1
|
Chen Z, Seman M, Fyodorova Y, Farhat A, Ames A, Levashkevich A, Biswas S, Huang F, Freddolino L, Biteen JS, Ragunathan K. Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions. Nucleic Acids Res 2024; 52:10731-10746. [PMID: 39142658 DOI: 10.1093/nar/gkae692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in single-molecule super-resolution microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression, but several important mechanistic details of this process remain unexplored. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and their binding partners, and we inferred their most likely interaction sites. Our results demonstrate that H3K9 methylation spatially restricts HP1 proteins and their interactors, thereby promoting ternary complex formation on chromatin while simultaneously suppressing off-chromatin binding. As opposed to being an inert platform to direct HP1 binding, our studies propose a novel function for H3K9me in promoting ternary complex formation by enhancing the specificity and stimulating the assembly of HP1-protein complexes in living cells.
Collapse
Affiliation(s)
- Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | | | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Amanda Ames
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | | | - Saikat Biswas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Fengting Huang
- Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | - Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Julie S Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | | |
Collapse
|
2
|
Yu J, Zhang Y, Fang Y, Paulo JA, Yaghoubi D, Hua X, Shipkovenska G, Toda T, Zhang Z, Gygi SP, Jia S, Li Q, Moazed D. A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance. Cell 2024; 187:5010-5028.e24. [PMID: 39094570 PMCID: PMC11380579 DOI: 10.1016/j.cell.2024.07.006] [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: 08/17/2023] [Revised: 03/17/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.
Collapse
Affiliation(s)
- Juntao Yu
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yujie Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Dadmehr Yaghoubi
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gergana Shipkovenska
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Toda T, Fang Y, Shan CM, Hua X, Kim JK, Tang LC, Jovanovic M, Tong L, Qiao F, Zhang Z, Jia S. Mrc1 regulates parental histone segregation and heterochromatin inheritance. Mol Cell 2024; 84:3223-3236.e4. [PMID: 39094566 PMCID: PMC11414769 DOI: 10.1016/j.molcel.2024.07.002] [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: 10/19/2023] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Chromatin-based epigenetic memory relies on the symmetric distribution of parental histones to newly synthesized daughter DNA strands, aided by histone chaperones within the DNA replication machinery. However, the mechanism of parental histone transfer remains elusive. Here, we reveal that in fission yeast, the replisome protein Mrc1 plays a crucial role in promoting the transfer of parental histone H3-H4 to the lagging strand, ensuring proper heterochromatin inheritance. In addition, Mrc1 facilitates the interaction between Mcm2 and DNA polymerase alpha, two histone-binding proteins critical for parental histone transfer. Furthermore, Mrc1's involvement in parental histone transfer and epigenetic inheritance is independent of its known functions in DNA replication checkpoint activation and replisome speed control. Instead, Mrc1 interacts with Mcm2 outside of its histone-binding region, creating a physical barrier to separate parental histone transfer pathways. These findings unveil Mrc1 as a key player within the replisome, coordinating parental histone segregation to regulate epigenetic inheritance.
Collapse
Affiliation(s)
- Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jin-Kwang Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | | | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
4
|
Braun S. Heterochromatin as a balancing act between transcription and gene silencing. Nat Rev Mol Cell Biol 2024; 25:676. [PMID: 38961267 DOI: 10.1038/s41580-024-00762-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Affiliation(s)
- Sigurd Braun
- Institute for Genetics, Justus Liebig University, Giessen, Germany.
| |
Collapse
|
5
|
Marin H, Simental E, Allen C, Martin E, Panning B, Al-Sady B, Buchwalter A. The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602542. [PMID: 39026839 PMCID: PMC11257442 DOI: 10.1101/2024.07.08.602542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the effect of spatial position on heterochromatin function has not been defined. Here, we remove three nuclear lamins and lamin B receptor (LBR) in mouse embryonic stem cells (mESCs) and show that heterochromatin detaches from the nuclear periphery. Mutant mESCs sustain naïve pluripotency and maintain H3K9me2 across the genome but cannot repress H3K9me2-marked genes or transposons. Further, mutant cells fail to differentiate into epiblast-like cells (EpiLCs), a transition that requires the expansion of H3K9me2 across the genome. Mutant EpiLCs can silence naïve pluripotency genes and activate epiblast-stage genes. However, H3K9me2 cannot repress markers of alternative fates, including primitive endoderm. We conclude that the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of H3K9me2-marked heterochromatin to shape cell fate decisions.
Collapse
Affiliation(s)
- Harold Marin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Simental
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Charlie Allen
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Eric Martin
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Barbara Panning
- Department of Biochemistry, University of California, San Francisco, CA, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
| |
Collapse
|
6
|
Yabe K, Kamio A, Oya S, Kakutani T, Hirayama M, Tanaka Y, Inagaki S. H3K9 methylation regulates heterochromatin silencing through incoherent feedforward loops. SCIENCE ADVANCES 2024; 10:eadn4149. [PMID: 38924413 PMCID: PMC11204290 DOI: 10.1126/sciadv.adn4149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Histone H3 lysine-9 methylation (H3K9me) is a hallmark of the condensed and transcriptionally silent heterochromatin. It remains unclear how H3K9me controls transcription silencing and how cells delimit H3K9me domains to avoid silencing essential genes. Here, using Arabidopsis genetic systems that induce H3K9me2 in genes and transposons de novo, we show that H3K9me2 accumulation paradoxically also causes the deposition of the euchromatic mark H3K36me3 by a SET domain methyltransferase, ASHH3. ASHH3-induced H3K36me3 confers anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2. These results demonstrate that H3K9me2 not only facilitates but orchestrates silencing by actuating antagonistic silencing and anti-silencing pathways, providing insights into the molecular basis underlying proper partitioning of chromatin domains and the creation of metastable epigenetic variation.
Collapse
Affiliation(s)
| | | | - Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Hirayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuriko Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | |
Collapse
|
7
|
Khanduja JS, Joh RI, Perez MM, Paulo JA, Palmieri CM, Zhang J, Gulka AOD, Haas W, Gygi SP, Motamedi M. RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly. Cell 2024; 187:3262-3283.e23. [PMID: 38815580 PMCID: PMC11227895 DOI: 10.1016/j.cell.2024.04.042] [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: 01/19/2023] [Revised: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024]
Abstract
In eukaryotes, the Suv39 family of proteins tri-methylate lysine 9 of histone H3 (H3K9me) to form constitutive heterochromatin. However, how Suv39 proteins are nucleated at heterochromatin is not fully described. In the fission yeast, current models posit that Argonaute1-associated small RNAs (sRNAs) nucleate the sole H3K9 methyltransferase, Clr4/SUV39H, to centromeres. Here, we show that in the absence of all sRNAs and H3K9me, the Mtl1 and Red1 core (MTREC)/PAXT complex nucleates Clr4/SUV39H at a heterochromatic long noncoding RNA (lncRNA) at which the two H3K9 deacetylases, Sir2 and Clr3, also accumulate by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4/SUV39H from the nucleation center in an sRNA-independent manner, generating a basal H3K9me state. This is acted upon by the RNAi machinery to augment and amplify the Clr4/H3K9me signal at centromeres to establish heterochromatin. Overall, our data reveal that lncRNAs and RNA quality control factors can nucleate heterochromatin and function as epigenetic silencers in eukaryotes.
