1
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Gao J, Qin Y, Schimenti JC. Gene regulation during meiosis. Trends Genet 2024; 40:326-336. [PMID: 38177041 PMCID: PMC11003842 DOI: 10.1016/j.tig.2023.12.006] [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: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Meiosis is essential for gamete production in all sexually reproducing organisms. It entails two successive cell divisions without DNA replication, producing haploid cells from diploid ones. This process involves complex morphological and molecular differentiation that varies across species and between sexes. Specialized genomic events like meiotic recombination and chromosome segregation are tightly regulated, including preparation for post-meiotic development. Research in model organisms, notably yeast, has shed light on the genetic and molecular aspects of meiosis and its regulation. Although mammalian meiosis research faces challenges, particularly in replicating gametogenesis in vitro, advances in genetic and genomic technologies are providing mechanistic insights. Here we review the genetics and molecular biology of meiotic gene expression control, focusing on mammals.
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Affiliation(s)
- Jingyi Gao
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Yiwen Qin
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - John C Schimenti
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA.
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2
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Halblander FN, Meng FW, Murphy PJ. Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation. Dev Biol 2024; 507:34-43. [PMID: 38159623 PMCID: PMC10922954 DOI: 10.1016/j.ydbio.2023.12.010] [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: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Epigenetic regulation of chromatin states is crucial for proper gene expression programs and progression during development, but precise mechanisms by which epigenetic factors influence differentiation remain poorly understood. Here we find that the histone variant H2A.Z accumulates at Sox motif-containing promoters during zebrafish gastrulation while neighboring genes become transcriptionally active. These changes coincide with reduced expression of anp32e, the H2A.Z histone removal chaperone, suggesting that loss of Anp32e may lead to increases in H2A.Z binding during differentiation. Remarkably, genetic removal of Anp32e in embryos leads to H2A.Z accumulation prior to gastrulation and developmental genes become precociously active. Accordingly, H2A.Z accumulation occurs most extensively at Sox motif-associated genes, including many which are normally activated following gastrulation. Altogether, our results provide compelling evidence for a mechanism in which Anp32e preferentially restricts H2A.Z accumulation at Sox motifs to regulate the initial phases of developmental differentiation in zebrafish.
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Affiliation(s)
- Fabian N Halblander
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Fanju W Meng
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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3
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Leszczynska KB, Freitas-Huhtamäki A, Jayaprakash C, Dzwigonska M, Vitorino FNL, Horth C, Wojnicki K, Gielniewski B, Szadkowska P, Kaza B, Nazarian J, Ciolkowski MK, Trubicka J, Grajkowska W, Garcia BA, Majewski J, Kaminska B, Mieczkowski J. H2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in pediatric high-grade glioma cells. Cell Rep 2024; 43:113707. [PMID: 38306270 PMCID: PMC11026119 DOI: 10.1016/j.celrep.2024.113707] [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: 05/29/2023] [Revised: 10/22/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024] Open
Abstract
Diffuse intrinsic pontine gliomas (DIPGs) are deadly pediatric brain tumors, non-resectable due to brainstem localization and diffusive growth. Over 80% of DIPGs harbor a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine-to-methionine substitution (H3K27M). Patients with DIPG have a dismal prognosis with no effective therapy. We show that histone deacetylase (HDAC) inhibitors lead to a significant reduction in the H3.3K27M protein (up to 80%) in multiple glioma cell lines. We discover that the SB939-mediated H3.3K27M loss is partially blocked by a lysosomal inhibitor, chloroquine. The H3.3K27M loss is facilitated by co-occurrence of H2A.Z, as evidenced by the knockdown of H2A.Z isoforms. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis confirms the occupancy of H3.3K27M and H2A.Z at the same SB939-inducible genes. We discover a mechanism showing that HDAC inhibition in DIPG leads to pharmacological modulation of the oncogenic H3.3K27M protein levels. These findings show the possibility of directly targeting the H3.3K27M oncohistone.
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Affiliation(s)
- Katarzyna B Leszczynska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
| | | | - Chinchu Jayaprakash
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Monika Dzwigonska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Francisca N L Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kamil Wojnicki
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Paulina Szadkowska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA; Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland
| | | | | | | | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.
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4
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Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development 2023; 150:dev202338. [PMID: 37938830 PMCID: PMC10651094 DOI: 10.1242/dev.202338] [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: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, long interspersed nuclear elements and long terminal repeats, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the levels of the repressive histone modification H3K9me3 and a moderate increase in chromatin accessibility. Notably, however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein via transgenic overexpression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes.
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Affiliation(s)
- Fanju W. Meng
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | - Benjamin Delatte
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA 92008, USA
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5
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Zhao H, Shao X, Guo M, Xing Y, Wang J, Luo L, Cai L. Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro. Int J Mol Sci 2023; 24:15846. [PMID: 37958827 PMCID: PMC10647764 DOI: 10.3390/ijms242115846] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles.
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Affiliation(s)
- Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Xueqin Shao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
| | - Mingxin Guo
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
| | - Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Jingyan Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Liaofu Luo
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China; (H.Z.); (X.S.); (M.G.); (Y.X.); (J.W.); (L.L.)
- Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, Inner Mongolia University of Science and Technology, Baotou 014010, China
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6
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Jamge B, Lorković ZJ, Axelsson E, Osakabe A, Shukla V, Yelagandula R, Akimcheva S, Kuehn AL, Berger F. Histone variants shape chromatin states in Arabidopsis. eLife 2023; 12:RP87714. [PMID: 37467143 PMCID: PMC10393023 DOI: 10.7554/elife.87714] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Akihisa Osakabe
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-kuTokyoJapan
- PRESTO, Japan Science and Technology Agency, HonchoKawaguchiJapan
| | - Vikas Shukla
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Vienna BioCenterViennaAustria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
- Institute of Molecular Biotechnology, IMBA, Dr. Bohr-Gasse 3ViennaAustria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Annika Luisa Kuehn
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenterViennaAustria
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7
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Ji X, Liu W, Zhang F, Su Y, Ding Y, Li H. H3K36me3 and H2A.Z coordinately modulate flowering time in Arabidopsis. J Genet Genomics 2023:S1673-8527(23)00122-4. [PMID: 37302474 DOI: 10.1016/j.jgg.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Affiliation(s)
- Xiaoru Ji
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenqian Liu
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fei Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yanhua Su
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yong Ding
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei, Anhui 230027, China; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Hefei, Anhui 230027, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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8
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Li X, Mei Q, Yu Q, Wang M, He F, Xiao D, Liu H, Ge F, Yu X, Li S. The TORC1 activates Rpd3L complex to deacetylate Ino80 and H2A.Z and repress autophagy. SCIENCE ADVANCES 2023; 9:eade8312. [PMID: 36888706 PMCID: PMC9995077 DOI: 10.1126/sciadv.ade8312] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Autophagy is a critical process to maintain homeostasis, differentiation, and development. How autophagy is tightly regulated by nutritional changes is poorly understood. Here, we identify chromatin remodeling protein Ino80 and histone variant H2A.Z as the deacetylation targets for histone deacetylase Rpd3L complex and uncover how they regulate autophagy in response to nutrient availability. Mechanistically, Rpd3L deacetylates Ino80 K929, which protects Ino80 from being degraded by autophagy. The stabilized Ino80 promotes H2A.Z eviction from autophagy-related genes, leading to their transcriptional repression. Meanwhile, Rpd3L deacetylates H2A.Z, which further blocks its deposition into chromatin to repress the transcription of autophagy-related genes. Rpd3-mediated deacetylation of Ino80 K929 and H2A.Z is enhanced by the target of rapamycin complex 1 (TORC1). Inactivation of TORC1 by nitrogen starvation or rapamycin inhibits Rpd3L, leading to induction of autophagy. Our work provides a mechanism for chromatin remodelers and histone variants in modulating autophagy in response to nutrient availability.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Min Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Fei He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Duncheng Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Huan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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9
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Morioka S, Sato S, Horikoshi N, Kujirai T, Tomita T, Baba Y, Kakuta T, Ogoshi T, Puppulin L, Sumino A, Umeda K, Kodera N, Kurumizaka H, Shibata M. High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale. NANO LETTERS 2023; 23:1696-1704. [PMID: 36779562 DOI: 10.1021/acs.nanolett.2c04346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nucleosome dynamics, such as nucleosome sliding and DNA unwrapping, are important for gene regulation in eukaryotic chromatin. H2A.Z, a variant of histone H2A that is highly evolutionarily conserved, participates in gene regulation by forming unstable multipositioned nucleosomes in vivo and in vitro. However, the subsecond dynamics of this unstable nucleosome have not been directly visualized under physiological conditions. Here, we used high-speed atomic force microscopy (HS-AFM) to directly visualize the subsecond dynamics of human H2A.Z.1-nucleosomes. HS-AFM videos show nucleosome sliding along 4 nm of DNA within 0.3 s in any direction. This sliding was also visualized in an H2A.Z.1 mutant, in which the C-terminal half was replaced by the corresponding canonical H2A amino acids, indicating that the interaction between the N-terminal region of H2A.Z.1 and the DNA is responsible for nucleosome sliding. These results may reveal the relationship between nucleosome dynamics and gene regulation by histone H2A.Z.
