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Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. J Biol Chem 2024:107604. [PMID: 39059488 DOI: 10.1016/j.jbc.2024.107604] [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: 06/21/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition.
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Affiliation(s)
- Austin Vogt
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, PA, 19104 USA
| | - Mary Szurgot
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, PA, 19104 USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, PA, 19104 USA
| | - Lauren Gardner
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, PA, 19104 USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, PA, 19104 USA.
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2
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Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [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: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
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Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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3
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Zhao Y, Liu W, Li Y, Ma J, Liu T, Cui H, Deng Y, Liao X, Wang Z. Human Bocavirus 1 NP1 acts as an ssDNA-binding protein to help AAV2 DNA replication and cooperates with RPA to regulate AAV2 capsid expression. J Virol 2024; 98:e0151523. [PMID: 38323812 PMCID: PMC10949510 DOI: 10.1128/jvi.01515-23] [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: 09/28/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Adeno-associated virus (AAV) requires co-infection with helper virus for efficient replication. We previously reported that Human Bocavirus 1 (HBoV1) genes, including NP1, NS2, and BocaSR, were critical for AAV2 replication. Here, we first demonstrate the essential roles of the NP1 protein in AAV2 DNA replication and protein expression. We show that NP1 binds to single-strand DNA (ssDNA) at least 30 nucleotides (nt) in length in a sequence-independent manner. Furthermore, NP1 colocalized with the BrdU-labeled AAV2 DNA replication center, and the loss of the ssDNA-binding ability of NP1 by site-directed mutation completely abolished AAV2 DNA replication. We used affinity-tagged NP1 protein to identify host cellular proteins associated with NP1 in cells cotransfected with the HBoV1 helper genes and AAV2 duplex genome. Of the identified proteins, we demonstrate that NP1 directly binds to the DBD-F domain of the RPA70 subunit with a high affinity through the residues 101-121. By reconstituting the heterotrimer protein RPA in vitro using gel filtration, we demonstrate that NP1 physically associates with RPA to form a heterologous complex characterized by typical fast-on/fast-off kinetics. Following a dominant-negative strategy, we found that NP1-RPA complex mainly plays a role in expressing AAV2 capsid protein by enhancing the transcriptional activity of the p40 promoter. Our study revealed a novel mechanism by which HBoV1 NP1 protein supports AAV2 DNA replication and capsid protein expression through its ssDNA-binding ability and direct interaction with RPA, respectively.IMPORTANCERecombinant adeno-associated virus (rAAV) vectors have been extensively used in clinical gene therapy strategies. However, a limitation of these gene therapy strategies is the efficient production of the required vectors, as AAV alone is replication-deficient in the host cells. HBoV1 provides the simplest AAV2 helper genes consisting of NP1, NS2, and BocaSR. An important question regarding the helper function of HBoV1 is whether it provides any direct function that supports AAV2 DNA replication and protein expression. Also of interest is how HBoV1 interplays with potential host factors to constitute a permissive environment for AAV2 replication. Our studies revealed that the multifunctional protein NP1 plays important roles in AAV2 DNA replication via its sequence-independent ssDNA-binding ability and in regulating AAV2 capsid protein expression by physically interacting with host protein RPA. Our findings present theoretical guidance for the future application of the HBoV1 helper genes in the rAAV vector production.
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Affiliation(s)
- Yanqun Zhao
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Wei Liu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Yanjie Li
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Jing Ma
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Ting Liu
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Huichan Cui
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Yongheng Deng
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Xiaochen Liao
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
| | - Zekun Wang
- Joint National Laboratory for Antibody Drug Engineering, The First Affiliated Hospital, Henan University, Kaifeng, Henan, China
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4
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Choi J, Kim T, Cho EJ. HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape. Exp Mol Med 2024; 56:251-263. [PMID: 38297159 PMCID: PMC10907377 DOI: 10.1038/s12276-023-01145-3] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 02/02/2024] Open
Abstract
H3.3, the most common replacement variant for histone H3, has emerged as an important player in chromatin dynamics for controlling gene expression and genome integrity. While replicative variants H3.1 and H3.2 are primarily incorporated into nucleosomes during DNA synthesis, H3.3 is under the control of H3.3-specific histone chaperones for spatiotemporal incorporation throughout the cell cycle. Over the years, there has been progress in understanding the mechanisms by which H3.3 affects domain structure and function. Furthermore, H3.3 distribution and relative abundance profoundly impact cellular identity and plasticity during normal development and pathogenesis. Recurrent mutations in H3.3 and its chaperones have been identified in neoplastic transformation and developmental disorders, providing new insights into chromatin biology and disease. Here, we review recent findings emphasizing how two distinct histone chaperones, HIRA and DAXX, take part in the spatial and temporal distribution of H3.3 in different chromatin domains and ultimately achieve dynamic control of chromatin organization and function. Elucidating the H3.3 deposition pathways from the available histone pool will open new avenues for understanding the mechanisms by which H3.3 epigenetically regulates gene expression and its impact on cellular integrity and pathogenesis.
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Affiliation(s)
- Jinmi Choi
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Taewan Kim
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Eun-Jung Cho
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea.
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5
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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Girasol MJ, Krasilnikova M, Marques CA, Damasceno JD, Lapsley C, Lemgruber L, Burchmore R, Beraldi D, Carruthers R, Briggs EM, McCulloch R. RAD51-mediated R-loop formation acts to repair transcription-associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proc Natl Acad Sci U S A 2023; 120:e2309306120. [PMID: 37988471 PMCID: PMC10691351 DOI: 10.1073/pnas.2309306120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 11/23/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of all genomes that intersect with many processes, including transcription, telomere homeostasis, and centromere function. Increasing evidence suggests that RNA-DNA hybrids can provide two conflicting roles in the maintenance and transmission of genomes: They can be the triggers of DNA damage, leading to genome change, or can aid the DNA repair processes needed to respond to DNA lesions. Evasion of host immunity by African trypanosomes, such as Trypanosoma brucei, relies on targeted recombination of silent Variant Surface Glycoprotein (VSG) genes into a specialized telomeric locus that directs transcription of just one VSG from thousands. How such VSG recombination is targeted and initiated is unclear. Here, we show that a key enzyme of T. brucei homologous recombination, RAD51, interacts with RNA-DNA hybrids. In addition, we show that RNA-DNA hybrids display a genome-wide colocalization with DNA breaks and that this relationship is impaired by mutation of RAD51. Finally, we show that RAD51 acts to repair highly abundant, localised DNA breaks at the single transcribed VSG and that mutation of RAD51 alters RNA-DNA hybrid abundance at 70 bp repeats both around the transcribed VSG and across the silent VSG archive. This work reveals a widespread, generalised role for RNA-DNA hybrids in directing RAD51 activity during recombination and uncovers a specialised application of this interplay during targeted DNA break repair needed for the critical T. brucei immune evasion reaction of antigenic variation.