Collapse
Affiliation(s)
- Jasbeer S Khanduja
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Richard I Joh
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Monica M Perez
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christina M Palmieri
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jingyu Zhang
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alex O D Gulka
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Willhelm Haas
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mo Motamedi
- Massachusetts General Hospital Krantz Family Center for Cancer Research and Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA.
| |
Collapse
|
8
|
Yue B, Wang HY, Huang Y, Li S, Ma W, Liu Q, Shao C. Molecular functional characterization of the setdb1 and its potential target gene sox5 illuminate the histone modification-mediated orchestration of gonadal development in Chinese tongue sole (Cynoglossus semilaevis). Gene 2024; 901:148199. [PMID: 38253299 DOI: 10.1016/j.gene.2024.148199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/31/2023] [Accepted: 01/19/2024] [Indexed: 01/24/2024]
Abstract
SET (SuVar3-9, Enhancer of Zeste, Trithorax) domain bifurcated histone lysine methyltransferase 1, setdb1, is the predominant histone lysine methyltransferase catalyzing H3K9me3. Prior studies have illustrated that setdb1 and H3K9me3 critically regulate sex differentiation and gametogenesis. However, the molecular details by which setdb1 is involved in these processes in fish have been poorly reported. Here, we cloned and characterized the setdb1 ORF (open reading frame) sequence from Chinese tongue sole (Cynoglossus semilaevis). The setdb1 ORF sequence was 3,669 bp, encoding a 1,222-amino-acid protein. Phylogenetic analysis showed that setdb1 was structurally conserved. qRT-PCR revealed that setdb1 had a high expression level in the testes at 12 mpf (months post fertilization). Single-cell RNA-seq data at 24 mpf indicated that setdb1 was generally expressed in spermatogenic cells at each stage except for sperm and was centrally expressed in oogonia. H3K9me3 modification was observed in gonads with the immunofluorescence technique. Furthermore, the overexpression experiment suggested that sox5 was a candidate target of setdb1. sox5 was abundantly expressed in male and pseudomale gonads at 24 mpf. Single-cell RNA-seq data showed that sox5 was mainly expressed in spermatogonia and its expression gradually declined with differentiation. Taken together, our findings imply that setdb1 regulates sox5 transcription in gonads, which provides molecular clues into histone modification-mediated orchestration of sex differentiation and gametogenesis.
Collapse
Affiliation(s)
- Bowen Yue
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Yingyi Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Shuo Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Wenxiu Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266237, China.
| |
Collapse
|
9
|
Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [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: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
Collapse
Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| |
Collapse
|
10
|
Sun L, Liu L, Song C, Wang Y, Jin QW. Heat stress-induced activation of MAPK pathway attenuates Atf1-dependent epigenetic inheritance of heterochromatin in fission yeast. eLife 2024; 13:e90525. [PMID: 38289024 PMCID: PMC10863984 DOI: 10.7554/elife.90525] [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: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
Eukaryotic cells are constantly exposed to various environmental stimuli. It remains largely unexplored how environmental cues bring about epigenetic fluctuations and affect heterochromatin stability. In the fission yeast Schizosaccharomyces pombe, heterochromatic silencing is quite stable at pericentromeres but unstable at the mating-type (mat) locus under chronic heat stress, although both loci are within the major constitutive heterochromatin regions. Here, we found that the compromised gene silencing at the mat locus at elevated temperature is linked to the phosphorylation status of Atf1, a member of the ATF/CREB superfamily. Constitutive activation of mitogen-activated protein kinase (MAPK) signaling disrupts epigenetic maintenance of heterochromatin at the mat locus even under normal temperature. Mechanistically, phosphorylation of Atf1 impairs its interaction with heterochromatin protein Swi6HP1, resulting in lower site-specific Swi6HP1 enrichment. Expression of non-phosphorylatable Atf1, tethering Swi6HP1 to the mat3M-flanking site or absence of the anti-silencing factor Epe1 can largely or partially rescue heat stress-induced defective heterochromatic maintenance at the mat locus.
Collapse
Affiliation(s)
- Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Libo Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Chunlin Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Quan-wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| |
Collapse
|
11
|
MacKinnon S, Pagé V, Chen JJ, Shariat-Panahi A, Martin RD, Hébert TE, Tanny JC. Spt5 C-terminal repeat domain phosphorylation and length negatively regulate heterochromatin through distinct mechanisms. PLoS Genet 2023; 19:e1010492. [PMID: 37939109 PMCID: PMC10659198 DOI: 10.1371/journal.pgen.1010492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/20/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
Heterochromatin is a condensed chromatin structure that represses transcription of repetitive DNA elements and developmental genes, and is required for genome stability. Paradoxically, transcription of heterochromatic sequences is required for establishment of heterochromatin in diverse eukaryotic species. As such, components of the transcriptional machinery can play important roles in establishing heterochromatin. How these factors coordinate with heterochromatin proteins at nascent heterochromatic transcripts remains poorly understood. In the model eukaryote Schizosaccharomyces pombe (S. pombe), heterochromatin nucleation can be coupled to processing of nascent transcripts by the RNA interference (RNAi) pathway, or to other post-transcriptional mechanisms that are RNAi-independent. Here we show that the RNA polymerase II processivity factor Spt5 negatively regulates heterochromatin in S. pombe through its C-terminal domain (CTD). The Spt5 CTD is analogous to the CTD of the RNA polymerase II large subunit, and is comprised of multiple repeats of an amino acid motif that is phosphorylated by Cdk9. We provide evidence that genetic ablation of Spt5 CTD phosphorylation results in aberrant RNAi-dependent nucleation of heterochromatin at an ectopic location, as well as inappropriate spread of heterochromatin proximal to centromeres. In contrast, truncation of Spt5 CTD repeat number enhanced RNAi-independent heterochromatin formation and bypassed the requirement for RNAi. We relate these phenotypes to the known Spt5 CTD-binding factor Prf1/Rtf1. This separation of function argues that Spt5 CTD phosphorylation and CTD length restrict heterochromatin through unique mechanisms. More broadly, our findings argue that length and phosphorylation of the Spt5 CTD repeat array have distinct regulatory effects on transcription.