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Affiliation(s)
- Shin Morioka
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Naoki Horikoshi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takuya Tomita
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yudai Baba
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takahiro Kakuta
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Tomoki Ogoshi
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Leonardo Puppulin
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Ayumi Sumino
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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10
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Long J, Carter B, Johnson ET, Ogas J. Contribution of the histone variant H2A.Z to expression of responsive genes in plants. Semin Cell Dev Biol 2023; 135:85-92. [PMID: 35474148 PMCID: PMC9588091 DOI: 10.1016/j.semcdb.2022.04.006] [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: 01/10/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/19/2022]
Abstract
The histone variant H2A.Z plays a critical role in chromatin-based processes such as transcription, replication, and repair in eukaryotes. Although many H2A.Z-associated processes and features are conserved in plants and animals, a distinguishing feature of plant chromatin is the enrichment of H2A.Z in the bodies of genes that exhibit dynamic expression, particularly in response to differentiation and the environment. Recent work sheds new light on the plant machinery that enables dynamic changes in H2A.Z enrichment and identifies additional chromatin-based pathways that contribute to transcriptional properties of H2A.Z-enriched chromatin. In particular, analysis of a variety of responsive loci reveals a repressive role for H2A.Z in expression of responsive genes and identifies roles for SWR1 and INO80 chromatin remodelers in enabling dynamic regulation of H2A.Z levels and transcription. These studies lay the groundwork for understanding how this ancient histone variant is harnessed by plants to enable responsive and dynamic gene expression (Graphical Abstract).
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Affiliation(s)
- Jiaxin Long
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Benjamin Carter
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Emily T Johnson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA.
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Interplay Between the Histone Variant H2A.Z and the Epigenome in Pancreatic Cancer. Arch Med Res 2022; 53:840-858. [PMID: 36470770 DOI: 10.1016/j.arcmed.2022.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND The oncogenic process is orchestrated by a complex network of chromatin remodeling elements that shape the cancer epigenome. Histone variant H2A.Z regulates DNA control elements such as promoters and enhancers in different types of cancer; however, the interplay between H2A.Z and the pancreatic cancer epigenome is unknown. OBJECTIVE This study analyzed the role of H2A.Z in different DNA regulatory elements. METHODS We performed Chromatin Immunoprecipitation Sequencing assays (ChiP-seq) with total H2A.Z and acetylated H2A.Z (acH2A.Z) antibodies and analyzed published data from ChIP-seq, RNA-seq, bromouridine labeling-UV and sequencing (BruUV-seq), Hi-C and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) in the pancreatic cancer cell line PANC-1. RESULTS The results indicate that total H2A.Z facilitates the recruitment of RNA polymerase II and transcription factors at promoters and enhancers allowing the expression of pro-oncogenic genes. Interestingly, we demonstrated that H2A.Z is enriched in super-enhancers (SEs) contributing to the transcriptional activation of key genes implicated in tumor development. Importantly, we established that H2A.Z contributes to the three-dimensional (3D) genome organization of pancreatic cancer and that it is a component of the Topological Associated Domains (TADs) boundaries in PANC-1 and that total H2A.Z and acH2A.Z are associated with A and B compartments, respectively. CONCLUSIONS H2A.Z participates in the biology and development of pancreatic cancer by generating a pro-oncogenic transcriptome through its posttranslational modifications, interactions with different partners, and regulatory elements, contributing to the oncogenic 3D genome organization. These data allow us to understand the molecular mechanisms that promote an oncogenic transcriptome in pancreatic cancer mediated by H2A.Z.
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12
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Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun 2022; 13:7052. [PMID: 36396651 PMCID: PMC9672302 DOI: 10.1038/s41467-022-34861-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.
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Affiliation(s)
- Jiayi Fan
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Interdisciplinary Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Andrew T. Moreno
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Alexander S. Baier
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Joseph J. Loparo
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Craig L. Peterson
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
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13
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Fuglerud BM, Drissler S, Lotto J, Stephan TL, Thakur A, Cullum R, Hoodless PA. SOX9 reprograms endothelial cells by altering the chromatin landscape. Nucleic Acids Res 2022; 50:8547-8565. [PMID: 35904801 PMCID: PMC9410909 DOI: 10.1093/nar/gkac652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/08/2023] Open
Abstract
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 displays features of a pioneer transcription factor, such as opening of chromatin and leading to deposition of active histone modifications at silent chromatin regions, guided by SOX dimer motifs and H2A.Z enrichment. We further observe highly transient and dynamic SOX9 binding, possibly promoted through its eviction by histone phosphorylation. However, while SOX9 binding is dynamic, changes in the chromatin landscape and cell fate induced by SOX9 are persistent. Finally, our analysis of single-cell chromatin accessibility indicates that SOX9 opens chromatin to drive EndMT in atherosclerotic lesions in vivo. This study provides new insight into key molecular functions of SOX9 and mechanisms of EndMT and highlights the crucial developmental role of SOX9 and relevance to human disease.
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Affiliation(s)
- Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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14
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Zhao Q, Dai B, Wu H, Zhu W, Chen J. Ino80 is required for H2A.Z eviction from hypha-specific promoters and hyphal development of Candida albicans. Mol Microbiol 2022; 118:92-104. [PMID: 35713098 PMCID: PMC9543228 DOI: 10.1111/mmi.14954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
ATP‐dependent chromatin remodeling complexes play important roles in many essential cellular processes, including transcription regulation, DNA replication, and repair. Evicting H2A.Z, a variant of histone H2A, from the promoter of hypha‐specific genes is required for hyphal formation in Candida albicans. However, the mechanism that regulates H2A.Z removal during hyphal formation remains unknown. In this study, we demonstrated that Ino80, the core catalytic subunit of the INO80 complex, was recruited to hypha‐specific promoters during hyphal induction in Arp8 dependent manner and facilitated the removal of H2A.Z. Deleting INO80 or mutating the ATPase site of Ino80 impairs the expression of hypha‐specific genes (HSGs) and hyphal development. In addition, we showed that Ino80 was essential for the virulence of C. albicans during systemic infections in mice. Interestingly, Arp5, an INO80 complex‐specific component, acts in concert with Ino80 during DNA damage responses but is dispensable for hyphal induction. Our findings clarified that Ino80 was critical for hyphal development, DNA damage response, and pathogenesis in C. albicans.
