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Krajewski WA. Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes. Front Genet 2022; 13:873398. [PMID: 35571051 PMCID: PMC9096104 DOI: 10.3389/fgene.2022.873398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022] Open
Abstract
Tight packaging of DNA in chromatin severely constrains DNA accessibility and dynamics. In contrast, nucleosomes in active chromatin state are highly flexible, can exchange their histones, and are virtually “transparent” to RNA polymerases, which transcribe through gene bodies at rates comparable to that of naked DNA. Defining mechanisms that revert nucleosome repression, in addition to their value for basic science, is of key importance for the diagnosis and treatment of genetic diseases. Chromatin activity is largely regulated by histone posttranslational modifications, ranging from small chemical groups up to the yet understudied “bulky” ubiquitylation and sumoylation. However, it is to be revealed how histone marks are “translated” to permissive or repressive changes in nucleosomes: it is a general opinion that histone modifications act primarily as “signals” for recruiting the regulatory proteins or as a “neutralizer” of electrostatic shielding of histone tails. Here, we would like to discuss recent evidence suggesting that histone ubiquitylation, in a DNA stress–dependent manner, can directly regulate the dynamics of the nucleosome and their primary structure and can promote nucleosome decomposition to hexasome particles or additionally stabilize nucleosomes against unwrapping. In addition, nucleosome repression/ derepression studies are usually performed with single mononucleosomes as a model. We would like to review and discuss recent findings showing that internucleosomal interactions could strongly modulate the dynamics and rearrangements of nucleosomes. Our hypothesis is that bulky histone modifications, nucleosome inherent dynamics, internucleosome interactions, and DNA torsions could act in cooperation to orchestrate the formation of different dynamic states of arrayed nucleosomes and thus promote chromatin functionality and diversify epigenetic programming methods.
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2
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Hsieh FK, Ji F, Damle M, Sadreyev RI, Kingston RE. HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7. Life Sci Alliance 2021; 5:5/1/e202101127. [PMID: 34663690 PMCID: PMC8548210 DOI: 10.26508/lsa.202101127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in CHD7 are diagnostic for human CHARGE syndrome. RNAs expressed from the HERVH repeats modulate CHD7 function providing one mechanism for regulation of differentiation of pluripotent cells. Chd7 encodes an ATP-dependent chromatin remodeler which has been shown to target specific genomic loci and alter local transcription potentially by remodeling chromatin structure. De novo mutations in CHD7 are the major cause of CHARGE syndrome which features multiple developmental defects. We examined whether nuclear RNAs might contribute to its targeting and function and identified a preferential interaction between CHD7 and lncRNAs derived from HERVH loci in pluripotent stem cells. Knockdown of HERVH family lncRNAs using LNAs or knockout of an individual copy of HERVH by CRISPR-Cas9 both resulted in increased binding of CHD7 and increased levels of H3K27ac at a subset of enhancers. Depletion of HERVH family RNAs led to the activation of multiple genes. CHD7 bound HERVH RNA with high affinity but low specificity and this interaction decreased the ability of CHD7 to bind and remodel nucleosomes. We present a model in which HERVH lncRNAs act as a decoy to modulate the dynamics of CHD7 binding to enhancers in pluripotent cells and the activation of numerous genes that might impact the differentiation process.
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Affiliation(s)
- Fu-Kai Hsieh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA .,Department of Genetics, Harvard Medical School, Boston, MA, USA
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Krajewski WA, Li J, Dou Y. Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics. Nucleic Acids Res 2019; 46:7631-7642. [PMID: 29931239 PMCID: PMC6125632 DOI: 10.1093/nar/gky526] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/25/2018] [Indexed: 01/01/2023] Open
Abstract
DNA in nucleosomes has restricted nucleosome dynamics and is refractory to DNA-templated processes. Histone post-translational modifications play important roles in regulating DNA accessibility in nucleosomes. Whereas most histone modifications function either by mitigating the electrostatic shielding of histone tails or by recruiting 'reader' proteins, we show that ubiquitylation of H2B K34, which is located in a tight space protected by two coils of DNA superhelix, is able to directly influence the canonical nucleosome conformation via steric hindrances by ubiquitin groups. H2B K34 ubiquitylation significantly enhances nucleosome dynamics and promotes generation of hexasomes both with symmetrically or asymmetrically modified nucleosomes. Our results indicate a direct mechanism by which a histone modification regulates the chromatin structural states.
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Affiliation(s)
- Wladyslaw A Krajewski
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow, 119334, Russia.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiabin Li
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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Chang HW, Hsieh FK, Patel SS, Studitsky VM. Time-resolved analysis of transcription through chromatin. Methods 2019; 159-160:90-95. [PMID: 30707952 DOI: 10.1016/j.ymeth.2019.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 01/03/2023] Open
Abstract
During transcription along nucleosomal DNA, RNA polymerase II (Pol II) pauses at multiple positions and induces formation of multiple intermediates that aid in maintaining proper chromatin structure. To describe the kinetics of this multiple-step reaction, we utilized a computational model-based approach and KinTek Explorer software to analyze the time courses. Here we describe the stepwise protocol for analysis of the kinetics of transcription through a nucleosome that provides the rate constants for each step of this complex process. We also present an example where this time-resolved approach was applied to study the mechanism of histone chaperone FACT action during Pol II transcription through a single nucleosome by comparing the rate constants derived in the presence or in the absence of FACT.
