWI/SNF (SWItch/Sucrose NonFermentable) complex: SWI/SNF interacts with WCC in vivo and in vitro, binds to the Clock box in the frq promoter, and is required both for circadian remodeling of nucleosomes at frq and for rhythmic frq expression; interestingly, SWI/SNF is not required for light-induced frq expression. These data suggest a model in which WC-1 recruits SWI/SNF to remodel and loop chromatin at frq, thereby activating frq expression to initiate the circadian cycle. Circadian clocks govern behavior in a wide variety of organisms. These clocks are assembled in such a way that proteins encoded by a few dedicated “clock genes” form a complex that acts to reduce their own expression. That is, the genes and proteins participate in a negative feedback loop, and so long as the feedback has delays built in, this system will oscillate. The feedback loops that underlie circadian rhythms in fungi and animals are quite similar in many ways, and while much is known about the proteins themselves, both those that activate the dedicated clock genes and the clock proteins that repress their own expression, relatively little is known about how the initial expression of the clock genes is activated. In Neurospora, a fungal model for these clocks, the proteins that activate expression of the clock gene “frequency” bind to DNA far away from where the coding part of the gene begins, and a mystery has been how this action-at-a-distance works. The answer revealed here is that the activating proteins recruit other proteins to unwrap the DNA and bring the distal site close to the place where the coding part of the gene begins.
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Affiliation(s)
- Bin Wang
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Arminja N. Kettenbach
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Scott A. Gerber
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biochemistry, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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Tartey S, Matsushita K, Vandenbon A, Ori D, Imamura T, Mino T, Standley DM, Hoffmann JA, Reichhart JM, Akira S, Takeuchi O. Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex. EMBO J 2014; 33:2332-48. [PMID: 25107474 DOI: 10.15252/embj.201488447] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcription of inflammatory genes in innate immune cells is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. However, it remains unclear how microbial sensing initiates chromatin remodeling. Here, we show that Akirin2, an evolutionarily conserved nuclear protein, bridges NF-κB and the chromatin remodeling SWI/SNF complex by interacting with BRG1-Associated Factor 60 (BAF60) proteins as well as IκB-ζ, which forms a complex with the NF-κB p50 subunit. These interactions are essential for Toll-like receptor-, RIG-I-, and Listeria-mediated expression of proinflammatory genes including Il6 and Il12b in macrophages. Consistently, effective clearance of Listeria infection required Akirin2. Furthermore, Akirin2 and IκB-ζ recruitment to the Il6 promoter depend upon the presence of IκB-ζ and Akirin2, respectively, for regulation of chromatin remodeling. BAF60 proteins were also essential for the induction of Il6 in response to LPS stimulation. Collectively, the IκB-ζ-Akirin2-BAF60 complex physically links the NF-κB and SWI/SNF complexes in innate immune cell activation. By recruiting SWI/SNF chromatin remodellers to IκB-ζ, transcriptional coactivator for NF-κB, the conserved nuclear protein Akirin2 stimulates pro-inflammatory gene promoters in mouse macrophages during innate immune responses to viral or bacterial infection.