Collapse
Affiliation(s)
- Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jennifer J. Chen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ali Shariat-Panahi
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ryan D. Martin
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Terence E. Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| |
Collapse
|
12
|
Hamali B, Amine AAA, Al-Sady B. Regulation of the heterochromatin spreading reaction by trans-acting factors. Open Biol 2023; 13:230271. [PMID: 37935357 PMCID: PMC10645111 DOI: 10.1098/rsob.230271] [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: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
Heterochromatin is a gene-repressive protein-nucleic acid ultrastructure that is initially nucleated by DNA sequences. However, following nucleation, heterochromatin can then propagate along the chromatin template in a sequence-independent manner in a reaction termed spreading. At the heart of this process are enzymes that deposit chemical information on chromatin, which attracts the factors that execute chromatin compaction and transcriptional or co/post-transcriptional gene silencing. Given that these enzymes deposit guiding chemical information on chromatin they are commonly termed 'writers'. While the processes of nucleation and central actions of writers have been extensively studied and reviewed, less is understood about how the spreading process is regulated. We discuss how the chromatin substrate is prepared for heterochromatic spreading, and how trans-acting factors beyond writer enzymes regulate it. We examine mechanisms by which trans-acting factors in Suv39, PRC2, SETDB1 and SIR writer systems regulate spreading of the respective heterochromatic marks across chromatin. While these systems are in some cases evolutionarily and mechanistically quite distant, common mechanisms emerge which these trans-acting factors exploit to tune the spreading reaction.
Collapse
Affiliation(s)
- Bulut Hamali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ahmed A A Amine
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| |
Collapse
|
13
|
Hisanaga T, Romani F, Wu S, Kowar T, Wu Y, Lintermann R, Fridrich A, Cho CH, Chaumier T, Jamge B, Montgomery SA, Axelsson E, Akimcheva S, Dierschke T, Bowman JL, Fujiwara T, Hirooka S, Miyagishima SY, Dolan L, Tirichine L, Schubert D, Berger F. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 2023; 33:4367-4380.e9. [PMID: 37738971 DOI: 10.1016/j.cub.2023.08.073] [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: 10/28/2022] [Revised: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.
Collapse
Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Teresa Kowar
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Ruth Lintermann
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Arie Fridrich
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chung Hyun Cho
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Liam Dolan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Daniel Schubert
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
14
|
Challal D, Menant A, Goksal C, Leroy E, Al-Sady B, Rougemaille M. A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading. Genetics 2023; 224:iyad108. [PMID: 37279920 PMCID: PMC10411572 DOI: 10.1093/genetics/iyad108] [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: 04/11/2023] [Revised: 04/11/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
Heterochromatic gene silencing relies on combinatorial control by specific histone modifications, the occurrence of transcription, and/or RNA degradation. Once nucleated, heterochromatin propagates within defined chromosomal regions and is maintained throughout cell divisions to warrant proper genome expression and integrity. In the fission yeast Schizosaccharomyces pombe, the Ccr4-Not complex partakes in gene silencing, but its relative contribution to distinct heterochromatin domains and its role in nucleation versus spreading have remained elusive. Here, we unveil major functions for Ccr4-Not in silencing and heterochromatin spreading at the mating type locus and subtelomeres. Mutations of the catalytic subunits Caf1 or Mot2, involved in RNA deadenylation and protein ubiquitinylation, respectively, result in impaired propagation of H3K9me3 and massive accumulation of nucleation-distal heterochromatic transcripts. Both silencing and spreading defects are suppressed upon disruption of the heterochromatin antagonizing factor Epe1. Overall, our results position the Ccr4-Not complex as a critical, dual regulator of heterochromatic gene silencing and spreading.
Collapse
Affiliation(s)
- Drice Challal
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Alexandra Menant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Can Goksal
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, CA 94143, USA
| | - Estelle Leroy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Bassem Al-Sady
- Department of Microbiology & Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| |
Collapse
|
15
|
Heterochromatin and RNAi act independently to ensure genome stability in Mucorales human fungal pathogens. Proc Natl Acad Sci U S A 2023; 120:e2220475120. [PMID: 36745785 PMCID: PMC9963178 DOI: 10.1073/pnas.2220475120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Chromatin modifications play a fundamental role in controlling transcription and genome stability and yet despite their importance, are poorly understood in early-diverging fungi. We present a comprehensive study of histone lysine and DNA methyltransferases across the Mucoromycota, emphasizing heterochromatin formation pathways that rely on the Clr4 complex involved in H3K9-methylation, the Polycomb-repressive complex 2 driving H3K27-methylation, or DNMT1-like methyltransferases that catalyze 5mC DNA methylation. Our analysis uncovered H3K9-methylated heterochromatin as the major chromatin modification repressing transcription in these fungi, which lack both Polycomb silencing and cytosine methylation. Although small RNAs generated by RNA interference (RNAi) pathways facilitate the formation of heterochromatin in many eukaryotic organisms, we show that RNAi is not required to maintain either genomic or centromeric heterochromatin in Mucor. H3K9-methylation and RNAi act independently to control centromeric regions, suggesting a functional subspecialization. Whereas the H3K9 methyltransferase Clr4 and heterochromatin formation are essential for cell viability, RNAi is dispensable for viability yet acts as the main epigenetic, regulatory force repressing transposition of centromeric GremLINE1 elements. Mutations inactivating canonical RNAi lead to rampant transposition and insertional inactivation of targets resulting in antimicrobial drug resistance. This fine-tuned, Rdrp2-dependent RNAi activity is critical for genome stability, restricting GremLINE1 retroelements to the centromeres where they occupy long heterochromatic islands. Taken together, our results suggest that RNAi and heterochromatin formation are independent genome defense and regulatory mechanisms in the Mucorales, contributing to a paradigm shift from the cotranscriptional gene silencing observed in fission yeasts to models in which heterochromatin and RNAi operate independently in early-diverging fungi.
Collapse
|
16
|
MacDonald KM, Nicholson-Puthenveedu S, Tageldein MM, Khasnis S, Arrowsmith CH, Harding SM. Antecedent chromatin organization determines cGAS recruitment to ruptured micronuclei. Nat Commun 2023; 14:556. [PMID: 36732527 PMCID: PMC9894866 DOI: 10.1038/s41467-023-36195-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Micronuclei (MN) are cytosolic bodies that sequester acentric fragments or mis-segregated chromosomes from the primary nucleus. Spontaneous rupture of the MN envelope allows recognition by the viral receptor cyclic GMP-AMP synthase (cGAS), initiating interferon signaling downstream of DNA damage. Here, we demonstrate that MN rupture is permissive but not sufficient for cGAS localization. Chromatin characteristics such as histone 3, lysine 79 dimethylation (H3K79me2) are present in the nucleus before DNA damage, retained in ruptured MN, and regulate cGAS recruitment. cGAS is further responsive to dynamic intra-MN processes occurring prior to rupture, including transcription. MN chromatin tethering via the nucleosome acidic patch is necessary for cGAS-dependent interferon signaling. Our data suggest that both damage-antecedent nuclear chromatin status and MN-contained chromatin organizational changes dictate cGAS recruitment and the magnitude of the cGAS-driven interferon cascade. Our work defines MN as integrative signaling hubs for the cellular response to genotoxic stress.
Collapse
Affiliation(s)
- Kate M MacDonald
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Maha M Tageldein
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarika Khasnis
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Shane M Harding
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada.