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Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Fu-Kai Hsieh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Smita S Patel
- Department of Biochemistry & Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Biology Faculty, Lomonosov Moscow State University, Moscow 119992, Russia.
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Kozlova AL, Valieva ME, Maluchenko NV, Studitsky VM. HMGB Proteins as DNA Chaperones That Modulate Chromatin Activity. Mol Biol 2018. [DOI: 10.1134/s0026893318050096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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6
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Safina A, Cheney P, Pal M, Brodsky L, Ivanov A, Kirsanov K, Lesovaya E, Naberezhnov D, Nesher E, Koman I, Wang D, Wang J, Yakubovskaya M, Winkler D, Gurova K. FACT is a sensor of DNA torsional stress in eukaryotic cells. Nucleic Acids Res 2017; 45:1925-1945. [PMID: 28082391 PMCID: PMC5389579 DOI: 10.1093/nar/gkw1366] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/29/2016] [Indexed: 02/01/2023] Open
Abstract
Transitions of B-DNA to alternative DNA structures (ADS) can be triggered by negative torsional strain, which occurs during replication and transcription, and may lead to genomic instability. However, how ADS are recognized in cells is unclear. We found that the binding of candidate anticancer drug, curaxin, to cellular DNA results in uncoiling of nucleosomal DNA, accumulation of negative supercoiling and conversion of multiple regions of genomic DNA into left-handed Z-form. Histone chaperone FACT binds rapidly to the same regions via the SSRP1 subunit in curaxin-treated cells. In vitro binding of purified SSRP1 or its isolated CID domain to a methylated DNA fragment containing alternating purine/pyrimidines, which is prone to Z-DNA transition, is much stronger than to other types of DNA. We propose that FACT can recognize and bind Z-DNA or DNA in transition from a B to Z form. Binding of FACT to these genomic regions triggers a p53 response. Furthermore, FACT has been shown to bind to other types of ADS through a different structural domain, which also leads to p53 activation. Thus, we propose that FACT acts as a sensor of ADS formation in cells. Recognition of ADS by FACT followed by a p53 response may explain the role of FACT in DNA damage prevention.
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Affiliation(s)
- Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Peter Cheney
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Mahadeb Pal
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Leonid Brodsky
- Department of Evolutionary & Environmental Biology, Tauber Bioinformatics Research Center, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Alexander Ivanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Kirill Kirsanov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Ekaterina Lesovaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia.,I.P. Pavlov Ryazan State Medical University, Ryazan, Russia
| | - Denis Naberezhnov
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Elimelech Nesher
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA.,Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Igor Koman
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Dan Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Jianming Wang
- Department of Bioinformatics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
| | - Marianna Yakubovskaya
- Department of Chemical Carcinogenesis, Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Moscow 115478, Russia
| | - Duane Winkler
- Department of Molecular and Cell Biology, University of Texas at Dallas, 800 W. Campbell Rd., Richardson, TX 75080, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14127, USA
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Fleyshman D, Prendergast L, Safina A, Paszkiewicz G, Commane M, Morgan K, Attwood K, Gurova K. Level of FACT defines the transcriptional landscape and aggressive phenotype of breast cancer cells. Oncotarget 2017; 8:20525-20542. [PMID: 28423528 PMCID: PMC5400524 DOI: 10.18632/oncotarget.15656] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 01/11/2017] [Indexed: 02/07/2023] Open
Abstract
Although breast cancer (BrCa) may be detected at an early stage, there is a shortage of markers that predict tumor aggressiveness and a lack of targeted therapies. Histone chaperone FACT, expressed in a limited number of normal cells, is overexpressed in different types of cancer, including BrCa. Recently, we found that FACT expression in BrCa correlates with markers of aggressive BrCa, which prompted us to explore the consequences of FACT inhibition in BrCa cells with varying levels of FACT. FACT inhibition using a small molecule or shRNA caused reduced growth and viability of all BrCa cells tested. Phenotypic changes were more severe in high- FACT cells (death or growth arrest) than in low-FACT cells (decreased proliferation). Though inhibition had no effect on the rate of general transcription, expression of individual genes was changed in a cell-specific manner. Initially distinct transcriptional profiles of BrCa cells became similar upon equalizing FACT expression. In high-FACT cells, FACT supports expression of genes involved in the regulation of cell cycle, DNA replication, maintenance of an undifferentiated cell state and regulated by the activity of several proto-oncogenes. In low-FACT cells, the presence of FACT reduces expression of genes encoding enzymes of steroid metabolism that are characteristic of differentiated mammary epithelia. Thus, we propose that FACT is both a marker and a target of aggressive BrCa cells, whose inhibition results in the death of BrCa or convertion of them to a less aggressive subtype.
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Affiliation(s)
- Daria Fleyshman
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Laura Prendergast
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Alfiya Safina
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Mairead Commane
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kelsey Morgan
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kristopher Attwood
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Biostatistics, University of Buffalo, SUNY, Buffalo, NY, USA
| | - Katerina Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
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