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Affiliation(s)
- Sarang Tartey
- Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan Laboratory of Host Defense WPI Immunology Frontier Research Center (IFReC), Osaka University Suita, Osaka, Japan Research Institute for Microbial Diseases Osaka University, Suita Osaka, Japan
| | - Kazufumi Matsushita
- Laboratory of Allergic Diseases Institute for Advanced Medical Sciences Hyogo College of Medicine, Suita Osaka, Japan
| | - Alexis Vandenbon
- Laboratory of Systems Immunology WPI Immunology Frontier Research Center (IFReC), Nishinomiya Hyogo, Japan
| | - Daisuke Ori
- Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan
| | - Tomoko Imamura
- Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan
| | - Takashi Mino
- Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan
| | - Daron M Standley
- Laboratory of Systems Immunology WPI Immunology Frontier Research Center (IFReC), Nishinomiya Hyogo, Japan
| | | | | | - Shizuo Akira
- Laboratory of Host Defense WPI Immunology Frontier Research Center (IFReC), Osaka University Suita, Osaka, Japan Research Institute for Microbial Diseases Osaka University, Suita Osaka, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan Laboratory of Host Defense WPI Immunology Frontier Research Center (IFReC), Osaka University Suita, Osaka, Japan
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48
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Hepp MI, Alarcon V, Dutta A, Workman JL, Gutiérrez JL. Nucleosome remodeling by the SWI/SNF complex is enhanced by yeast high mobility group box (HMGB) proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:764-72. [PMID: 24972368 DOI: 10.1016/j.bbagrm.2014.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 12/01/2022]
Abstract
The regulation of gene expression at the level of transcription involves the concerted action of several proteins and protein complexes committed to dynamically alter the surrounding chromatin environment of a gene being activated or repressed. ATP-dependent chromatin remodeling complexes are key factors in chromatin remodeling, and the SWI/SNF complex is the founding member. While many studies have linked the action of these complexes to specific transcriptional regulation of a large number of genes and much is known about their catalytic activity, less is known about the nuclear elements that can enhance or modulate their activity. A number of studies have found that certain High Mobility Group (HMG) proteins are able to stimulate ATP-dependent chromatin remodeling activity, but their influence on the different biochemical outcomes of this activity is still unknown. In this work we studied the influence of the yeast Nhp6A, Nhp6B and Hmo1 proteins (HMGB family members) on different biochemical outcomes of yeast SWI/SNF remodeling activity. We found that all these HMG proteins stimulate the sliding activity of ySWI/SNF, while transient exposure of nucleosomal DNA and octamer transfer catalyzed by this complex are only stimulated by Hmo1. Consistently, only Hmo1 stimulates SWI/SNF binding to the nucleosome. Additionally, the sliding activity of another chromatin remodeling complex, ISW1a, is only stimulated by Hmo1. Further analyses show that these differential stimulatory effects of Hmo1 are dependent on the presence of its C-terminal tail, which contains a stretch of acidic and basic residues.
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Affiliation(s)
- Matias I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Valentina Alarcon
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile
| | - Arnob Dutta
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City 64110, MO, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City 64110, MO, USA
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción 4070043, Chile.
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49
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Two distinct domains of Flo8 activator mediates its role in transcriptional activation and the physical interaction with Mss11. Biochem Biophys Res Commun 2014; 449:202-7. [DOI: 10.1016/j.bbrc.2014.04.161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 04/30/2014] [Indexed: 11/23/2022]
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50
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Duan MR, Smerdon MJ. Histone H3 lysine 14 (H3K14) acetylation facilitates DNA repair in a positioned nucleosome by stabilizing the binding of the chromatin Remodeler RSC (Remodels Structure of Chromatin). J Biol Chem 2014; 289:8353-63. [PMID: 24515106 DOI: 10.1074/jbc.m113.540732] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Histone H3 acetylation is induced by UV damage in yeast and may play an important role in regulating the repair of UV photolesions in nucleosome-loaded genomic loci. However, it remains elusive how H3 acetylation facilitates repair. We generated a strongly positioned nucleosome containing homogeneously acetylated H3 at Lys-14 (H3K14ac) and investigated possible mechanisms by which H3K14 acetylation modulates repair. We show that H3K14ac does not alter nucleosome unfolding dynamics or enhance the repair of UV-induced cyclobutane pyrimidine dimers by UV photolyase. Importantly, however, nucleosomes with H3K14ac have a higher affinity for purified chromatin remodeling complex RSC (Remodels the Structure of Chromatin) and show greater cyclobutane pyrimidine dimer repair compared with unacetylated nucleosomes. Our study indicates that, by anchoring RSC, H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage.
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Affiliation(s)
- Ming-Rui Duan
- From Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520
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