- Departments of Radiation Oncology and Immunology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
17
|
Kuzdere T, Flury V, Schalch T, Iesmantavicius V, Hess D, Bühler M. Differential phosphorylation of Clr4 SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis. EMBO Rep 2022; 24:e55928. [PMID: 36408846 PMCID: PMC9827552 DOI: 10.15252/embr.202255928] [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: 08/08/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Methylation of histone H3 at lysine 9 (H3K9) is a hallmark of heterochromatin that plays crucial roles in gene silencing, genome stability, and chromosome segregation. In Schizosaccharomyces pombe, Clr4 mediates both di- and tri-methylation of H3K9. Although H3K9 methylation has been intensely studied in mitotic cells, its role during sexual differentiation remains unclear. Here, we map H3K9 methylation genome-wide during meiosis and show that constitutive heterochromatin temporarily loses H3K9me2 and becomes H3K9me3 when cells commit to meiosis. Cells lacking the ability to tri-methylate H3K9 exhibit meiotic chromosome segregation defects. Finally, the H3K9 methylation switch is accompanied by differential phosphorylation of Clr4 by the cyclin-dependent kinase Cdk1. Our results suggest that a conserved master regulator of the cell cycle controls the specificity of an H3K9 methyltransferase to prevent ectopic H3K9 methylation and to ensure faithful gametogenesis.
Collapse
Affiliation(s)
- Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Valentin Flury
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Thomas Schalch
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| |
Collapse
|
18
|
Fraser CJ, Whitehall SK. Heterochromatin in the fungal plant pathogen, Zymoseptoria tritici: Control of transposable elements, genome plasticity and virulence. Front Genet 2022; 13:1058741. [DOI: 10.3389/fgene.2022.1058741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Heterochromatin is a repressive chromatin state that plays key roles in the functional organisation of eukaryotic genomes. In fungal plant pathogens, effector genes that are required for host colonization tend to be associated with heterochromatic regions of the genome that are enriched with transposable elements. It has been proposed that the heterochromatin environment silences effector genes in the absence of host and dynamic chromatin remodelling facilitates their expression during infection. Here we discuss this model in the context of the key wheat pathogen, Zymoseptoria tritici. We cover progress in understanding the deposition and recognition of heterochromatic histone post translational modifications in Z. tritici and the role that heterochromatin plays in control of genome plasticity and virulence.
Collapse
|
19
|
Esquivel-Chávez A, Maki T, Tsubouchi H, Handa T, Kimura H, Haber JE, Thon G, Iwasaki H. Euchromatin factors HULC and Set1C affect heterochromatin organization and mating-type switching in fission yeast Schizosaccharomyces pombe. Genes Genet Syst 2022; 97:123-138. [PMID: 35908934 DOI: 10.1266/ggs.22-00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mating-type (P or M) of fission yeast Schizosaccharomyces pombe is determined by the transcriptionally active mat1 cassette and is switched by gene conversion using a donor, either mat2 or mat3, located in an adjacent heterochromatin region (mating-type switching; MTS). In the switching process, heterochromatic donors of genetic information are selected based on the P or M cell type and on the action of two recombination enhancers, SRE2 promoting the use of mat2-P and SRE3 promoting the use of mat3-M, leading to replacement of the content of the expressed mat1 cassette. Recently, we found that the histone H3K4 methyltransferase complex Set1C participates in donor selection, raising the question of how a complex best known for its effects in euchromatin controls recombination in heterochromatin. Here, we report that the histone H2BK119 ubiquitin ligase complex HULC functions with Set1C in MTS, as mutants in the shf1, brl1, brl2 and rad6 genes showed defects similar to Set1C mutants and belonged to the same epistasis group as set1Δ. Moreover, using H3K4R and H2BK119R histone mutants and a Set1-Y897A catalytic mutant, we found that ubiquitylation of histone H2BK119 by HULC and methylation of histone H3K4 by Set1C are functionally coupled in MTS. Cell-type biases in MTS in these mutants suggested that HULC and Set1C inhibit the use of the SRE3 recombination enhancer in M cells, thus favoring SRE2 and mat2-P. Consistent with this, imbalanced switching in the mutants was traced to compromised association of the directionality factor Swi6 with the recombination enhancers in M cells. Based on their known effects at other chromosomal locations, we speculate that HULC and Set1C control nucleosome mobility and strand invasion near the SRE elements. In addition, we uncovered distinct effects of HULC and Set1C on histone H3K9 methylation and gene silencing, consistent with additional functions in the heterochromatic domain.
Collapse
Affiliation(s)
- Alfredo Esquivel-Chávez
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Takahisa Maki
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Hideo Tsubouchi
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Testuya Handa
- Institute of Innovative Research, Tokyo Institute of Technology
| | - Hiroshi Kimura
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University
| | | | - Hiroshi Iwasaki
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology
- Institute of Innovative Research, Tokyo Institute of Technology
| |
Collapse
|
20
|
Biswas S, Chen Z, Karslake JD, Farhat A, Ames A, Raiymbek G, Freddolino PL, Biteen JS, Ragunathan K. HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization. SCIENCE ADVANCES 2022; 8:eabk0793. [PMID: 35857444 PMCID: PMC9269880 DOI: 10.1126/sciadv.abk0793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 05/24/2022] [Indexed: 05/31/2023]
Abstract
HP1 proteins traverse a complex and crowded chromatin landscape to bind with low affinity but high specificity to histone H3K9 methylation (H3K9me) and form transcriptionally inactive genomic compartments called heterochromatin. Here, we visualize single-molecule dynamics of an HP1 homolog, the fission yeast Swi6, in its native chromatin environment. By tracking single Swi6 molecules, we identify mobility states that map to discrete biochemical intermediates. Using Swi6 mutants that perturb H3K9me recognition, oligomerization, or nucleic acid binding, we determine how each biochemical property affects protein dynamics. We estimate that Swi6 recognizes H3K9me3 with ~94-fold specificity relative to unmodified nucleosomes in living cells. While nucleic acid binding competes with Swi6 oligomerization, as few as four tandem chromodomains can overcome these inhibitory effects to facilitate Swi6 localization at heterochromatin formation sites. Our studies indicate that HP1 oligomerization is essential to form dynamic, higher-order complexes that outcompete nucleic acid binding to enable specific H3K9me recognition.