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Affiliation(s)
- Qun Zhao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Baodi Dai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongyu Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wencheng Zhu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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15
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Mammalian PERIOD2 regulates H2A.Z incorporation in chromatin to orchestrate circadian negative feedback. Nat Struct Mol Biol 2022; 29:549-562. [PMID: 35606517 DOI: 10.1038/s41594-022-00777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
Mammalian circadian oscillators are built on a feedback loop in which the activity of the transcription factor CLOCK-BMAL1 is repressed by the PER-CRY complex. Here, we show that murine Per-/- fibroblasts display aberrant nucleosome occupancy around transcription start sites (TSSs) and at promoter-proximal and distal CTCF sites due to impaired histone H2A.Z deposition. Knocking out H2A.Z mimicked the Per null chromatin state and disrupted cellular rhythms. We found that endogenous mPER2 complexes retained CTCF as well as the specific H2A.Z-deposition chaperone YL1-a component of the ATP-dependent remodeler SRCAP and p400-TIP60 complex. While depleting YL1 or mutating chaperone-binding sites on H2A.Z lengthened the circadian period, H2A.Z deletion abrogated BMAL1 chromatin recruitment and promoted its proteasomal degradation. We propose that a PER2-mediated H2A.Z deposition pathway (1) compacts CLOCK-BMAL1 binding sites to establish negative feedback, (2) organizes circadian chromatin landscapes using CTCF and (3) bookmarks genomic loci for BMAL1 binding to impinge on the positive arm of the subsequent cycle.
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16
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Sun S, Jiang Y, Zhang Q, Pan H, Li X, Yang L, Huang M, Wei W, Wang X, Qiu M, Cao L, He H, Yu M, Liu H, Zhao B, Jiang N, Li R, Lin X. Znhit1 controls meiotic initiation in male germ cells by coordinating with Stra8 to activate meiotic gene expression. Dev Cell 2022; 57:901-913.e4. [PMID: 35413238 DOI: 10.1016/j.devcel.2022.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 01/25/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
Abstract
The switch from mitosis to meiosis ensures the successive formation of gametes. However, it remains unclear how meiotic initiation occurs within the context of chromatin. Recent studies have shown that zinc finger HIT-type containing 1 (Znhit1), a subunit of the SRCAP chromatin remodeling complex, plays essential roles in modulating the chromatin structure. Herein, we report that the germline-conditional deletion of Znhit1 in male mice specifically blocks meiotic initiation. We show that Znhit1 is required for meiotic prophase events, including synapsis, DNA double-strand break formation, and meiotic DNA replication. Mechanistically, Znhit1 controls the histone variant H2A.Z deposition, which facilitates the expression of meiotic genes, such as Meiosin, but not the expression of Stra8. Interestingly, Znhit1 deficiency disrupts the transcription bubbles of meiotic genes. Thus, our findings identify the essential role of Znhit1-dependent H2A.Z deposition in allowing activation of meiotic gene expression, thereby controlling the initiation of meiosis.
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Affiliation(s)
- Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yamei Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Qiaoli Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hongjie Pan
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Xinyang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Li Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Meina Huang
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Wei Wei
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Xiaoye Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Mengdi Qiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Lihuan Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hua He
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Miao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Hanmin Liu
- The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China.
| | - Runsheng Li
- National Health Commission (NHC) Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China.
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai 200438, China; The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, Chengdu 610041, China.
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17
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Ikram AU, Zhang F, Xu Z, Li E, Xue G, Wang S, Zhang C, Yang Y, Su Y, Ding Y. Chromatin remodeling factors OsYAF9 and OsSWC4 interact to promote internode elongation in rice. PLANT PHYSIOLOGY 2022; 188:2199-2214. [PMID: 35157083 PMCID: PMC8968431 DOI: 10.1093/plphys/kiac031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/15/2021] [Indexed: 05/09/2023]
Abstract
Deposition of H2A.Z and H4 acetylation by SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) and Nucleosome Acetyltransferase of H4 (NuA4) complexes in specific regulatory regions modulates transcription and development. However, little is known about these complexes in Oryza sativa (rice) development. Here, we reported that OsYAF9 and OsSWC4, two subunits of SWR1 and NuA4 complexes, are involved in rice vegetative and reproductive development. Loss of OsYAF9 resulted in reduced height, fewer tillers, fewer pollen grains, and defects in embryogenesis and seed filling. OsYAF9 directly interacted with OsSWC4 in vitro and in vivo. Loss of OsSWC4 function exhibited defects in pollen germination and failure to generate seeds, whereas knockdown of OsSWC4 resulted in reduced height and fewer tillers. The reduced height caused by OsYAF9 mutation and OsSWC4 knockdown was due to shorter internodes and defects in cell elongation, and this phenotype was rescued with gibberellin (GA) treatment, suggesting that both OsYAF9 and OsSWC4 are involved in the GA biosynthesis pathway. OsSWC4 was directly bound to the AT-rich region of GA biosynthesis genes, which in turn accomplished H2A.Z deposition and H4 acetylation at the GA biosynthesis genes with OsYAF9. Together, our study provides insights into the mechanisms involving OsSWC4 and OsYAF9 forming a protein complex to promote rice internode elongation with H2A.Z deposition and H4 acetylation.
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Affiliation(s)
| | | | - Zuntao Xu
- Division of Life Sciences and Medicine, School of Life Sciences; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Enze Li
- Division of Life Sciences and Medicine, School of Life Sciences; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Gan Xue
- Division of Life Sciences and Medicine, School of Life Sciences; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Shiliang Wang
- Division of Life Sciences and Medicine, School of Life Sciences; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Cheng Zhang
- Division of Life Sciences and Medicine, School of Life Sciences; Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics; Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, University of Science and Technology of China, Anhui 230027, China
| | - Yachun Yang
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
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Braghini MR, Lo Re O, Romito I, Fernandez-Barrena MG, Barbaro B, Pomella S, Rota R, Vinciguerra M, Avila MA, Alisi A. Epigenetic remodelling in human hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:107. [PMID: 35331312 PMCID: PMC8943959 DOI: 10.1186/s13046-022-02297-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/19/2022] [Indexed: 04/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications.In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches.In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine.Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches.
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Affiliation(s)
- Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Oriana Lo Re
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Ilaria Romito
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Barbara Barbaro
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Silvia Pomella
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Matias A Avila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy.
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Genome-Wide Characterization and Analysis of Expression of the Histone Gene Family in Razor Clam, Sinonovacula constricta. FISHES 2021. [DOI: 10.3390/fishes7010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Chinese razor clam (Sinonovacula constricta), a bivalve species widely distributed in estuaries and mudflats, is often exposed to extreme environmental and microbial stresses. Histones are fundamental components of chromatin and play an important role in innate immunity, as demonstrated by its antimicrobial activities in clams. However, little attention has been paid to histones in bivalves. To fill this gap, we investigated the genomic distribution, structural characteristics, conserved motifs, and phylogenetic relationships of histones in S. constricta. A total of 114 histone genes were detected in the S. constricta genome, which were divided into 25 types in phylogenetic analysis. Among them, partial histones exhibited a tissue-dependent expression pattern, indicating that they may be involved in sustaining the homeostasis of organs/tissues in adult S. constricta. Furthermore, mRNA expression of certain histones changed significantly in S. constricta when infected with Vibrio parahaemolyticus, suggesting that histones play a role in the immune defense of S. constricta. All together, this study on histone genes in S. constricta not only greatly expands our knowledge of histone function in the clam, but also histone evolution in molluscs.