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Affiliation(s)
- Mark John Girasol
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Faculty of the MD-PhD in Molecular Medicine Program, College of Medicine, University of the Philippines Manila, Manila1000, Philippines
| | - Marija Krasilnikova
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Catarina A. Marques
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Jeziel D. Damasceno
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Craig Lapsley
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Richard Burchmore
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Dario Beraldi
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Ross Carruthers
- College of Medical, Veterinary and Life Sciences, School of Cancer Sciences, University of Glasgow, GlasgowG12 0YN, United Kingdom
| | - Emma M. Briggs
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Richard McCulloch
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
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7
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Girasol MJ, Briggs EM, Marques CA, Batista JM, Beraldi D, Burchmore R, Lemgruber L, McCulloch R. Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Res 2023; 51:11123-11141. [PMID: 37843098 PMCID: PMC10639054 DOI: 10.1093/nar/gkad836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA-DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
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Affiliation(s)
- Mark J Girasol
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of the Philippines Manila, College of Medicine, Manila, Philippines
| | - Emma M Briggs
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
| | - Catarina A Marques
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - José M Batista
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Dario Beraldi
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard Burchmore
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Leandro Lemgruber
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard McCulloch
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
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8
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Jaiswal A, Roy R, Tamrakar A, Singh AK, Kar P, Kodgire P. Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells. Sci Rep 2023; 13:19615. [PMID: 37949972 PMCID: PMC10638239 DOI: 10.1038/s41598-023-46448-7] [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: 12/15/2022] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is the key mediator of antibody diversification in activated B-cells by the process of somatic hypermutation (SHM) and class switch recombination (CSR). Targeting AID to the Ig genes requires transcription (initiation and elongation), enhancers, and its interaction with numerous factors. Furthermore, the HIRA chaperon complex, a regulator of chromatin architecture, is indispensable for SHM. The HIRA chaperon complex consists of UBN1, ASF1a, HIRA, and CABIN1 that deposit H3.3 onto the DNA, the SHM hallmark. We explored whether UBN1 interacts with AID using computational and in-vitro experiments. Interestingly, our in-silico studies, such as molecular docking and molecular dynamics simulation results, predict that AID interacts with UBN1. Subsequently, co-immunoprecipitation and pull-down experiments established interactions between UBN1 and AID inside B-cells. Additionally, a double immunofluorescence assay confirmed that AID and UBN1 were co-localized in the human and chicken B-cell lines. Moreover, proximity ligation assay studies validated that AID interacts with UBN1. Ours is the first report on the interaction of genome mutator enzyme AID with UBN1. Nevertheless, the fate of interaction between UBN1 and AID is yet to be explored in the context of SHM or CSR.
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Affiliation(s)
- Ankit Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India
| | - Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India
| | - Anubhav Tamrakar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India
| | - Amit Kumar Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, Madhya Pradesh, 453 552, India.
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9
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Wu P, Lin SJ, Chen D, Jin C. Characterization of histone chaperone MCM2 as a key regulator in arsenic-induced depletion of H3.3 at genomic loci. Toxicol Appl Pharmacol 2023; 477:116697. [PMID: 37734572 PMCID: PMC10591817 DOI: 10.1016/j.taap.2023.116697] [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: 08/03/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Arsenic exposure is associated with an increased risk of many cancers, and epigenetic mechanisms play a crucial role in arsenic-mediated carcinogenesis. Our previous studies have shown that arsenic exposure induces polyadenylation of H3.1 mRNA and inhibits the deposition of H3.3 at critical gene regulatory elements. However, the precise underling mechanisms are not yet understood. To characterize the factors governing arsenic-induced inhibition of H3.3 assembly through H3.1 mRNA polyadenylation, we utilized mass spectrometry to identify the proteins, especially histone chaperones, with reduced binding affinity to H3.3 under conditions of arsenic exposure and polyadenylated H3.1 mRNA overexpression. Our findings reveal that the interaction between H3.3 and the histone chaperon protein MCM2 is diminished by both polyadenylated H3.1 mRNA overexpression and arsenic treatment in human lung epithelial BEAS-2B cells. The increased binding of MCM2 to H3.1, resulting from elevated H3.1 protein levels, appears to contribute to the reduced availability of MCM2 for H3.3. To further investigate the role of MCM2 in H3.3 deposition during arsenic exposure and H3.1 mRNA polyadenylation, we overexpressed MCM2 in BEAS-2B cells overexpressing polyadenylated H3.1 or exposed to arsenic. Our results demonstrate that MCM2 overexpression attenuates H3.3 depletion at several genomic loci, suggesting its involvement in the arsenic-induced displacement of H3.3 mediated by H3.1 mRNA polyadenylation. These findings suggest that changes in the association between histone chaperone MCM2 and H3.3 due to polyadenylation of H3.1 mRNA may play a pivotal role in arsenic-induced carcinogenesis.
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Affiliation(s)
- Peipei Wu
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Su-Jiun Lin
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Danqi Chen
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA
| | - Chunyuan Jin
- Department of Medicine, New York University Grossman School of Medicine, New York, NY 10010, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA.
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10
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Mizumoto A, Yokoyama Y, Miyoshi T, Takikawa M, Ishikawa F, Sadaie M. DHX36 maintains genomic integrity by unwinding G-quadruplexes. Genes Cells 2023; 28:694-708. [PMID: 37632696 DOI: 10.1111/gtc.13061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 08/28/2023]
Abstract
The guanine-rich stretch of single-stranded DNA (ssDNA) forms a G-quadruplex (G4) in a fraction of genic and intergenic chromosomal regions. The probability of G4 formation increases during events causing ssDNA generation, such as transcription and replication. In turn, G4 abrogates these events, leading to DNA damage. DHX36 unwinds G4-DNA in vitro and in human cells. However, its spatial correlation with G4-DNA in vivo and its role in genome maintenance remain unclear. Here, we demonstrate a connection between DHX36 and G4-DNA and its implications for genomic integrity. The nuclear localization of DHX36 overlapped with that of G4-DNA, RNA polymerase II, and a splicing-related factor. Depletion of DHX36 resulted in accumulated DNA damage, slower cell growth, and enhanced cell growth inhibition upon treatment with a G4-stabilizing compound; DHX36 expression reversed these defects. In contrast, the reversal upon expression of DHX36 mutants that could not bind G4 was imperfect. Thus, DHX36 may suppress DNA damage by promoting the clearance of G4-DNA for cell growth and survival. Our findings deepen the understanding of G4 resolution in the maintenance of genomic integrity.