Collapse
Affiliation(s)
- Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Joshua D. Karslake
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
| | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda Ames
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L. Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Julie S. Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48104, USA
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
21
|
Liu C, Xiong Q, Li Q, Lin W, Jiang S, Zhang D, Wang Y, Duan X, Gong P, Kang N. CHD7 regulates bone-fat balance by suppressing PPAR-γ signaling. Nat Commun 2022; 13:1989. [PMID: 35418650 PMCID: PMC9007978 DOI: 10.1038/s41467-022-29633-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 03/23/2022] [Indexed: 02/08/2023] Open
Abstract
Chromodomain helicase DNA-binding protein 7 (CHD7), an ATP-dependent eukaryotic chromatin remodeling enzyme, is essential for the development of organs. The mutation of CHD7 is the main cause of CHARGE syndrome, but its function and mechanism in skeletal system remain unclear. Here, we show conditional knockout of Chd7 in bone marrow mesenchymal stem cells (MSCs) and preosteoblasts leads to a pathological phenotype manifested as low bone mass and severely high marrow adiposity. Mechanistically, we identify enhancement of the peroxisome proliferator-activated receptor (PPAR) signaling in Chd7-deficient MSCs. Loss of Chd7 reduces the restriction of PPAR-γ and then PPAR-γ associates with trimethylated histone H3 at lysine 4 (H3K4me3), which subsequently activates the transcription of downstream adipogenic genes and disrupts the balance between osteogenic and adipogenic differentiation. Our data illustrate the pathological manifestations of Chd7 mutation in MSCs and reveal an epigenetic mechanism in skeletal health and diseases. CHD7 is chromatin remodeler and mutations of CHD7 are the main cause of CHARGE syndrome. Here the authors show that conditional knockout of Chd7 in bone marrow mesenchymal stem cells (MSCs) and pre-osteoblasts leads to a skeletal system development disorder in mice and upregulated PPAR signaling, disrupting the balance between osteogenic and adipogenic differentiation.
Collapse
Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Qiuchan Xiong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Qiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Shuang Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Danting Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Yuan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Xiaobo Duan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
| | - Ning Kang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, PR China.
| |
Collapse
|
22
|
Murawska M, Braun S. Chaperoning heterochromatin: new roles of FACT in chromatin silencing. Trends Genet 2022; 38:646-649. [PMID: 35303999 DOI: 10.1016/j.tig.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/11/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
The multitasking histone chaperone FACT (FAcilitates Chromatin Transcription) contributes to actively transcribed euchromatin and repressed heterochromatin. However, its precise role in gene silencing has remained obscure. Here, we discuss new insights into the silent chromatin functions and recruitment mechanisms of FACT, and their possible implications in cell identity and cancer.
Collapse
Affiliation(s)
- Magdalena Murawska
- Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
| | - Sigurd Braun
- Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
23
|
Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nat Commun 2022; 13:1072. [PMID: 35228526 PMCID: PMC8885841 DOI: 10.1038/s41467-022-28471-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/21/2022] [Indexed: 01/04/2023] Open
Abstract
DNA modifications are used to regulate gene expression and defend against invading genetic elements. In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic mark in eukaryotes. Bdelloid rotifers, tiny freshwater invertebrates with transposon-poor genomes rich in foreign genes, lack canonical eukaryotic C5-methyltransferases for 5mC addition, but encode an amino-methyltransferase, N4CMT, captured from bacteria >60 Mya. N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its “histone-read-DNA-write” architecture recognizing silent chromatin marks. Furthermore, amplification of SETDB1 H3K9me3 histone methyltransferases yields variants preferentially binding 4mC-DNA, suggesting “DNA-read-histone-write” partnership to maintain chromatin-based silencing. Our results show how non-native DNA methyl groups can reshape epigenetic systems to silence transposons and demonstrate the potential of horizontal gene transfer to drive regulatory innovation in eukaryotes. Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.
Collapse
|
24
|
De Luca C, Virtuoso A, Cerasuolo M, Gargano F, Colangelo AM, Lavitrano M, Cirillo G, Papa M. Matrix metalloproteinases, purinergic signaling, and epigenetics: hubs in the spinal neuroglial network following peripheral nerve injury. Histochem Cell Biol 2022; 157:557-567. [PMID: 35175413 DOI: 10.1007/s00418-022-02082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
Activation of glial cells (reactive gliosis) and the purinergic pathway, together with metalloproteinase (MMP)-induced remodeling of the neural extracellular matrix (nECM), drive maladaptive changes in the spinal cord following peripheral nerve injury (PNI). We evaluated the effects on spinal maladaptive plasticity through administration of oxidized ATP (oxATP), an antagonist of P2X receptors (P2XR), and/or GM6001, an inhibitor of MMPs, in rats following spared nerve injury (SNI) of the sciatic nerve. With morpho-molecular techniques, we demonstrated a reduction in spinal reactive gliosis and changes in the neuro-glial-nECM crosstalk via expression remodeling of P2XR, nerve growth factor (NGF) receptors (TrkA and p75), and histone deacetylase 2 (HDAC2) after treatments with oxATP/GM6001. Altogether, our data suggest that MMPs and purinergic inhibition have a modulatory impact on key proteins in the neuro-glial-nECM network, acting at different levels from intracellular signaling to epigenetic modifications.
Collapse
Affiliation(s)
- Ciro De Luca
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Assunta Virtuoso
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Michele Cerasuolo
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Francesca Gargano
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Maria Colangelo
- Laboratory of Neuroscience "R. Levi-Montalcini", Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,SYSBIO Centre of Systems Biology ISBE-IT, University of Milano-Bicocca, Milan, Italy
| | | | - Giovanni Cirillo
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Michele Papa
- Neuronal Network Morphology and Systems Biology Lab, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.,SYSBIO Centre of Systems Biology ISBE-IT, University of Milano-Bicocca, Milan, Italy
| |
Collapse
|
25
|
Maeda R, Tachibana M. HP1 maintains protein stability of H3K9 methyltransferases and demethylases. EMBO Rep 2022; 23:e53581. [PMID: 35166421 PMCID: PMC8982598 DOI: 10.15252/embr.202153581] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/09/2022] Open
Abstract
Di- or tri-methylated H3K9 (H3K9me2/3) is an epigenetic mark of heterochromatin. Heterochromatin protein 1 (HP1) specifically recognizes H3K9me2/3, contributing to transcriptional suppression and spread of H3K9me2/3. Here, we demonstrate another role of HP1 in heterochromatin organization: regulation of protein stability of H3K9 methyltransferases (H3K9 MTs) and demethylases (H3K9 DMs). We show that HP1 interaction-defective mutants of H3K9 MTs, Suv39h1 and Setdb1, undergo protein degradation. We further establish mouse embryonic stem cell lines lacking all three HP1 paralogs. In the HP1-deficient cells, Suv39h1, Suv39h2, Setdb1, and G9a/GLP complex decrease at the protein level, and the enzymes are released from chromatin. HP1 mutants that cannot recognize H3K9me2/3 or form dimers cannot stabilize these enzymes, indicating that the tethering of H3K9 MTs to chromatin is critical for their protein stability. We show that HP1 also stabilizes H3K9 DMs, Jmjd1a and Jmjd1b. Our study indicates that mammalian HP1 forms a heterochromatin hub that governs protein stability of H3K9 MTs and H3K9 DMs.