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20
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Salmerón-Bárcenas EG, Zacapala-Gómez AE, Lozano-Amado D, Castro-Muñoz LJ, Leyva-Vázquez MA, Manzo-Merino J, Ávila-López PA. Comprehensive bioinformatic analysis reveals oncogenic role of H2A.Z isoforms in cervical cancer progression. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1470-1481. [PMID: 35317119 PMCID: PMC8917839 DOI: 10.22038/ijbms.2021.58287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/11/2021] [Indexed: 12/20/2022]
Abstract
Objectives Cervical cancer ranks as the fourth most common neoplasia in women worldwide in which epigenetic alterations play an important role. Several studies have reported pro-oncogenic role of the histone variant H2A.Z in different types of cancer; however, the role of H2A.Z in cervical cancer remains poorly studied. This study aimed to determine the potential role of H2A.Z in cervical cancer through a bioinformatic approach. Materials and Methods H2A.Z expression was analyzed in The Human Protein Atlas, The Cancer Genome Atlas, and Gene Expression Omnibus datasets. The promoter regions of H2AZ1 and H2AZ2 genes were downloaded from Expasy, and the prediction of transcription factor binding motifs was performed using CONSITE, Alibaba, and ALGGEN. ChIP-seq and RNA-seq data from HeLa-S3 cells were downloaded from ENCODE. The discovery motif was investigated using MEME-ChIP. The functional annotation was examined in Enrich. Results The expression of H2A.Z is elevated in cervical cancer. Interestingly, DNA methylation, copy number, and transcription factors AP2α and ELK1 are involved in H2A.Z overexpression. Additionally, H2A.Z is enriched on promoter and enhancer regions of genes involved in pathways associated with cancer development. In these regions, H2A.Z enables the recruitment of transcription factors such as NRF1, NFYA, and RNA Pol II. Finally, H2A.Z allows the expression of genes associated with proliferation in patients with cervical cancer. Conclusion Our findings suggest that H2A.Z overexpression and its presence in promoters and enhancers could be regulating the transcription of genes involved in cervical carcinogenesis.
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Affiliation(s)
- Eric G. Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto
| | - Ana E. Zacapala-Gómez
- Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México
| | - Daniela Lozano-Amado
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, 39090, Gro
| | | | - Marco A. Leyva-Vázquez
- Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México
| | | | - Pedro A. Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto ,Corresponding author: Pedro A. Ávila-López. Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, Ciudad de México. Tel: +52 55 6098 2694;
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21
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Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG. Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag. Dev Dyn 2021; 251:729-742. [PMID: 34647658 DOI: 10.1002/dvdy.430] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis. RESULTS To overcome these challenges, we adapted the chromatin profiling methods Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and CUT&Tag for use in zebrafish and applied these methods to generate high-resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences. CONCLUSIONS Our results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
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Affiliation(s)
| | | | - Fanju W Meng
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, Georgia, USA
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22
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Linking nuclear matrix-localized PIAS1 to chromatin SUMOylation via direct binding of histones H3 and H2A.Z. J Biol Chem 2021; 297:101200. [PMID: 34537242 PMCID: PMC8496182 DOI: 10.1016/j.jbc.2021.101200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
As a conserved posttranslational modification, SUMOylation has been shown to play important roles in chromatin-related biological processes including transcription. However, how the SUMOylation machinery associates with chromatin is not clear. Here, we present evidence that multiple SUMOylation machinery components, including SUMO E1 proteins SAE1 and SAE2 and the PIAS (protein inhibitor of activated STAT) family SUMO E3 ligases, are primarily associated with the nuclear matrix rather than with chromatin. We show using nuclease digestion that all PIAS family proteins maintain nuclear matrix association in the absence of chromatin. Of importance, we identify multiple histones including H3 and H2A.Z as directly interacting with PIAS1 and demonstrate that this interaction requires the PIAS1 SAP (SAF-A/B, Acinus, and PIAS) domain. We demonstrate that PIAS1 promotes SUMOylation of histones H3 and H2B in both a SAP domain– and an E3 ligase activity–dependent manner. Furthermore, we show that PIAS1 binds to heat shock–induced genes and represses their expression and that this function also requires the SAP domain. Altogether, our study reveals for the first time the nuclear matrix as the compartment most enriched in SUMO E1 and PIAS family E3 ligases. Our finding that PIAS1 interacts directly with histone proteins also suggests a molecular mechanism as to how nuclear matrix–associated PIAS1 is able to regulate transcription and other chromatin-related processes.
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23
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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24
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Itoh T, Inoue S, Sun X, Kusuda R, Hibi M, Shimizu T. Cfdp1 controls the cell cycle and neural differentiation in the zebrafish cerebellum and retina. Dev Dyn 2021; 250:1618-1633. [PMID: 33987914 DOI: 10.1002/dvdy.371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although the cell cycle and cell differentiation should be coordinately regulated to generate a variety of neurons in the brain, the molecules that are involved in this coordination still remain largely unknown. In this study, we analyzed the roles of a nuclear protein Cfdp1, which is thought to be involved in chromatin remodeling, in zebrafish neurogenesis. RESULTS Zebrafish cfdp1 mutants maintained the progenitors of granule cells (GCs) in the cerebellum, but showed defects in their differentiation to GCs. cfdp1 mutants showed an increase in phospho-histone 3 (pH 3)-positive cells and apoptotic cells, as well as a delayed cell cycle transition from the G2 to the M phase in the cerebellum. The inhibition of tp53 prevented apoptosis but not GC differentiation in the cfdp1 mutant cerebellum. A similar increase in apoptotic cells and pH 3-positive cells, and defective cell differentiation, were observed in the cfdp1 mutant retina. Although mitotic spindles formed, mitosis was blocked before anaphase in both the cerebellum and retina of cfdp1 mutant larvae. Furthermore, expression of the G2/mitotic-specific cyclin B1 gene increased in the cfdp1 mutant cerebellum. CONCLUSIONS Our findings suggest that Cfdp1 regulates the cell cycle of neural progenitors, thereby promoting neural differentiation in the brain.
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Affiliation(s)
- Tsubasa Itoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Shinsuke Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Xiaoding Sun
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Ryo Kusuda
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Masahiko Hibi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takashi Shimizu
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
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25
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Mylonas C, Lee C, Auld AL, Cisse II, Boyer LA. A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation. Nat Struct Mol Biol 2021; 28:435-442. [PMID: 33972784 DOI: 10.1038/s41594-021-00589-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
RNA polymerase II (RNAPII) pausing immediately downstream of the transcription start site is a critical rate-limiting step for the expression of most metazoan genes. During pause release, RNAPII encounters a highly conserved +1 H2A.Z nucleosome, yet how this histone variant contributes to transcription is poorly understood. Here, using an inducible protein degron system combined with genomic approaches and live cell super-resolution microscopy, we show that H2A.Z.1 modulates RNAPII dynamics across most genes in murine embryonic stem cells. Our quantitative analysis shows that H2A.Z.1 slows the rate of RNAPII pause release and consequently impacts negative elongation factor dynamics as well as nascent transcription. Consequently, H2A.Z.1 also impacts re-loading of the pre-initiation complex components TFIIB and TBP. Altogether, this work provides a critical mechanistic link between H2A.Z.1 and the proper induction of mammalian gene expression programs through the regulation of RNAPII dynamics and pause release.
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Affiliation(s)
- Constantine Mylonas
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Choongman Lee
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander L Auld
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ibrahim I Cisse
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laurie A Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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26
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Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun 2020; 11:5063. [PMID: 33033242 PMCID: PMC7546623 DOI: 10.1038/s41467-020-18821-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels. Chromatin state underlies cellular function, and transcription factor binding patterns along with epigenetic marks define chromatin state. Here the authors show that the histone chaperone ANP32E functions through regulation of H2A.Z to restrict genome-wide chromatin accessibility and to inhibit gene transcriptional activation.
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27
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Courtney AJ, Kamei M, Ferraro AR, Gai K, He Q, Honda S, Lewis ZA. Normal Patterns of Histone H3K27 Methylation Require the Histone Variant H2A.Z in Neurospora crassa. Genetics 2020; 216:51-66. [PMID: 32651262 PMCID: PMC7463285 DOI: 10.1534/genetics.120.303442] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/05/2020] [Indexed: 12/14/2022] Open
Abstract
Neurospora crassa contains a minimal Polycomb repression system, which provides rich opportunities to explore Polycomb-mediated repression across eukaryotes and enables genetic studies that can be difficult in plant and animal systems. Polycomb Repressive Complex 2 is a multi-subunit complex that deposits mono-, di-, and trimethyl groups on lysine 27 of histone H3, and trimethyl H3K27 is a molecular marker of transcriptionally repressed facultative heterochromatin. In mouse embryonic stem cells and multiple plant species, H2A.Z has been found to be colocalized with H3K27 methylation. H2A.Z is required for normal H3K27 methylation in these experimental systems, though the regulatory mechanisms are not well understood. We report here that Neurospora crassa mutants lacking H2A.Z or SWR-1, the ATP-dependent histone variant exchanger, exhibit a striking reduction in levels of H3K27 methylation. RNA-sequencing revealed downregulation of eed, encoding a subunit of PRC2, in an hH2Az mutant compared to wild type, and overexpression of EED in a ΔhH2Az;Δeed background restored most H3K27 methylation. Reduced eed expression leads to region-specific losses of H3K27 methylation, suggesting that differential dependence on EED concentration is critical for normal H3K27 methylation at certain regions in the genome.