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Affiliation(s)
- Ayaka Mizumoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuta Yokoyama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahiro Takikawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Mahito Sadaie
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
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11
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Wen Q, Zhou J, Tian C, Li X, Song G, Gao Y, Sun Y, Ma C, Yao S, Liang X, Kang X, Wang N, Yao Y, Wang H, Liang X, Tang J, Offer SM, Lei X, Yu C, Liu X, Liu Z, Wang Z, Gan H. Symmetric inheritance of parental histones contributes to safeguarding the fate of mouse embryonic stem cells during differentiation. Nat Genet 2023; 55:1555-1566. [PMID: 37666989 PMCID: PMC10777717 DOI: 10.1038/s41588-023-01477-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
Parental histones, the carriers of posttranslational modifications, are deposited evenly onto the replicating DNA of sister chromatids in a process dependent on the Mcm2 subunit of DNA helicase and the Pole3 subunit of leading-strand DNA polymerase. The biological significance of parental histone propagation remains unclear. Here we show that Mcm2-mutated or Pole3-deleted mouse embryonic stem cells (ESCs) display aberrant histone landscapes and impaired neural differentiation. Mutation of the Mcm2 histone-binding domain causes defects in pre-implantation development and embryonic lethality. ESCs with biased parental histone transfer exhibit increased epigenetic heterogeneity, showing altered histone variant H3.3 and H3K27me3 patterning at genomic sites regulating differentiation genes. Our results indicate that the lagging strand pattern of H3.3 leads to the redistribution of H3K27me3 in Mcm2-2A ESCs. We demonstrate that symmetric parental histone deposition to sister chromatids contributes to cellular differentiation and development.
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Affiliation(s)
- Qing Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Congcong Tian
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xinran Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guibing Song
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yaping Sun
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chiyuan Ma
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sitong Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoyan Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xing Kang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuan Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohuan Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jialin Tang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Xiaohua Lei
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Xiangyu Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Department of Hematology, The Second People's Hospital of Shenzhen, Shenzhen, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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12
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [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: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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13
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Karthik N, Lee JJH, Soon JLJ, Chiu HY, Loh AHP, Ong DST, Tam WL, Taneja R. Histone variant H3.3 promotes metastasis in alveolar rhabdomyosarcoma. J Pathol 2023; 259:342-356. [PMID: 36573560 DOI: 10.1002/path.6048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
The relatively quiet mutational landscape of rhabdomyosarcoma (RMS) suggests that epigenetic deregulation could be central to oncogenesis and tumour aggressiveness. Histone variants have long been recognised as important epigenetic regulators of gene expression. However, the role of histone variants in RMS has not been studied hitherto. In this study, we show that histone variant H3.3 is overexpressed in alveolar RMS (ARMS), an aggressive subtype of RMS. Functionally, knockdown of H3F3A, which encodes for H3.3, significantly impairs the ability of ARMS cells to undertake migration and invasion and reduces Rho activation. In addition, a striking reduction in metastatic tumour burden and improved survival is apparent in vivo. Using RNA-sequencing and ChIP-sequencing analyses, we identified melanoma cell adhesion molecule (MCAM/CD146) as a direct downstream target of H3.3. Loss of H3.3 resulted in a reduction in the presence of active marks and an increase in the occupancy of H1 at the MCAM promoter. Cell migration and invasion were rescued in H3F3A-depleted cells through MCAM overexpression. Moreover, we identified G9a, a lysine methyltransferase encoded by EHMT2, as an upstream regulator of H3F3A. Therefore, this study identifies a novel H3.3 dependent axis involved in ARMS metastasis. These findings establish the potential of MCAM as a therapeutic target for high-risk ARMS patients. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jane Jia Hui Lee
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Joshua Ling Jun Soon
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hsin Yao Chiu
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amos Hong Pheng Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, KK Women's and Children's Hospital, Singapore, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology and NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Healthy Longevity and NUS Cancer Centre for Cancer Research Translation Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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14
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Tafessu A, O’Hara R, Martire S, Dube AL, Saha P, Gant VU, Banaszynski LA. H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells. Genome Biol 2023; 24:25. [PMID: 36782260 PMCID: PMC9926682 DOI: 10.1186/s13059-023-02867-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND The histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are highly accessible, creating an environment that is permissive to transcription factor binding and the recruitment of transcriptional coactivators that establish a unique chromatin post-translational landscape. How H3.3 contributes to the establishment and function of chromatin states at these regions is poorly understood. RESULTS We perform genomic analyses of features associated with active promoter chromatin in mouse embryonic stem cells (ESCs) and find evidence of subtle yet widespread promoter dysregulation in the absence of H3.3. Loss of H3.3 results in reduced chromatin accessibility and transcription factor (TF) binding at promoters of expressed genes in ESCs. Likewise, enrichment of the transcriptional coactivator p300 and downstream histone H3 acetylation at lysine 27 (H3K27ac) is reduced at promoters in the absence of H3.3, along with reduced enrichment of the acetyl lysine reader BRD4. Despite the observed chromatin dysregulation, H3.3 KO ESCs maintain transcription from ESC-specific genes. However, upon undirected differentiation, H3.3 KO cells retain footprinting of ESC-specific TF motifs and fail to generate footprints of lineage-specific TF motifs, in line with their diminished capacity to differentiate. CONCLUSIONS H3.3 facilitates DNA accessibility, transcription factor binding, and histone post-translational modification at active promoters. While H3.3 is not required for maintaining transcription in ESCs, it does promote de novo transcription factor binding which may contribute to the dysregulation of cellular differentiation in the absence of H3.3.
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Affiliation(s)
- Amanuel Tafessu
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Ryan O’Hara
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Sara Martire
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Altair L. Dube
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Purbita Saha
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Vincent U. Gant
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
| | - Laura A. Banaszynski
- grid.267313.20000 0000 9482 7121Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children’s Medical Center Research Institute, Harold C. Simmons Comprehensive Cancer Center, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390 USA
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15
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Murat P, Perez C, Crisp A, van Eijk P, Reed SH, Guilbaud G, Sale JE. DNA replication initiation shapes the mutational landscape and expression of the human genome. SCIENCE ADVANCES 2022; 8:eadd3686. [PMID: 36351018 PMCID: PMC9645720 DOI: 10.1126/sciadv.add3686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation-dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins' genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome.
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Affiliation(s)
- Pierre Murat
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Consuelo Perez
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alastair Crisp
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patrick van Eijk
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Simon H. Reed
- Broken String Biosciences Ltd., BioData Innovation Centre, Unit AB3-03, Level 3, Wellcome Genome Campus, Hinxton, Cambridge CB10 1DR, UK
- Division of Cancer & Genetics School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Guillaume Guilbaud
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E. Sale
- Division of Protein & Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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16
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Reske JJ, Wilson MR, Armistead B, Harkins S, Perez C, Hrit J, Adams M, Rothbart SB, Missmer SA, Fazleabas AT, Chandler RL. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers. BMC Biol 2022; 20:209. [PMID: 36153585 PMCID: PMC9509632 DOI: 10.1186/s12915-022-01407-y] [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: 04/25/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium. RESULTS Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 toward genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas. CONCLUSIONS These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers.