Collapse
Affiliation(s)
- Ryo Maeda
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
| | - Makoto Tachibana
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
| |
Collapse
|
26
|
Oh J, Yeom S, Park J, Lee JS. The regional sequestration of heterochromatin structural proteins is critical to form and maintain silent chromatin. Epigenetics Chromatin 2022; 15:5. [PMID: 35101096 PMCID: PMC8805269 DOI: 10.1186/s13072-022-00435-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/06/2022] [Indexed: 12/20/2022] Open
Abstract
Budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe are good models for heterochromatin study. In S. pombe, H3K9 methylation and Swi6, an ortholog of mammalian HP1, lead to heterochromatin formation. However, S. cerevisiae does not have known epigenetic silencing markers and instead has Sir proteins to regulate silent chromatin formation. Although S. cerevisiae and S. pombe form and maintain heterochromatin via mechanisms that appear to be fundamentally different, they share important common features in the heterochromatin structural proteins. Heterochromatin loci are localized at the nuclear periphery by binding to perinuclear membrane proteins, thereby producing distinct heterochromatin foci, which sequester heterochromatin structural proteins. In this review, we discuss the nuclear peripheral anchoring of heterochromatin foci and its functional relevance to heterochromatin formation and maintenance.
Collapse
Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jiyeon Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, 1 Kangwondeahak-gil, Chuncheon, 24341, Republic of Korea.
| |
Collapse
|
27
|
Yao Y, Wen Q, Zhang T, Yu C, Chan KM, Gan H. Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory. ACS Synth Biol 2022; 11:16-25. [PMID: 34965084 DOI: 10.1021/acssynbio.1c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.
Collapse
Affiliation(s)
- Yuan Yao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qing Wen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianjun Zhang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Chuanhe Yu
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518172, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
28
|
Rizavi HS, Chase KA, Liu C, Gavin H, Rosen C, Xia C, Guidotti A, Sharma RP. Differential H3K9me2 heterochromatin levels and concordant mRNA expression in postmortem brain tissue of individuals with schizophrenia, bipolar, and controls. Front Psychiatry 2022; 13:1006109. [PMID: 36386965 PMCID: PMC9644155 DOI: 10.3389/fpsyt.2022.1006109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
The existence of repressive and durable chromatin assemblies along gene promoters or networks, especially in the brain, is of theoretical and therapeutic relevance in a subset of individuals diagnosed with schizophrenia who experience a chronic, persistent, and treatment-resistant trajectory. We used chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) to generate an epigenomic map that includes differential sites occupied by di-methylated lysine 9 of histone 3 (H3K9me2), a repressive modification that is yet unexplored in human postmortem brain tissue. We have discovered over 150 significantly differential promoter sites in the postmortem prefrontal cortex tissue of individuals diagnosed with schizophrenia (n = 15) when compared to controls (n = 15). Potentially dysregulated gene categories include postsynaptic proteins, processing enzymes (for proproteins, lipids, and oxidative stress), cadherin family genes, the complement system, and peptide hormones. Ten genes with significantly increased or decreased H3K9me2 promoter occupation were selected through statistical analysis, function, or previous GWAS association, and Quantitative RT-PCR (qRT-PCR) was performed on an extended sample of postmortem brain tissue, adding an additional 17 controls, 7 individuals with schizophrenia, and 19 individuals with bipolar samples (n = 32 control, 22 schizophrenia, 19 bipolar). This approach revealed that mRNA expression levels correlated with chromatin modification levels in eight of 10 selected genes, and mRNA expression in the total sample could be predicted by the occupancy of H3K9me2. Utilization of this method and replication in a larger sample open a pathway to durable and restrictive epigenomic assemblies whose accumulation across the lifespan of individuals diagnosed with schizophrenia may explain treatment resistance, and advance therapeutic options.
Collapse
Affiliation(s)
- Hooriyah S Rizavi
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| | - Kayla A Chase
- Department of Biochemistry and Molecular Biology, University of Illinois at Chicago, Chicago, IL, United States
| | - Chunyu Liu
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States.,Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Hannah Gavin
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Cherise Rosen
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Cuihua Xia
- School of Life Sciences, Central South University, Changsha, China
| | - Alessandro Guidotti
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States
| | - Rajiv P Sharma
- Department of Psychiatry, The Psychiatric Institute, University of Illinois at Chicago, Chicago, IL, United States.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| |
Collapse
|
29
|
Tsouris A, Schacherer J, Ishchuk OP. RNA Interference (RNAi ) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata. Methods Mol Biol 2022; 2477:313-330. [PMID: 35524125 DOI: 10.1007/978-1-0716-2257-5_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
After its discovery RNA interference (RNAi) has become a powerful tool to study gene functions in different organisms. RNAi has been applied at genome-wide scale and can be nowadays performed using high-throughput automated systems (robotics). The simplest RNAi process requires the expression of two genes (Dicer and Argonaute) to function. To initiate the silencing, constructs generating either double-strand RNA or antisense RNA are required. Recently, RNAi was reconstituted by expressing Saccharomyces castellii genes in the human pathogenic yeast Candida glabrata and was used to identify new genes related to the virulence of this pathogen.In this chapter, we describe a method to make the C. glabrata pathogenic yeast competent for RNAi and to use RNA silencing as a tool for low- or high-resolution phenotypic screening in this species.
Collapse
Affiliation(s)
- Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Olena P Ishchuk
- Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
30
|
The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states. Cell Rep 2021; 37:109944. [PMID: 34731638 PMCID: PMC8608617 DOI: 10.1016/j.celrep.2021.109944] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin formation requires three distinct steps: nucleation, self-propagation (spreading) along the chromosome, and faithful maintenance after each replication cycle. Impeding any of those steps induces heterochromatin defects and improper gene expression. The essential histone chaperone FACT (facilitates chromatin transcription) has been implicated in heterochromatin silencing, but the mechanisms by which FACT engages in this process remain opaque. Here, we pinpoint its function to the heterochromatin spreading process in fission yeast. FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries. FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading. FACT mutant spreading defects are suppressed by removal of the H3K9 methylation antagonist Epe1. Together, our study identifies FACT as a histone chaperone that promotes heterochromatin spreading and lends support to the model that regulated histone turnover controls the propagation of repressive methylation marks. Heterochromatin establishment requires distinct nucleation and spreading steps. Murawska et al. show that the conserved and essential histone chaperone FACT facilitates the heterochromatin spreading process by maintaining low heterochromatic histone turnover, which enables a productive H3K9 trimethylation step by the methyltransferase Clr4 in fission yeast.
Collapse
|
31
|
Stirpe A, Guidotti N, Northall SJ, Kilic S, Hainard A, Vadas O, Fierz B, Schalch T. SUV39 SET domains mediate crosstalk of heterochromatic histone marks. eLife 2021; 10:62682. [PMID: 34524082 PMCID: PMC8443253 DOI: 10.7554/elife.62682] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast Schizosaccharomyces pombe, and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.