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Affiliation(s)
- Abigail J Courtney
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Masayuki Kamei
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Aileen R Ferraro
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Kexin Gai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shinji Honda
- Division of Chromosome Biology, Faculty of Medical Sciences, University of Fukui, 910-1193, Japan
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
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28
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Sex-specific effects of the histone variant H2A.Z on fear memory, stress-enhanced fear learning and hypersensitivity to pain. Sci Rep 2020; 10:14331. [PMID: 32868857 PMCID: PMC7458907 DOI: 10.1038/s41598-020-71229-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023] Open
Abstract
Emerging evidence suggests that histone variants are novel epigenetic regulators of memory, whereby histone H2A.Z suppresses fear memory. However, it is not clear if altered fear memory can also modify risk for PTSD, and whether these effects differ in males and females. Using conditional-inducible H2A.Z knockout (cKO) mice, we showed that H2A.Z binding is higher in females and that H2A.Z cKO enhanced fear memory only in males. However, H2A.Z cKO improved memory on the non-aversive object-in-place task in both sexes, suggesting that H2A.Z suppresses non-stressful memory irrespective of sex. Given that risk for fear-related disorders, such as PTSD, is biased toward females, we examined whether H2A.Z cKO also has sex-specific effects on fear sensitization in the stress-enhanced fear learning (SEFL) model of PTSD, as well as associated changes in pain sensitivity. We found that H2A.Z cKO reduced stress-induced sensitization of fear learning and pain responses preferentially in female mice, indicating that the effects of H2A.Z depend on sex and the type of task, and are influenced by history of stress. These data suggest that H2A.Z may be a sex-specific epigenetic risk factor for PTSD susceptibility, with implications for developing sex-specific therapeutic interventions.
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29
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Abstract
Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.
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Affiliation(s)
- Benjamin Loppin
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007 Lyon, France;
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria;
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30
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Sun S, Jiang N, Jiang Y, He Q, He H, Wang X, Yang L, Li R, Liu F, Lin X, Zhao B. Chromatin remodeler Znhit1 preserves hematopoietic stem cell quiescence by determining the accessibility of distal enhancers. Leukemia 2020; 34:3348-3358. [PMID: 32694618 PMCID: PMC7685981 DOI: 10.1038/s41375-020-0988-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 01/10/2023]
Abstract
Hematopoietic stem cell (HSC) utilizes its quiescence feature to combat exhaustion for lifetime blood cell supply. To date, how certain chromatin architecture and subsequent transcription profile permit HSC quiescence remains unclear. Here, we show an essential role of chromatin remodeler zinc finger HIT-type containing 1 (Znhit1) in maintaining HSC quiescence. We find that loss of Znhit1 leads to exhaustion of stem cell pool and impairment of hematopoietic function. Mechanically, Znhit1 determines the chromatin accessibility at distal enhancers of HSC quiescence genes, including Pten, Fstl1, and Klf4, for sustained transcription and consequent PI3K-Akt signaling inhibition. Moreover, Znhit1-Pten-PI3K-Akt axis also participates in controlling myeloid expansion and B-lymphoid specification. Our findings therefore identify a dominant role of Znhit1-mediated chromatin remodeling in preserving HSC function for hematopoietic homeostasis.
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Affiliation(s)
- Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.,National Health Commission Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yamei Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Qiuping He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hua He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Li Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Runsheng Li
- National Health Commission Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Shanghai, 200032, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
| | - Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
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31
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Abstract
Chromatin is a highly dynamic structure that closely relates with gene expression in eukaryotes. ATP-dependent chromatin remodelling, histone post-translational modification and DNA methylation are the main ways that mediate such plasticity. The histone variant H2A.Z is frequently encountered in eukaryotes, and can be deposited or removed from nucleosomes by chromatin remodelling complex SWR1 or INO80, respectively, leading to altered chromatin state. H2A.Z has been found to be involved in a diverse range of biological processes, including genome stability, DNA repair and transcriptional regulation. Due to their formidable production of secondary metabolites, filamentous fungi play outstanding roles in pharmaceutical production, food safety and agriculture. During the last few years, chromatin structural changes were proven to be a key factor associated with secondary metabolism in fungi. However, studies on the function of H2A.Z are scarce. Here, we summarize current knowledge of H2A.Z functions with a focus on filamentous fungi. We propose that H2A.Z is a potential target involved in the regulation of secondary metabolite biosynthesis by fungi.
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32
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McFarlane M, Almire F, Kean J, Donald CL, McDonald A, Wee B, Lauréti M, Varjak M, Terry S, Vazeille M, Gestuveo RJ, Dietrich I, Loney C, Failloux AB, Schnettler E, Pondeville E, Kohl A. The Aedes aegypti Domino Ortholog p400 Regulates Antiviral Exogenous Small Interfering RNA Pathway Activity and ago-2 Expression. mSphere 2020; 5:e00081-20. [PMID: 32269152 PMCID: PMC7142294 DOI: 10.1128/msphere.00081-20] [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: 01/28/2020] [Accepted: 03/13/2020] [Indexed: 02/03/2023] Open
Abstract
Arboviruses are pathogens of humans and animals. A better understanding of the interactions between these pathogens and the arthropod vectors, such as mosquitoes, that transmit them is necessary to develop novel control measures. A major antiviral pathway in the mosquito vector is the exogenous small interfering RNA (exo-siRNA) pathway, which is induced by arbovirus-derived double-stranded RNA in infected cells. Although recent work has shown the key role played by Argonaute-2 (Ago-2) and Dicer-2 (Dcr-2) in this pathway, the regulatory mechanisms that govern these pathways have not been studied in mosquitoes. Here, we show that the Domino ortholog p400 has antiviral activity against the alphavirus Semliki Forest virus (Togaviridae) both in Aedes aegypti-derived cells and in vivo Antiviral activity of p400 was also demonstrated against chikungunya virus (Togaviridae) and Bunyamwera virus (Peribunyaviridae) but not Zika virus (Flaviviridae). p400 was found to be expressed across mosquito tissues and regulated ago-2 but not dcr-2 transcript levels in A. aegypti mosquitoes. These findings provide novel insights into the regulation of an important aedine exo-siRNA pathway effector protein, Ago-2, by the Domino ortholog p400. They add functional insights to previous observations of this protein's antiviral and RNA interference regulatory activities in Drosophila melanogasterIMPORTANCE Female Aedes aegypti mosquitoes are vectors of human-infecting arthropod-borne viruses (arboviruses). In recent decades, the incidence of arthropod-borne viral infections has grown dramatically. Vector competence is influenced by many factors, including the mosquito's antiviral defenses. The exogenous small interfering RNA (siRNA) pathway is a major antiviral response restricting arboviruses in mosquitoes. While the roles of the effectors of this pathway, Argonaute-2 and Dicer-2 are well characterized, nothing is known about its regulation in mosquitoes. In this study, we demonstrate that A. aegypti p400, whose ortholog Domino in Drosophila melanogaster is a chromatin-remodeling ATPase member of the Tip60 complex, regulates siRNA pathway activity and controls ago-2 expression levels. In addition, we found p400 to have antiviral activity against different arboviruses. Therefore, our study provides new insights into the regulation of the antiviral response in A. aegypti mosquitoes.