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Affiliation(s)
- Jake J. Reske
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Mike R. Wilson
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Brooke Armistead
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Shannon Harkins
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Cristina Perez
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA
| | - Joel Hrit
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Marie Adams
- grid.251017.00000 0004 0406 2057Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Scott B. Rothbart
- grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Stacey A. Missmer
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Asgerally T. Fazleabas
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
| | - Ronald L. Chandler
- grid.17088.360000 0001 2150 1785Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503 USA ,grid.251017.00000 0004 0406 2057Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503 USA ,grid.416230.20000 0004 0406 3236Department of Women’s Health, Spectrum Health System, Grand Rapids, MI 49341 USA
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17
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Thakar T, Dhoonmoon A, Straka J, Schleicher EM, Nicolae CM, Moldovan GL. Lagging strand gap suppression connects BRCA-mediated fork protection to nucleosome assembly through PCNA-dependent CAF-1 recycling. Nat Commun 2022; 13:5323. [PMID: 36085347 PMCID: PMC9463168 DOI: 10.1038/s41467-022-33028-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The inability to protect stalled replication forks from nucleolytic degradation drives genome instability and underlies chemosensitivity in BRCA-deficient tumors. An emerging hallmark of BRCA-deficiency is the inability to suppress replication-associated single-stranded DNA (ssDNA) gaps. Here, we report that lagging strand ssDNA gaps interfere with the ASF1-CAF-1 nucleosome assembly pathway, and drive fork degradation in BRCA-deficient cells. We show that CAF-1 function at replication forks is lost in BRCA-deficient cells, due to defects in its recycling during replication stress. This CAF-1 recycling defect is caused by lagging strand gaps which preclude PCNA unloading, causing sequestration of PCNA-CAF-1 complexes on chromatin. Importantly, correcting PCNA unloading defects in BRCA-deficient cells restores CAF-1-dependent fork stability. We further show that the activation of a HIRA-dependent compensatory histone deposition pathway restores fork stability to BRCA-deficient cells. We thus define lagging strand gap suppression and nucleosome assembly as critical enablers of BRCA-mediated fork stability. Efficient DNA replication is crucial for genome stability. Here, Thakar et al. report that accumulation of lagging strand ssDNA gaps during replication interferes with nucleosome assembly and drives replication fork degradation in BRCA-deficient cells.
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Affiliation(s)
- Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Joshua Straka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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18
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Huang YC, Yuan W, Jacob Y. The Role of the TSK/TONSL-H3.1 Pathway in Maintaining Genome Stability in Multicellular Eukaryotes. Int J Mol Sci 2022; 23:9029. [PMID: 36012288 PMCID: PMC9409234 DOI: 10.3390/ijms23169029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with H3.3, the H3.1 variant has been hypothesized to play unique roles in cells, as it is specifically expressed and inserted into chromatin during DNA replication. However, identifying a function that is unique to H3.1 during replication has remained elusive. In this review, we discuss recent findings regarding the involvement of the H3.1 variant in regulating the TSK/TONSL-mediated resolution of stalled or broken replication forks. Uncovering this new function for the H3.1 variant has been made possible by the identification of the first proteins containing domains that can selectively bind or modify the H3.1 variant. The functional characterization of H3-variant-specific readers and writers reveals another layer of chromatin-based information regulating transcription, DNA replication, and DNA repair.
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Affiliation(s)
| | | | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
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19
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Xu X, Duan S, Hua X, Li Z, He R, Zhaang Z. Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. Nat Commun 2022; 13:2514. [PMID: 35523900 PMCID: PMC9076889 DOI: 10.1038/s41467-022-30298-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
Newly synthesized H3.1 and H3.3 histones are assembled into nucleosomes by different histone chaperones in replication-coupled and replication-independent pathways, respectively. However, it is not clear how parental H3.3 molecules are transferred following DNA replication, especially when compared to H3.1. Here, by monitoring parental H3.1- and H3.3-SNAP signals, we show that parental H3.3, like H3.1, are stably transferred into daughter cells. Moreover, Mcm2-Pola1 and Pole3-Pole4, two pathways involved in parental histone transfer based upon the analysis of modifications on parental histones, participate in the transfer of both H3.1 and H3.3 following DNA replication. Lastly, we found that Mcm2, Pole3 and Pole4 mutants defective in parental histone transfer show defects in chromosome segregation. These results indicate that in contrast to deposition of newly synthesized H3.1 and H3.3, transfer of parental H3.1 and H3.3 is mediated by these shared mechanisms, which contributes to epigenetic memory of gene expression and maintenance of genome stability. How nucleosome assembly of parental histones is regulated following DNA replication is still an open question. Here the authors show that unlike deposition of new histones H3.1 and H3.3 that utilizes different histone chaperones, parental H3.1 and H3.3 are both stably inherited during mitotic cell division in mouse embryonic stem cells, and this involves histone chaperones Mcm2, Pole3 and Pole4.
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Affiliation(s)
- Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard He
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiguo Zhaang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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20
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Zhang M, Zhao X, Feng X, Hu X, Zhao X, Lu W, Lu X. Histone chaperone HIRA complex regulates retrotransposons in embryonic stem cells. Stem Cell Res Ther 2022; 13:137. [PMID: 35365225 PMCID: PMC8973876 DOI: 10.1186/s13287-022-02814-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone cell cycle regulator (HIRA) complex is an important histone chaperone that mediates the deposition of the H3.3 histone variant onto chromatin independently from DNA synthesis. However, it is still unknown whether it participates in the expression control of retrotransposons and cell fate determination. METHODS We screened the role of HIRA complex members in repressing the expression of retrotransposons by shRNA depletion in embryonic stem cells (ESCs) followed by RT-qPCR. RNA-seq was used to study the expression profiles after depletion of individual HIRA member. RT-qPCR and western blot were used to determine overexpression of HIRA complex members. Chromatin immunoprecipitation (ChIP)-qPCR was used to find the binding of H3.3, HIRA members to chromatin. Co-immunoprecipitation was used to identify the interaction between Hira mutant and Ubn2. ChIP-qPCR was used to identify H3.3 deposition change and western blot of chromatin extract was used to validate the epigenetic change. Bioinformatics analysis was applied for the analysis of available ChIP-seq data. RESULTS We revealed that Hira, Ubn2, and Ubn1 were the main repressors of 2-cell marker retrotransposon MERVL among HIRA complex members. Surprisingly, Ubn2 and Hira targeted different groups of retrotransposons and retrotransposon-derived long noncoding RNAs (lncRNAs), despite that they partially shared target genes. Furthermore, Ubn2 prevented ESCs to gain a 2-cell like state or activate trophectodermal genes upon differentiation. Mechanistically, Ubn2 and Hira suppressed retrotransposons by regulating the deposition of histone H3.3. Decreased H3.3 deposition, that was associated with the loss of Ubn2 or Hira, caused the reduction of H3K9me2 and H3K9me3, which are known repressive marks of retrotransposons. CONCLUSIONS Overall, our findings shed light on the distinct roles of HIRA complex members in controlling retrotransposons and cell fate conversion in ESCs.