Collapse
Affiliation(s)
- Alessandro Stirpe
- Department of Molecular Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nora Guidotti
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sarah J Northall
- Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom.,Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Sinan Kilic
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Hainard
- University Medical Center, University of Geneva, Geneva, Switzerland
| | - Oscar Vadas
- School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Thomas Schalch
- Department of Molecular Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.,Leicester Institute for Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom.,Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
32
|
Li CL, Pu M, Wang W, Chaturbedi A, Emerson FJ, Lee SS. Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009432. [PMID: 34506495 PMCID: PMC8457455 DOI: 10.1371/journal.pgen.1009432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/22/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic alterations occur as organisms age, and lead to chromatin deterioration, loss of transcriptional silencing and genomic instability. Dysregulation of the epigenome has been associated with increased susceptibility to age-related disorders. In this study, we aimed to characterize the age-dependent changes of the epigenome and, in turn, to understand epigenetic processes that drive aging phenotypes. We focused on the aging-associated changes in the repressive histone marks H3K9me3 and H3K27me3 in C. elegans. We observed region-specific gain and loss of both histone marks, but the changes are more evident for H3K9me3. We further found alteration of heterochromatic boundaries in aged somatic tissues. Interestingly, we discovered that the most statistically significant changes reflected H3K9me3-marked regions that are formed during aging, and are absent in developing worms, which we termed "aging-specific repressive regions" (ASRRs). These ASRRs preferentially occur in genic regions that are marked by high levels of H3K9me2 and H3K36me2 in larval stages. Maintenance of high H3K9me2 levels in these regions have been shown to correlate with a longer lifespan. Next, we examined whether the changes in repressive histone marks lead to de-silencing of repetitive DNA elements, as reported for several other organisms. We observed increased expression of active repetitive DNA elements but not global re-activation of silent repeats in old worms, likely due to the distributed nature of repetitive elements in the C. elegans genome. Intriguingly, CELE45, a putative short interspersed nuclear element (SINE), was greatly overexpressed at old age and upon heat stress. SINEs have been suggested to regulate transcription in response to various cellular stresses in mammals. It is likely that CELE45 RNAs also play roles in stress response and aging in C. elegans. Taken together, our study revealed significant and specific age-dependent changes in repressive histone modifications and repetitive elements, providing important insights into aging biology.
Collapse
Affiliation(s)
- Cheng-Lin Li
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mintie Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Wenke Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Felicity J Emerson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
33
|
Epimutations and mutations, nurturing phenotypic diversity. Genetica 2021; 150:171-181. [PMID: 34114171 DOI: 10.1007/s10709-021-00124-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/26/2021] [Indexed: 12/22/2022]
Abstract
Epimutations and mutations are two dissimilar mechanisms that have contributed to the phenotypic diversities in organisms. Though dissimilar, many previous studies have revealed that the consequences of epimutations and mutations are not mutually exclusive. DNA rich in epigenetic modifications can be prone to mutations and vice versa. In order to get a better insight into the molecular evolution in organisms, it is important to consider the information of both genetic and epigenetic changes in their genomes. Understanding the similarities and differences between the consequences of epimutations and mutations is required for a better interpretation of phenotypic diversities in organisms. Factors contributing to epigenetic changes such as paramutations and mutation hotspots and, the correlation of the interdependence of mutations and epigenetic changes in DNA are important aspects that need to be considered for molecular evolutionary studies. Thus, this review explains what epimutations are, their causes, how they are similar/different from mutations, and the influence of epigenetic changes and mutations on each other, further emphasizing how molecular evolution involving both mutations and epimutations can lead to speciation. Considering this approach will aid in reorganizing taxonomic classifications, importantly, solving disparities in species identification.
Collapse
|
34
|
Ren X, Wang R, Yu XT, Cai B, Guo F. Regulation of histone H3 lysine 9 methylation in inflammation. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1931477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xin Ren
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Rong Wang
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Xiao-ting Yu
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Bo Cai
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Fei Guo
- Department of Burn, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| |
Collapse
|
35
|
Krug B, Harutyunyan AS, Deshmukh S, Jabado N. Polycomb repressive complex 2 in the driver's seat of childhood and young adult brain tumours. Trends Cell Biol 2021; 31:814-828. [PMID: 34092471 DOI: 10.1016/j.tcb.2021.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/19/2022]
Abstract
Deregulation of the epigenome underlies oncogenesis in numerous primary brain tumours in children and young adults. In this review, we describe how recurrent mutations in isocitrate dehydrogenases or histone 3 variants (oncohistones) in gliomas, expression of the oncohistone mimic enhancer of Zeste homologs inhibiting protein (EZHIP) in a subgroup of ependymoma, and epigenetic alterations in other embryonal tumours promote oncogenicity. We review the proposed mechanisms of cellular transformation, current tumorigenesis models and their link to development. We further stress the narrow developmental windows permissive to their oncogenic potential and how this may stem from converging effects deregulating polycomb repressive complex (PRC)2 function and targets. As altered chromatin states may be reversible, improved understanding of aberrant cancer epigenomes could orient the design of effective therapies.
Collapse
Affiliation(s)
- Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Shriya Deshmukh
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Division of Experimental Medicine, McGill University, Montreal, QC, Canada; Department of Pediatrics, McGill University, Montreal, QC, Canada; The Research Institute of the McGill University Health Center, Montreal, H4A 3J, Canada.
| |
Collapse
|
36
|
Oki M, Masai H. Regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle. J Biochem 2021; 169:629-632. [PMID: 33772590 DOI: 10.1093/jb/mvab040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 11/12/2022] Open
Abstract
HP1 (Heterochromatin Protein 1), a key factor for the formation of heterochromatin, binds to the methylated lysine 9 of histone H3 (H3K9me), and represses transcription. While the H3K9me mark and HP1 binding are thought to be faithfully propagated to daughter cells, the heterochromatin structure could be dynamically regulated during cell cycle. As evidenced by the well-known phenomenon called Position Effect Variegation (PEV), heterochromatin structure is dynamically and stochastically altered during developmental processes, and thus the expression of genes within or in the vicinity of heterochromatin could be affected by mutations in factors regulating DNA replication as well as by other epigenetic factors. Recent reports show that HP1 also plays an important role in the maintenance and transmission of chromosomes. Like many other factors ensuring faithful chromosome segregation, HP1 family proteins are subjected to posttranslational modifications, most notably phosphorylation, in a cell-cycle dependent manner. Recent studies identified a conserved phosphorylation site that profoundly affects the functions of HP1 during mitotic phase. In this commentary, we discuss dynamic regulation of HP1 protein by phosphorylation during transcriptional repression and cell cycle.