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Affiliation(s)
- Melanie McFarlane
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Floriane Almire
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Joy Kean
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Claire L Donald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Alma McDonald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Bryan Wee
- Usher Institute for Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Mathilde Lauréti
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Sandra Terry
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Marie Vazeille
- Arboviruses and Insect Vectors Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Rommel J Gestuveo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
- Division of Biological Sciences, University of the Philippines Visayas, Miagao, Philippines
| | - Isabelle Dietrich
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Colin Loney
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Anna-Bella Failloux
- Arboviruses and Insect Vectors Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Emilie Pondeville
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland
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33
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Rao VK, Swarnaseetha A, Tham GH, Lin WQ, Han BB, Benoukraf T, Xu GL, Ong CT. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res 2020; 48:1225-1238. [PMID: 31807777 PMCID: PMC7026633 DOI: 10.1093/nar/gkz1144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.
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Affiliation(s)
- Vinay Kumar Rao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Adusumalli Swarnaseetha
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hong Tham
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Wei-Qi Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Bin-Bin Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chin-Tong Ong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D. Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. eLife 2020; 9:53375. [PMID: 32109204 PMCID: PMC7048395 DOI: 10.7554/elife.53375] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of their functions in gene expression using endogenously-tagged proteins. RNA-Seq analysis in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Furthermore, they have similar or antagonistic function depending on genes. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, which can mediate their functional antagonism. Our data indicate that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants.
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Affiliation(s)
- Assala Lamaa
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Marion Aguirrebengoa
- BigA Core Facility, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Didier Trouche
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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Lei B, Berger F. H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity. PLANT COMMUNICATIONS 2020; 1:100015. [PMID: 33404536 PMCID: PMC7747964 DOI: 10.1016/j.xplc.2019.100015] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 05/16/2023]
Abstract
The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.
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Neural progenitor cells mediated by H2A.Z.2 regulate microglial development via Cxcl14 in the embryonic brain. Proc Natl Acad Sci U S A 2019; 116:24122-24132. [PMID: 31712428 DOI: 10.1073/pnas.1913978116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microglia, the resident immune cells of the central nervous system, play an important role in the brain. Microglia have a special spatiotemporal distribution during the development of the cerebral cortex. Neural progenitor cells (NPCs) are the main source of neural-specific cells in the early brain. It is unclear whether NPCs affect microglial development and what molecular mechanisms control early microglial localization. H2A.Z.2, a histone variant of H2A, has a key role in gene expression regulation, genomic stability, and chromatin remodeling, but its function in brain development is not fully understood. Here, we found that the specific deletion of H2A.Z.2 in neural progenitor cells led to an abnormal increase in microglia in the ventricular zone/subventricular zone (VZ/SVZ) of the embryonic cortex. Mechanistically, H2A.Z.2 regulated microglial development by incorporating G9a into the promoter region of Cxcl14 and promoted H3k9me2 modification to inhibit the transcription of Cxcl14 in neural progenitor cells. Meanwhile, we found that the deletion of H2A.Z.2 in microglia itself had no significant effect on microglial development in the early cerebral cortex. Our findings demonstrate a key role of H2A.Z.2 in neural progenitor cells in controlling microglial development and broaden our knowledge of 2 different types of cells that may affect each other through crosstalk in the central nervous system.
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Crevillén P, Gómez-Zambrano Á, López JA, Vázquez J, Piñeiro M, Jarillo JA. Arabidopsis YAF9 histone readers modulate flowering time through NuA4-complex-dependent H4 and H2A.Z histone acetylation at FLC chromatin. THE NEW PHYTOLOGIST 2019; 222:1893-1908. [PMID: 30742710 DOI: 10.1111/nph.15737] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/02/2019] [Indexed: 05/27/2023]
Abstract
Posttranslational histone modifications and the dynamics of histone variant H2A.Z are key mechanisms underlying the floral transition. In yeast, SWR1-C and NuA4-C mediate the deposition of H2A.Z and the acetylation of histone H4, H2A and H2A.Z, respectively. Yaf9 is a subunit shared by both chromatin-remodeling complexes. The significance of the two Arabidopsis YAF9 homologues, YAF9A and YAF9B, is unknown. To get an insight into the role of Arabidopsis YAF9 proteins in plant developmental responses, we followed physiological, genetic, genomic, epigenetic, proteomics and cell biology approaches. Our data revealed that YAF9A and YAF9B are histone H3 readers with unequally redundant functions. Double mutant yaf9a yaf9b plants display pleiotropic developmental phenotypic alterations as well as misregulation of a wide variety of genes. We demonstrated that YAF9 proteins regulate flowering time by both FLC-dependent and independent mechanisms that work in parallel with SWR1-C. Interestingly, we show that YAF9A binds FLC chromatin and that YAF9 proteins regulate FLC expression by modulating the acetylation levels of H2A.Z and H4 but not H2A.Z deposition. Our work highlights the key role exerted by YAF9 homologues in the posttranslational modification of canonical histones and variants that regulate gene expression in plants to control development.
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Affiliation(s)
- Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Ángeles Gómez-Zambrano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Juan A López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029, Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029, Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón (Madrid), Spain
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The base pair-scale diffusion of nucleosomes modulates binding of transcription factors. Proc Natl Acad Sci U S A 2019; 116:12161-12166. [PMID: 31147470 DOI: 10.1073/pnas.1815424116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The structure of promoter chromatin determines the ability of transcription factors (TFs) to bind to DNA and therefore has a profound effect on the expression levels of genes. However, the role of spontaneous nucleosome movements in this process is not fully understood. Here, we developed a single-molecule optical tweezers assay capable of simultaneously characterizing the base pair-scale diffusion of a nucleosome on DNA and the binding of a TF, using the luteinizing hormone β subunit gene (Lhb) promoter and Egr-1 as a model system. Our results demonstrate that nucleosomes undergo confined diffusion, and that the incorporation of the histone variant H2A.Z serves to partially relieve this confinement, inducing a different type of nucleosome repositioning. The increase in diffusion leads to exposure of a TF's binding site and facilitates its association with the DNA, which, in turn, biases the subsequent movement of the nucleosome. Our findings suggest the use of mobile nucleosomes as a general transcriptional regulatory mechanism.
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Ishihara A, Sapon MA, Yamauchi K. Seasonal acclimatization and thermal acclimation induce global histone epigenetic changes in liver of bullfrog (Lithobates catesbeianus) tadpole. Comp Biochem Physiol A Mol Integr Physiol 2019; 230:39-48. [DOI: 10.1016/j.cbpa.2018.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 01/08/2023]
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40
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Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
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41
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Zhao B, Chen Y, Jiang N, Yang L, Sun S, Zhang Y, Wen Z, Ray L, Liu H, Hou G, Lin X. Znhit1 controls intestinal stem cell maintenance by regulating H2A.Z incorporation. Nat Commun 2019; 10:1071. [PMID: 30842416 PMCID: PMC6403214 DOI: 10.1038/s41467-019-09060-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
Lgr5+ stem cells are crucial to gut epithelium homeostasis; however, how these cells are maintained is not fully understood. Zinc finger HIT-type containing 1 (Znhit1) is an evolutionarily conserved subunit of the SRCAP chromosome remodeling complex. Currently, the function of Znhit1 in vivo and its working mechanism in the SRCAP complex are unknown. Here we show that deletion of Znhit1 in intestinal epithelium depletes Lgr5+ stem cells thus disrupts intestinal homeostasis postnatal establishment and maintenance. Mechanistically, Znhit1 incorporates histone variant H2A.Z into TSS region of genes involved in Lgr5+ stem cell fate determination, including Lgr5, Tgfb1 and Tgfbr2, for subsequent transcriptional regulation. Importantly, Znhit1 promotes the interaction between H2A.Z and YL1 (H2A.Z chaperone) by controlling YL1 phosphorylation. These results demonstrate that Znhit1/H2A.Z is essential for Lgr5+ stem cell maintenance and intestinal homeostasis. Our findings identified a dominant role of Znhit1/H2A.Z in controlling mammalian organ development and tissue homeostasis in vivo.