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Affiliation(s)
- Miao Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xiao Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | | | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China.
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21
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Wen T, Chen QY. Dynamic Activity of Histone H3-Specific Chaperone Complexes in Oncogenesis. Front Oncol 2022; 11:806974. [PMID: 35087762 PMCID: PMC8786718 DOI: 10.3389/fonc.2021.806974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Canonical histone H3.1 and variant H3.3 deposit at different sites of the chromatin via distinct histone chaperones. Histone H3.1 relies on chaperone CAF-1 to mediate replication-dependent nucleosome assembly during S-phase, while H3.3 variant is regulated and incorporated into the chromatin in a replication-independent manner through HIRA and DAXX/ATRX. Current literature suggests that dysregulated expression of histone chaperones may be implicated in tumor progression. Notably, ectopic expression of CAF-1 can promote a switch between canonical H3.1 and H3 variants in the chromatin, impair the chromatic state, lead to chromosome instability, and impact gene transcription, potentially contributing to carcinogenesis. This review focuses on the chaperone proteins of H3.1 and H3.3, including structure, regulation, as well as their oncogenic and tumor suppressive functions in tumorigenesis.
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Affiliation(s)
- Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
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22
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The role of HIRA-dependent H3.3 deposition and its modifications in the somatic hypermutation of immunoglobulin variable regions. Proc Natl Acad Sci U S A 2021; 118:2114743118. [PMID: 34873043 DOI: 10.1073/pnas.2114743118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
The H3.3 histone variant and its chaperone HIRA are involved in active transcription, but their detailed roles in regulating somatic hypermutation (SHM) of immunoglobulin variable regions in human B cells are not yet fully understood. In this study, we show that the knockout (KO) of HIRA significantly decreased SHM and changed the mutation pattern of the variable region of the immunoglobulin heavy chain (IgH) in the human Ramos B cell line without changing the levels of activation-induced deaminase and other major proteins known to be involved in SHM. Except for H3K79me2/3 and Spt5, many factors related to active transcription, including H3.3, were substantively decreased in HIRA KO cells, and this was accompanied by decreased nascent transcription in the IgH locus. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the IgH locus was also reduced in the HIRA KO. Somewhat surprisingly, HIRA loss increased the chromatin accessibility of the IgH V region locus. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit both the trimethylation of H3.3K36 and the recruitment of ZMYND11 significantly reduced SHM in Ramos cells, while the H3.3K79M did not. Consistent with the HIRA KO, the H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on the IgH variable and downstream switching regions. Our results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and extend our knowledge of how transcription-associated chromatin structure and accessibility contribute to SHM in human B cells.
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23
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Lin R, Zhong X, Zhou Y, Geng H, Hu Q, Huang Z, Hu J, Fu XD, Chen L, Chen JY. R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. Nucleic Acids Res 2021; 50:D303-D315. [PMID: 34792163 PMCID: PMC8728142 DOI: 10.1093/nar/gkab1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/28/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
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Affiliation(s)
- Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Yongli Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huichao Geng
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhihao Huang
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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24
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Schoberleitner I, Bauer I, Huang A, Andreyeva EN, Sebald J, Pascher K, Rieder D, Brunner M, Podhraski V, Oemer G, Cázarez-García D, Rieder L, Keller MA, Winkler R, Fyodorov DV, Lusser A. CHD1 controls H3.3 incorporation in adult brain chromatin to maintain metabolic homeostasis and normal lifespan. Cell Rep 2021; 37:109769. [PMID: 34610319 PMCID: PMC8607513 DOI: 10.1016/j.celrep.2021.109769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/26/2021] [Accepted: 09/08/2021] [Indexed: 01/31/2023] Open
Abstract
The ATP-dependent chromatin remodeling factor CHD1 is essential for the assembly of variant histone H3.3 into paternal chromatin during sperm chromatin remodeling in fertilized eggs. It remains unclear, however, if CHD1 has a similar role in normal diploid cells. Using a specifically tailored quantitative mass spectrometry approach, we show that Chd1 disruption results in reduced H3.3 levels in heads of Chd1 mutant flies. Chd1 deletion perturbs brain chromatin structure in a similar way as H3.3 deletion and leads to global de-repression of transcription. The physiological consequences are reduced food intake, metabolic alterations, and shortened lifespan. Notably, brain-specific CHD1 expression rescues these phenotypes. We further demonstrate a strong genetic interaction between Chd1 and H3.3 chaperone Hira. Thus, our findings establish CHD1 as a factor required for the assembly of H3.3-containing chromatin in adult cells and suggest a crucial role for CHD1 in the brain as a regulator of organismal health and longevity.
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Affiliation(s)
- Ines Schoberleitner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Anming Huang
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Evgeniya N Andreyeva
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Sebald
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Katharina Pascher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Valerie Podhraski
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Gregor Oemer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Daniel Cázarez-García
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Leila Rieder
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
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25
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Jia A, Xu L, Wang Y. Venn diagrams in bioinformatics. Brief Bioinform 2021; 22:6220174. [PMID: 33839742 DOI: 10.1093/bib/bbab108] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/04/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Venn diagrams are widely used tools for graphical depiction of the unions, intersections and distinctions among multiple datasets, and a large number of programs have been developed to generate Venn diagrams for applications in various research areas. However, a comprehensive review comparing these tools has not been previously performed. In this review, we collect Venn diagram generators (i.e. tools for visualizing the relationships of input lists within a Venn diagram) and Venn diagram application tools (i.e. tools for analyzing the relationships between biological data and visualizing them in a Venn diagram) to compare their functional capacity as follows: ability to generate high-quality diagrams; maximum datasets handled by each program; input data formats; output diagram styles and image output formats. We also evaluate the picture beautification parameters of the Venn diagram generators in terms of the graphical layout and briefly describe the functional characteristics of the most popular Venn diagram application tools. Finally, we discuss the challenges in improving Venn diagram application tools and provide a perspective on Venn diagram applications in bioinformatics. Our aim is to assist users in selecting suitable tools for analyzing and visualizing user-defined datasets.
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Affiliation(s)
- Anqiang Jia
- Biological Science Research Center at Southwest University, Chongqing 400715, China
| | - Ling Xu
- University of California, Berkeley 400715, China
| | - Yi Wang
- Biological Science Research Center at Southwest University, Chongqing 400715, China
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26
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Abstract
Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
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Affiliation(s)
| | - Dan Filipescu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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27
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Wang Z, Wu R, Nie Q, Bouchonville KJ, Diasio RB, Offer SM. Chromatin assembly factor 1 suppresses epigenetic reprogramming toward adaptive drug resistance. JOURNAL OF THE NATIONAL CANCER CENTER 2021; 1:15-22. [PMID: 39036786 PMCID: PMC11256593 DOI: 10.1016/j.jncc.2020.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
The long-term effectiveness of targeted cancer therapies is limited by the development of resistance. Although epigenetic reprogramming has been implicated in resistance, the mechanisms remain elusive. Herein, we demonstrate that increased chromatin accessibility is involved in adaptive BRAF inhibitor (BRAFi)-resistance in melanoma cells. We observed loss of chromatin assembly factor 1 (CAF-1) and its related histone H3 lysine 9 trimethylation (H3K9me3) with adaptive BRAFi resistance. We further showed that depletion of CAF-1 provides chromatin plasticity for effective reprogramming by AP1 components to promote BRAFi resistance. Our data suggest that therapeutic approaches to restore H3K9me3 levels may compensate for the loss of CAF-1 and, in turn, suppress resistance to BRAF inhibitors.
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Affiliation(s)
- Zhiquan Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Rentian Wu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Nie
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kelly J. Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert B. Diasio
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Rochester, MN 55905, USA
| | - Steven M. Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Rochester, MN 55905, USA
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28
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Misova I, Pitelova A, Budis J, Gazdarica J, Sedlackova T, Jordakova A, Benko Z, Smondrkova M, Mayerova N, Pichlerova K, Strieskova L, Prevorovsky M, Gregan J, Cipak L, Szemes T, Polakova SB. Repression of a large number of genes requires interplay between homologous recombination and HIRA. Nucleic Acids Res 2021; 49:1914-1934. [PMID: 33511417 PMCID: PMC7913671 DOI: 10.1093/nar/gkab027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
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Affiliation(s)
- Ivana Misova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Anna Jordakova
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Zsigmond Benko
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, H-4010 Debrecen, Hungary
| | - Maria Smondrkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Karoline Pichlerova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Lucia Strieskova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Martin Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
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29
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Wang J, Rojas P, Mao J, Mustè Sadurnì M, Garnier O, Xiao S, Higgs MR, Garcia P, Saponaro M. Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M. Cell Rep 2021; 34:108759. [PMID: 33596418 PMCID: PMC7900609 DOI: 10.1016/j.celrep.2021.108759] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 11/09/2020] [Accepted: 01/26/2021] [Indexed: 12/22/2022] Open
Abstract
As transcription and replication use DNA as substrate, conflicts between transcription and replication can occur, leading to genome instability with direct consequences for human health. To determine how the two processes are coordinated throughout S phase, we characterize both processes together at high resolution. We find that transcription occurs during DNA replication, with transcription start sites (TSSs) not fully replicated along with surrounding regions and remaining under-replicated until late in the cell cycle. TSSs undergo completion of DNA replication specifically when cells enter mitosis, when RNA polymerase II is removed. Intriguingly, G2/M DNA synthesis occurs at high frequency in unperturbed cell culture, but it is not associated with increased DNA damage and is fundamentally separated from mitotic DNA synthesis. TSSs duplicated in G2/M are characterized by a series of specific features, including high levels of antisense transcription, making them difficult to duplicate during S phase.
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Affiliation(s)
- Jianming Wang
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Patricia Rojas
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jingwen Mao
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Martina Mustè Sadurnì
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Olivia Garnier
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Songshu Xiao
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Martin R Higgs
- Lysine Methylation and DNA Damage Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Paloma Garcia
- Stem Cells and Genome Stability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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30
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Ray-Gallet D, Almouzni G. The Histone H3 Family and Its Deposition Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:17-42. [PMID: 33155135 DOI: 10.1007/978-981-15-8104-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.
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Affiliation(s)
- Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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31
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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32
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Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol 2020; 27:1152-1164. [PMID: 33046907 PMCID: PMC7809635 DOI: 10.1038/s41594-020-0512-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
The synthesis of poly(ADP-ribose) (PAR) reconfigures the local chromatin environment and recruits DNA-repair complexes to damaged chromatin. PAR degradation by poly(ADP-ribose) glycohydrolase (PARG) is essential for progression and completion of DNA repair. Here, we show that inhibition of PARG disrupts homology-directed repair (HDR) mechanisms that underpin alternative lengthening of telomeres (ALT). Proteomic analyses uncover a new role for poly(ADP-ribosyl)ation (PARylation) in regulating the chromatin-assembly factor HIRA in ALT cancer cells. We show that HIRA is enriched at telomeres during the G2 phase and is required for histone H3.3 deposition and telomere DNA synthesis. Depletion of HIRA elicits systemic death of ALT cancer cells that is mitigated by re-expression of ATRX, a protein that is frequently inactivated in ALT tumors. We propose that PARylation enables HIRA to fulfill its essential role in the adaptive response to ATRX deficiency that pervades ALT cancers.
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Affiliation(s)
- Song My Hoang
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelle L Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin L Roncaioli
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Callen T Wallace
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominic I James
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Ian D Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Donald Ogilvie
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | - Kate M Smith
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, Macclesfield, UK
| | | | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jianfeng Li
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Robert W Sobol
- Department of Pharmacology and the Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Genevieve Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée, Ligue contre le Cancer, Paris, France
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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33
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Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
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Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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34
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Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
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Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
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35
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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36
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Torné J, Ray-Gallet D, Boyarchuk E, Garnier M, Le Baccon P, Coulon A, Orsi GA, Almouzni G. Two HIRA-dependent pathways mediate H3.3 de novo deposition and recycling during transcription. Nat Struct Mol Biol 2020; 27:1057-1068. [PMID: 32895554 DOI: 10.1038/s41594-020-0492-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
Nucleosomes represent a challenge in regard to transcription. Histone eviction enables RNA polymerase II (RNAPII) progression through DNA, but compromises chromatin integrity. Here, we used the SNAP-tag system to distinguish new and old histones and monitor chromatin reassembly coupled to transcription in human cells. We uncovered a transcription-dependent loss of old histone variants H3.1 and H3.3. At transcriptionally active domains, H3.3 enrichment reflected both old H3.3 retention and new deposition. Mechanistically, we found that the histone regulator A (HIRA) chaperone is critical to processing both new and old H3.3 via different pathways. De novo H3.3 deposition is totally dependent on HIRA trimerization as well as on its partner ubinuclein 1 (UBN1), while antisilencing function 1 (ASF1) interaction with HIRA can be bypassed. By contrast, recycling of H3.3 requires HIRA but proceeds independently of UBN1 or HIRA trimerization and shows absolute dependency on ASF1-HIRA interaction. We propose a model whereby HIRA coordinates these distinct pathways during transcription to fine-tune chromatin states.