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Affiliation(s)
- Bing Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| | - Ying Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Li Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lorraine Ray
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Han Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Guoli Hou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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42
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Bowerman S, Hickok RJ, Wereszczynski J. Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability. J Phys Chem B 2019; 123:419-427. [PMID: 30557018 DOI: 10.1021/acs.jpcb.8b10668] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The fundamental unit of eukaryotic chromatin is the nucleosome core particle, a protein/DNA complex that binds ∼147 base pairs of DNA to a histone octamer. These histones-H3, H4, H2A, H2B-form the nucleosome core through a stacked interaction in which two H2A-H2B dimers flank the (H3-H4)2 tetramer. In vivo, genetic accessibility can be modulated by the substitution of canonical histones with variant proteins that contain the same structural motif but a different amino acid sequence, such as the transcriptional repression-associated macroH2A variant. Previously, Chakravarthy and Luger published a crystal study that showed that H2A substitution is not necessarily required of both H2A moieties, but that in vitro recombination of nucleosomes in the presence of both macroH2A and H2A histone folds results in a hybrid macroH2A-H2A nucleosome with one dimer of each type. Here, we present molecular dynamics simulations of this hybrid construct and compare the results to our previous study on homogeneous H2A- and macroH2A-containing nucleosomes. We find that the hybrid contains a unique set of dynamics that stabilize the interactions between protein constituents and create an altogether more stable nucleosome, both in terms of protein-DNA and protein-protein binding. While dimer-tetramer interactions are asymmetric, as the difference in moieties would suggest, we observe that it is the canonical dimer that is pulled further into the nucleosome core, resulting in more secure dimer-tetramer bonds and a more stable histone core, and we also find significantly more interaction between the dimer subunits. Together, these models provide evidence for hybrid H2A-macroH2A nucleosome formation being not only possible but actually energetically more favorable than a homogeneous construct, with dynamics that are unique from their homogeneous H2A or macroH2A nucleosome counterparts. These effects of hybrid substitution likely propagate into higher-order chromatin structures to hinder transcriptional activity.
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Affiliation(s)
- Samuel Bowerman
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Robert J Hickok
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Jeff Wereszczynski
- Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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Gretzinger TL, Tyagi M, Fontaine CJ, Cheema MS, González-Perez M, Freeman ME, Christie BR, Ausió J. Fetal alcohol spectrum disorder (FASD) affects the hippocampal levels of histone variant H2A.Z-2. Biochem Cell Biol 2019; 97:431-436. [PMID: 30605356 DOI: 10.1139/bcb-2018-0240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Fetal alcohol spectrum disorder (FASD) is caused by prenatal exposure to ethanol and has been linked to neurodevelopmental impairments. Alcohol has the potential to alter some of the epigenetic components that play a critical role during development. Previous studies have provided evidence that prenatal exposure to ethanol results in abnormal epigenetic patterns (i.e., hypomethylation) of the genome. The aim of this study was to determine how prenatal exposure to ethanol in rats affects the hippocampal levels of expression of two important brain epigenetic transcriptional regulators involved in synaptic plasticity and memory consolidation: methyl CpG-binding protein 2 (MeCP2) and histone variant H2A.Z. Unexpectedly, under the conditions used in this work we were not able to detect any changes in MeCP2. Interestingly, however, we observed a significant decrease in H2A.Z, accompanied by its chromatin redistribution in both female and male FASD rat pups. Moreover, the data from reverse-transcription qPCR later confirmed that this decrease in H2A.Z is mainly due to down-regulation of its H2A.Z-2 isoform gene expression. Altogether, these data provide strong evidence that prenatal exposure to ethanol alters histone variant H2A.Z during neurogenesis of rat hippocampus.
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Affiliation(s)
- Taylor L Gretzinger
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Monica Tyagi
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Christine J Fontaine
- b Division of Medical Sciences and Neuroscience Graduate Program, University of Victoria, Victoria, British Columbia, Canada
| | - Manjinder S Cheema
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - María González-Perez
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Melissa E Freeman
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
| | - Brian R Christie
- b Division of Medical Sciences and Neuroscience Graduate Program, University of Victoria, Victoria, British Columbia, Canada
| | - Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
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Cai H, Zhang M, Chai M, He Q, Huang X, Zhao L, Qin Y. Epigenetic regulation of anthocyanin biosynthesis by an antagonistic interaction between H2A.Z and H3K4me3. THE NEW PHYTOLOGIST 2019; 221:295-308. [PMID: 29959895 DOI: 10.1111/nph.15306] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/01/2018] [Indexed: 05/20/2023]
Abstract
The accumulation of anthocyanins in response to specific developmental cues or environmental conditions plays a vital role in plant development and protection against stresses. Extensive research has examined the regulation of anthocyanin biosynthetic genes at the transcriptional and post-transcriptional levels, but the role of chromatin in this regulation remains unknown. Chromatin immunoprecipitation and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were performed. Genetic interactions between trimethylation of lysine 4 on histone H3 (H3K4me3) and the chromatin remodeling complex SWR1 in the control of anthocyanin biosynthesis were further studied. In this study, we provide evidence that a conserved histone H2 variant, H2A.Z, negatively regulates anthocyanin accumulation through deposition at a set of anthocyanin biosynthetic genes and consequently represses their expression in Arabidopsis thaliana. Our data indicate that the accumulation of anthocyanin in H2A.Z deposition-deficient mutants is associated with increased H3K4me3, which is required for promotion of the expression of anthocyanin biosynthetic genes. We further provide evidence that H3K4me3 in anthocyanin biosynthetic genes is negatively associated with the presence of H2A.Z. Our results reveal an antagonistic relationship between H2A.Z and H3K4me3 in the regulation of the expression of anthocyanin biosynthesis genes, adding another layer of regulation to anthocyanin biosynthesis genes and highlighting the role of chromatin in gene regulation.
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Affiliation(s)
- Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengnan Chai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyu Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lihua Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Marshall PR, Bredy TW. Neuroepigenetic mechanisms underlying fear extinction: emerging concepts. Psychopharmacology (Berl) 2019; 236:133-142. [PMID: 30506235 PMCID: PMC7293886 DOI: 10.1007/s00213-018-5084-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022]
Abstract
An understanding of how memory is acquired and how it can be modified in fear-related anxiety disorders, with the enhancement of failing memories on one side and a reduction or elimination of traumatic memories on the other, is a key unmet challenge in the fields of neuroscience and neuropsychiatry. The latter process depends on an important form of learning called fear extinction, where a previously acquired fear-related memory is decoupled from its ability to control behaviour through repeated non-reinforced exposure to the original fear-inducing cue. Although simple in description, fear extinction relies on a complex pattern of brain region and cell-type specific processes, some of which are unique to this form of learning and, for better or worse, contribute to the inherent instability of fear extinction memory. Here, we explore an emerging layer of biology that may compliment and enrich the synapse-centric perspective of fear extinction. As opposed to the more classically defined role of protein synthesis in the formation of fear extinction memory, a neuroepigenetic view of the experience-dependent gene expression involves an appreciation of dynamic changes in the state of the entire cell: from a transient change in plasticity at the level of the synapse, to potentially more persistent long-term effects within the nucleus. A deeper understanding of neuroepigenetic mechanisms and how they influence the formation and maintenance of fear extinction memory has the potential to enable the development of more effective treatment approaches for fear-related neuropsychiatric conditions.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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46
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Zimmerman D, Patel K, Hall M, Elmer J. Enhancement of transgene expression by nuclear transcription factor Y and CCCTC-binding factor. Biotechnol Prog 2018; 34:1581-1588. [PMID: 30294957 DOI: 10.1002/btpr.2712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/03/2018] [Accepted: 08/17/2018] [Indexed: 12/23/2022]
Abstract
If a transgene is effectively delivered to a cell, its expression may still be limited by epigenetic mechanisms that silence the transgene. Indeed, once the transgene reaches the nucleus, it may be bound by histone proteins and condensed into heterochromatin or associated with repressor proteins that block transcription. In this study, we sought to enhance transgene expression by adding binding motifs for several different epigenetic enzymes either upstream or downstream of two promoters (CMV and EF1α). Screening these plasmids revealed that luciferase expression was enhanced 10-fold (10.4 ± 5.8) by the addition of a CCAAT box just upstream of the EF1α promoter to recruit nuclear transcription factor Y (NF-Y), while inserting a CCCTC-binding factor (CTCF) motif downstream of the EF1α promoter enhanced expression at least 14-fold (14.03 ± 6.54). ChIP assays confirmed that NF-Y and CTCF bound to the motifs that were added to each plasmid, but the presence of NF-Y and CTCF did not significantly affect the levels of histone acetylation (H3K9ac) or methylation (H3K9me3). Overall, these results show that transgene expression from the EF1α promoter can be significantly increased with motifs that recruit NF-Y or CTCF. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1581-1588, 2018.