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Affiliation(s)
- Júlia Torné
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Ekaterina Boyarchuk
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Mickaël Garnier
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris, France
| | - Patricia Le Baccon
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Guillermo A Orsi
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France. .,LBMC, Université de Lyon, ENS de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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37
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Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
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Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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38
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Abstract
Histone variants regulate chromatin accessibility and gene transcription. Given their distinct properties and functions, histone varint substitutions allow for profound alteration of nucleosomal architecture and local chromatin landscape. Skeletal myogenesis driven by the key transcription factor MyoD is characterized by precise temporal regulation of myogenic genes. Timed substitution of variants within the nucleosomes provides a powerful means to ensure sequential expression of myogenic genes. Indeed, growing evidence has shown H3.3, H2A.Z, macroH2A, and H1b to be critical for skeletal myogenesis. However, the relative importance of various histone variants and their associated chaperones in myogenesis is not fully appreciated. In this review, we summarize the role that histone variants play in altering chromatin landscape to ensure proper muscle differentiation. The temporal regulation and cross talk between histones variants and their chaperones in conjunction with other forms of epigenetic regulation could be critical to understanding myogenesis and their involvement in myopathies.
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Affiliation(s)
- Nandini Karthik
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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39
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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40
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Wooten M, Ranjan R, Chen X. Asymmetric Histone Inheritance in Asymmetrically Dividing Stem Cells. Trends Genet 2020; 36:30-43. [PMID: 31753528 PMCID: PMC6925335 DOI: 10.1016/j.tig.2019.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
Epigenetic mechanisms play essential roles in determining distinct cell fates during the development of multicellular organisms. Histone proteins represent crucial epigenetic components that help specify cell identities. Previous work has demonstrated that during the asymmetric cell division of Drosophila male germline stem cells (GSCs), histones H3 and H4 are asymmetrically inherited, such that pre-existing (old) histones are segregated towards the self-renewing GSC whereas newly synthesized (new) histones are enriched towards the differentiating daughter cell. In order to further understand the molecular mechanisms underlying this striking phenomenon, two key questions must be answered: when and how old and new histones are differentially incorporated by sister chromatids, and how epigenetically distinct sister chromatids are specifically recognized and segregated. Here, we discuss recent advances in our understanding of the molecular mechanisms and cellular bases underlying these fundamental and important biological processes responsible for generating two distinct cells through one cell division.
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Affiliation(s)
- Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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Morrow BE, McDonald-McGinn DM, Emanuel BS, Vermeesch JR, Scambler PJ. Molecular genetics of 22q11.2 deletion syndrome. Am J Med Genet A 2019; 176:2070-2081. [PMID: 30380194 DOI: 10.1002/ajmg.a.40504] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/11/2018] [Accepted: 07/17/2018] [Indexed: 02/02/2023]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is a congenital malformation and neuropsychiatric disorder caused by meiotic chromosome rearrangements. One of the goals of this review is to summarize the current state of basic research studies of 22q11.2DS. It highlights efforts to understand the mechanisms responsible for the 22q11.2 deletion that occurs in meiosis. This mechanism involves the four sets of low copy repeats (LCR22) that are dispersed in the 22q11.2 region and the deletion is mediated by nonallelic homologous recombination events. This review also highlights selected genes mapping to the 22q11.2 region that may contribute to the typical clinical findings associated with the disorder and explain that mutations in genes on the remaining allele can uncover rare recessive conditions. Another important aspect of 22q11.2DS is the existence of phenotypic heterogeneity. While some patients are mildly affected, others have severe medical, cognitive, and/or psychiatric challenges. Variability may be due in part to the presence of genetic modifiers. This review discusses current genome-wide efforts to identify such modifiers that could shed light on molecular pathways required for normal human development, cognition or behavior.
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Affiliation(s)
- Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Joris R Vermeesch
- Center for Human Genetics, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Peter J Scambler
- Institute of Child Health, University College London, London, UK
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Gomes AP, Ilter D, Low V, Rosenzweig A, Shen ZJ, Schild T, Rivas MA, Er EE, McNally DR, Mutvei AP, Han J, Ou YH, Cavaliere P, Mullarky E, Nagiec M, Shin S, Yoon SO, Dephoure N, Massagué J, Melnick AM, Cantley LC, Tyler JK, Blenis J. Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization. Cancer Cell 2019; 36:402-417.e13. [PMID: 31564638 PMCID: PMC6801101 DOI: 10.1016/j.ccell.2019.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/07/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022]
Abstract
Metastasis is the leading cause of cancer mortality. Chromatin remodeling provides the foundation for the cellular reprogramming necessary to drive metastasis. However, little is known about the nature of this remodeling and its regulation. Here, we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin, triggering deposition of H3.3 variant at the promoters of poor-prognosis genes and metastasis-inducing transcription factors. This specific incorporation of H3.3 into chromatin is both necessary and sufficient for the induction of aggressive traits that allow for metastasis formation. Together, our data clearly show incorporation of histone variant H3.3 into chromatin as a major regulator of cell fate during tumorigenesis, and histone chaperones as valuable therapeutic targets for invasive carcinomas.
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Affiliation(s)
- Ana P Gomes
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Didem Ilter
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam Rosenzweig
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zih-Jie Shen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Martin A Rivas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ekrem E Er
- Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Dylan R McNally
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anders P Mutvei
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julie Han
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yi-Hung Ou
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Paola Cavaliere
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Edouard Mullarky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michal Nagiec
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sejeong Shin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sang-Oh Yoon
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joan Massagué
- Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Ari M Melnick
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
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Michelena J, Gatti M, Teloni F, Imhof R, Altmeyer M. Basal CHK1 activity safeguards its stability to maintain intrinsic S-phase checkpoint functions. J Cell Biol 2019; 218:2865-2875. [PMID: 31366665 PMCID: PMC6719454 DOI: 10.1083/jcb.201902085] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/12/2019] [Accepted: 07/08/2019] [Indexed: 12/11/2022] Open
Abstract
The essential kinase CHK1 controls cell cycle checkpoint signaling and S-phase progression. Michelena et al. reveal that steady-state activity of CHK1 is required to sustain its own stability and that failure to do so results in CHK1 degradation and sensitizes cells to replication stress. The DNA replication machinery frequently encounters impediments that slow replication fork progression and threaten timely and error-free replication. The CHK1 protein kinase is essential to deal with replication stress (RS) and ensure genome integrity and cell survival, yet how basal levels and activity of CHK1 are maintained under physiological, unstressed conditions is not well understood. Here, we reveal that CHK1 stability is controlled by its steady-state activity during unchallenged cell proliferation. This autoactivatory mechanism, which depends on ATR and its coactivator ETAA1 and is tightly associated with CHK1 autophosphorylation at S296, counters CHK1 ubiquitylation and proteasomal degradation, thereby preventing attenuation of S-phase checkpoint functions and a compromised capacity to respond to RS. Based on these findings, we propose that steady-state CHK1 activity safeguards its stability to maintain intrinsic checkpoint functions and ensure genome integrity and cell survival.