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Affiliation(s)
- Devon Zimmerman
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Krupa Patel
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Matthew Hall
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
| | - Jacob Elmer
- Dept. of Chemical Engineering, Villanova University, Villanova, PA, 19085
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47
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Wang Y, Long H, Yu J, Dong L, Wassef M, Zhuo B, Li X, Zhao J, Wang M, Liu C, Wen Z, Chang L, Chen P, Wang QF, Xu X, Margueron R, Li G. Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells. BMC Biol 2018; 16:107. [PMID: 30249243 PMCID: PMC6151936 DOI: 10.1186/s12915-018-0568-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/24/2018] [Indexed: 01/27/2023] Open
Abstract
Background The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. The histone variants H3.3 and H2A.Z have recently been identified as key regulatory players in this process, but the underlying molecular mechanisms by which they permit or restrict gene expression remain unclear. Here, we investigated the regulatory function of H3.3 and H2A.Z on chromatin dynamics and Polycomb-mediated gene silencing. Results Our ChIP-seq analysis reveals that in mouse embryonic stem (mES) cells, H3K27me3 enrichment correlates strongly with H2A.Z. We further demonstrate that H2A.Z promotes PRC2 activity on H3K27 methylation through facilitating chromatin compaction both in vitro and in mES cells. In contrast, PRC2 activity is counteracted by H3.3 through impairing chromatin compaction. However, a subset of H3.3 may positively regulate PRC2-dependent H3K27 methylation via coordinating depositions of H2A.Z to developmental and signaling genes in mES cells. Using all-trans retinoic acid (tRA)-induced gene as a model, we show that the dynamic deposition of H2A.Z and H3.3 coordinately regulates the PRC2-dependent H3K27 methylation by modulating local chromatin structure at the promoter region during the process of turning genes off. Conclusions Our study provides key insights into the mechanism of how histone variants H3.3 and H2A.Z function coordinately to finely tune the PRC2 enzymatic activity during gene silencing, through promoting or impairing chromosome compaction respectively. Electronic supplementary material The online version of this article (10.1186/s12915-018-0568-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haizhen Long
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liping Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Michel Wassef
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 26 Rue d'Ulm, 75005, Paris, France
| | - Baowen Zhuo
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China
| | - Xia Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luyuan Chang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian-Fei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xueqing Xu
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, 518102, China
| | - Raphael Margueron
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 26 Rue d'Ulm, 75005, Paris, France.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Au-Yeung N, Horvath CM. Histone H2A.Z Suppression of Interferon-Stimulated Transcription and Antiviral Immunity Is Modulated by GCN5 and BRD2. iScience 2018; 6:68-82. [PMID: 30240626 PMCID: PMC6137307 DOI: 10.1016/j.isci.2018.07.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/27/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Type I interferon (IFN)-stimulated gene (ISG) expression requires interaction between a transcription factor complex, ISGF3, and target gene promoters to initiate transcription and protection against infection. To uncover chromatin regulatory features of this antiviral immune response, IFN-induced nucleosome and histone dynamics of human ISG loci were examined. ISGF3 recruitment after IFN stimulation was accompanied by nucleosome reorganization at promoters and gene bodies. IFN stimulation induced loss of core histones H2B, H3, and H4, as well as H2A.Z at ISG promoters. A strong correlation was found between H2A.Z occupancy and ISGF3 target sites, and IFN-stimulated H2A.Z removal requires STAT1, STAT2, and IRF9. Neither INO80 nor SWI/SNF participate in IFN-driven H2A.Z eviction, but GCN5 and BRD2 are required. Interference with H2A.Z expression enhanced ISGF3 recruitment to ISG promoters, ISG mRNA expression, and IFN-stimulated antiviral immunity. This indicates that H2A.Z nucleosomes at ISG promoters restrict optimal ISGF3 engagement and modulate the biological response to IFN.
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Affiliation(s)
- Nancy Au-Yeung
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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49
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Gómez-Zambrano Á, Crevillén P, Franco-Zorrilla JM, López JA, Moreno-Romero J, Roszak P, Santos-González J, Jurado S, Vázquez J, Köhler C, Solano R, Piñeiro M, Jarillo JA. Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes. MOLECULAR PLANT 2018; 11:815-832. [PMID: 29604400 DOI: 10.1016/j.molp.2018.03.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 05/07/2023]
Abstract
Deposition of the H2A.Z histone variant by the SWR1 complex (SWR1-C) in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWR1-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWR1-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo-lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and reproductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses transcription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWR1-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.
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Affiliation(s)
- Ángeles Gómez-Zambrano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - José M Franco-Zorrilla
- Plant Molecular Genetics Department and Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Juan A López
- Proteomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Pawel Roszak
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Silvia Jurado
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75652, Sweden
| | - Roberto Solano
- Plant Molecular Genetics Department and Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - José A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain.
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50
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Carter B, Bishop B, Ho KK, Huang R, Jia W, Zhang H, Pascuzzi PE, Deal RB, Ogas J. The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis. THE PLANT CELL 2018; 30:1337-1352. [PMID: 29802212 PMCID: PMC6048792 DOI: 10.1105/tpc.17.00867] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 05/20/2023]
Abstract
Selective, tissue-specific gene expression is facilitated by the epigenetic modification H3K27me3 (trimethylation of lysine 27 on histone H3) in plants and animals. Much remains to be learned about how H3K27me3-enriched chromatin states are constructed and maintained. Here, we identify a genetic interaction in Arabidopsis thaliana between the chromodomain helicase DNA binding chromatin remodeler PICKLE (PKL), which promotes H3K27me3 enrichment, and the SWR1-family remodeler PHOTOPERIOD INDEPENDENT EARLY FLOWERING1 (PIE1), which incorporates the histone variant H2A.Z. Chromatin immunoprecipitation-sequencing and RNA-sequencing reveal that PKL, PIE1, and the H3K27 methyltransferase CURLY LEAF act in a common gene expression pathway and are required for H3K27me3 levels genome-wide. Additionally, H3K27me3-enriched genes are largely a subset of H2A.Z-enriched genes, further supporting the functional linkage between these marks. We also found that recombinant PKL acts as a prenucleosome maturation factor, indicating that it promotes retention of H3K27me3. These data support the existence of an epigenetic pathway in which PIE1 promotes H2A.Z, which in turn promotes H3K27me3 deposition. After deposition, PKL promotes retention of H3K27me3 after DNA replication and/or transcription. Our analyses thus reveal roles for H2A.Z and ATP-dependent remodelers in construction and maintenance of H3K27me3-enriched chromatin in plants.
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Affiliation(s)
- Benjamin Carter
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brett Bishop
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Kwok Ki Ho
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Ru Huang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Songjiang District, Shanghai 201602, China
| | - Pete E Pascuzzi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue University Libraries, Purdue University, West Lafayette, Indiana 47907
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia 30322
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
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