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Affiliation(s)
- Jone Michelena
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Federico Teloni
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Ralph Imhof
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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Abstract
Cellular senescence defines an irreversible cell growth arrest state linked to loss of tissue function and aging in mammals. This transition from proliferation to senescence is typically characterized by increased expression of the cell-cycle inhibitor p16INK4a and formation of senescence-associated heterochromatin foci (SAHF). SAHF formation depends on HIRA-mediated nucleosome assembly of histone H3.3, which is regulated by the serine/threonine protein kinase Pak2. However, it is unknown if Pak2 contributes to cellular senescence. Here, we show that depletion of Pak2 delayed oncogene-induced senescence in IMR90 human fibroblasts and oxidative stress-induced senescence of mouse embryonic fibroblasts (MEFs), whereas overexpression of Pak2 accelerated senescence of IMR90 cells. Importantly, depletion of Pak2 in BubR1 progeroid mice attenuated the onset of aging-associated phenotypes and extended life span. Pak2 is required for expression of genes involved in cellular senescence and regulated the deposition of newly synthesized H3.3 onto chromatin in senescent cells. Together, our results demonstrate that Pak2 is an important regulator of cellular senescence and organismal aging, in part through the regulation of gene expression and H3.3 nucleosome assembly.
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Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation. Nat Genet 2019; 51:941-946. [PMID: 31152160 PMCID: PMC6598431 DOI: 10.1038/s41588-019-0428-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/25/2019] [Indexed: 02/07/2023]
Abstract
The histone variant H3.3 is enriched at enhancers and active genes, as well as repeat regions such as telomeres and retroelements, in mouse embryonic stem cells (mESCs)1–3. While recent studies demonstrate a role for H3.3 and its chaperones in establishing heterochromatin at repeat regions4–8, the function of H3.3 in transcription regulation has been less clear9–16. Here, we find that H3.3-specific phosphorylation17–19 stimulates activity of the acetyltransferase p300 in trans, suggesting that H3.3 acts as a nucleosomal cofactor for p300. Depletion of H3.3 from mESCs reduces acetylation on histone H3 at lysine 27 (H3K27ac) at enhancers. Cells lacking H3.3 demonstrate reduced capacity to acetylate enhancers that are activated upon differentiation, along with reduced ability to reprogram cell fate. Our study demonstrates that a single amino acid in a histone variant can integrate signaling information and globally impact genome regulation, which may help better understand how mutations in these proteins contribute to human cancers20,21.
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The histone chaperoning pathway: from ribosome to nucleosome. Essays Biochem 2019; 63:29-43. [PMID: 31015382 PMCID: PMC6484783 DOI: 10.1042/ebc20180055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022]
Abstract
Nucleosomes represent the fundamental repeating unit of eukaryotic DNA, and comprise eight core histones around which DNA is wrapped in nearly two superhelical turns. Histones do not have the intrinsic ability to form nucleosomes; rather, they require an extensive repertoire of interacting proteins collectively known as ‘histone chaperones’. At a fundamental level, it is believed that histone chaperones guide the assembly of nucleosomes through preventing non-productive charge-based aggregates between the basic histones and acidic cellular components. At a broader level, histone chaperones influence almost all aspects of chromatin biology, regulating histone supply and demand, governing histone variant deposition, maintaining functional chromatin domains and being co-factors for histone post-translational modifications, to name a few. In this essay we review recent structural insights into histone-chaperone interactions, explore evidence for the existence of a histone chaperoning ‘pathway’ and reconcile how such histone-chaperone interactions may function thermodynamically to assemble nucleosomes and maintain chromatin homeostasis.
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Synergy of Hir1, Ssn6, and Snf2 global regulators is the functional determinant of a Mac1 transcriptional switch in S. cerevisiae copper homeostasis. Curr Genet 2019; 65:799-816. [DOI: 10.1007/s00294-019-00935-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/21/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022]
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Briggs E, Hamilton G, Crouch K, Lapsley C, McCulloch R. Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome. Nucleic Acids Res 2018; 46:11789-11805. [PMID: 30304482 PMCID: PMC6294496 DOI: 10.1093/nar/gky928] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 01/09/2023] Open
Abstract
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, UK
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK
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Briggs E, Crouch K, Lemgruber L, Lapsley C, McCulloch R. Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. PLoS Genet 2018; 14:e1007729. [PMID: 30543624 PMCID: PMC6292569 DOI: 10.1371/journal.pgen.1007729] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022] Open
Abstract
Switching of the Variant Surface Glycoprotein (VSG) in Trypanosoma brucei provides a crucial host immune evasion strategy that is catalysed both by transcription and recombination reactions, each operating within specialised telomeric VSG expression sites (ES). VSG switching is likely triggered by events focused on the single actively transcribed ES, from a repertoire of around 15, but the nature of such events is unclear. Here we show that RNA-DNA hybrids, called R-loops, form preferentially within sequences termed the 70 bp repeats in the actively transcribed ES, but spread throughout the active and inactive ES, in the absence of RNase H1, which degrades R-loops. Loss of RNase H1 also leads to increased levels of VSG coat switching and replication-associated genome damage, some of which accumulates within the active ES. This work indicates VSG ES architecture elicits R-loop formation, and that these RNA-DNA hybrids connect T. brucei immune evasion by transcription and recombination.
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Affiliation(s)
- Emma Briggs
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Leandro Lemgruber
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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Nye J, Sturgill D, Athwal R, Dalal Y. HJURP antagonizes CENP-A mislocalization driven by the H3.3 chaperones HIRA and DAXX. PLoS One 2018; 13:e0205948. [PMID: 30365520 PMCID: PMC6203356 DOI: 10.1371/journal.pone.0205948] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/03/2018] [Indexed: 02/07/2023] Open
Abstract
The centromere specific histone H3 variant CENP-A/CENH3 specifies where the kinetochore is formed in most eukaryotes. Despite tight regulation of CENP-A levels in normal cells, overexpression of CENP-A is a feature shared by various types of solid tumors and results in its mislocalization to non-centromeric DNA. How CENP-A is assembled ectopically and the consequences of this mislocalization remain topics of high interest. Here, we report that in human colon cancer cells, the H3.3 chaperones HIRA and DAXX promote ectopic CENP-A deposition. Moreover, the correct balance between levels of the centromeric chaperone HJURP and CENP-A is essential to preclude ectopic assembly by H3.3 chaperones. In addition, we find that ectopic localization can recruit kinetochore components, and correlates with mitotic defects and DNA damage in G1 phase. Finally, CENP-A occupancy at the 8q24 locus is also correlated with amplification and overexpression of the MYC gene within that locus. Overall, these data provide insights into the causes and consequences of histone variant mislocalization in human cancer cells.
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Affiliation(s)
- Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, United States of America
| | - David Sturgill
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, United States of America
| | - Rajbir Athwal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, United States of America
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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