Collapse
Affiliation(s)
- Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, JAPAN
| | - Hisao Masai
- Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, JAPAN, Tel: 81-3-5316-3220
| |
Collapse
|
37
|
Misova I, Pitelova A, Budis J, Gazdarica J, Sedlackova T, Jordakova A, Benko Z, Smondrkova M, Mayerova N, Pichlerova K, Strieskova L, Prevorovsky M, Gregan J, Cipak L, Szemes T, Polakova SB. Repression of a large number of genes requires interplay between homologous recombination and HIRA. Nucleic Acids Res 2021; 49:1914-1934. [PMID: 33511417 PMCID: PMC7913671 DOI: 10.1093/nar/gkab027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
Collapse
Affiliation(s)
- Ivana Misova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Anna Jordakova
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Zsigmond Benko
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, H-4010 Debrecen, Hungary
| | - Maria Smondrkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Karoline Pichlerova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Lucia Strieskova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Martin Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| |
Collapse
|
38
|
Lax C, Tahiri G, Patiño-Medina JA, Cánovas-Márquez JT, Pérez-Ruiz JA, Osorio-Concepción M, Navarro E, Calo S. The Evolutionary Significance of RNAi in the Fungal Kingdom. Int J Mol Sci 2020; 21:E9348. [PMID: 33302447 PMCID: PMC7763443 DOI: 10.3390/ijms21249348] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/18/2022] Open
Abstract
RNA interference (RNAi) was discovered at the end of last millennium, changing the way scientists understood regulation of gene expression. Within the following two decades, a variety of different RNAi mechanisms were found in eukaryotes, reflecting the evolutive diversity that RNAi entails. The essential silencing mechanism consists of an RNase III enzyme called Dicer that cleaves double-stranded RNA (dsRNA) generating small interfering RNAs (siRNAs), a hallmark of RNAi. These siRNAs are loaded into the RNA-induced silencing complex (RISC) triggering the cleavage of complementary messenger RNAs by the Argonaute protein, the main component of the complex. Consequently, the expression of target genes is silenced. This mechanism has been thoroughly studied in fungi due to their proximity to the animal phylum and the conservation of the RNAi mechanism from lower to higher eukaryotes. However, the role and even the presence of RNAi differ across the fungal kingdom, as it has evolved adapting to the particularities and needs of each species. Fungi have exploited RNAi to regulate a variety of cell activities as different as defense against exogenous and potentially harmful DNA, genome integrity, development, drug tolerance, or virulence. This pathway has offered versatility to fungi through evolution, favoring the enormous diversity this kingdom comprises.
Collapse
Affiliation(s)
- Carlos Lax
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Ghizlane Tahiri
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - José Alberto Patiño-Medina
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán CP 58030, Mexico;
| | - José T. Cánovas-Márquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - José A. Pérez-Ruiz
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Macario Osorio-Concepción
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Eusebio Navarro
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain; (C.L.); (G.T.); (J.T.C.-M.); (J.A.P.-R.); (M.O.-C.); (E.N.)
| | - Silvia Calo
- School of Natural and Exact Sciences, Pontificia Universidad Católica Madre y Maestra, 51033 Santiago de los Caballeros, Dominican Republic
| |
Collapse
|
39
|
Khella MS, Bröhm A, Weirich S, Jeltsch A. Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation. Int J Mol Sci 2020; 21:ijms21228832. [PMID: 33266419 PMCID: PMC7700585 DOI: 10.3390/ijms21228832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Clr4 is a histone H3 lysine 9 methyltransferase in Schizosaccharomyces pombe that is essential for heterochromatin formation. Previous biochemical and structural studies have shown that Clr4 is in an autoinhibited state in which an autoregulatory loop (ARL) blocks the active site. Automethylation of lysine residues in the ARL relieves autoinhibition. To investigate the mechanism of Clr4 regulation by autoinhibition and automethylation, we exchanged residues in the ARL by site-directed mutagenesis leading to stimulation or inhibition of automethylation and corresponding changes in Clr4 catalytic activity. Furthermore, we demonstrate that Clr4 prefers monomethylated (H3K9me1) over unmodified (H3K9me0) histone peptide substrates, similar to related human enzymes and, accordingly, H3K9me1 is more efficient in overcoming autoinhibition. Due to enzyme activation by automethylation, we observed a sigmoidal dependence of Clr4 activity on the AdoMet concentration, with stimulation at high AdoMet levels. In contrast, an automethylation-deficient mutant showed a hyperbolic Michaelis–Menten type relationship. These data suggest that automethylation of the ARL could act as a sensor for AdoMet levels in cells and regulate the generation and maintenance of heterochromatin accordingly. This process could connect epigenome modifications with the metabolic state of cells. As other human protein lysine methyltransferases (for example, PRC2) also use automethylation/autoinhibition mechanisms, our results may provide a model to describe their regulation as well.
Collapse
Affiliation(s)
- Mina S. Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo 11566, Egypt
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
- Correspondence: or ; Tel.: +49-711-685-64390; Fax: +49-711-685-64392
| |
Collapse
|
40
|
Storck WK, Bicocca VT, Rountree MR, Honda S, Ormsby T, Selker EU. LSD1 prevents aberrant heterochromatin formation in Neurospora crassa. Nucleic Acids Res 2020; 48:10199-10210. [PMID: 32946564 PMCID: PMC7544195 DOI: 10.1093/nar/gkaa724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/17/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.
Collapse
Affiliation(s)
- William K Storck
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Vincent T Bicocca
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Michael R Rountree
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Tereza Ormsby
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
41
|
Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes. Nucleic Acids Res 2020; 48:5953-5966. [PMID: 32396165 PMCID: PMC7293002 DOI: 10.1093/nar/gkaa369] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/01/2023] Open
Abstract
The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.
Collapse
Affiliation(s)
- Soonkap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Sophie J M Piquerez
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Juan S Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Emmanouil Mastorakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Natalia Y Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles 78000, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Heribert Hirt
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Vardis Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France.,Institut Universitaire de France (IUF)
| |
Collapse
|
42
|
Wong CYY, Lee BCH, Yuen KWY. Epigenetic regulation of centromere function. Cell Mol Life Sci 2020; 77:2899-2917. [PMID: 32008088 PMCID: PMC11105045 DOI: 10.1007/s00018-020-03460-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/23/2019] [Accepted: 01/10/2020] [Indexed: 12/20/2022]
Abstract
The centromere is a specialized region on the chromosome that directs equal chromosome segregation. Centromeres are usually not defined by DNA sequences alone. How centromere formation and function are determined by epigenetics is still not fully understood. Active centromeres are often marked by the presence of centromeric-specific histone H3 variant, centromere protein A (CENP-A). How CENP-A is assembled into the centromeric chromatin during the cell cycle and propagated to the next cell cycle or the next generation to maintain the centromere function has been intensively investigated. In this review, we summarize current understanding of how post-translational modifications of CENP-A and other centromere proteins, centromeric and pericentric histone modifications, non-coding transcription and transcripts contribute to centromere function, and discuss their intricate relationships and potential feedback mechanisms.
Collapse
Affiliation(s)
- Charmaine Yan Yu Wong
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Bernard Chi Hang Lee
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China.
| |
Collapse
|
43
|
Shipkovenska G, Durango A, Kalocsay M, Gygi SP, Moazed D. A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin. eLife 2020; 9:54341. [PMID: 32491985 PMCID: PMC7269676 DOI: 10.7554/elife.54341] [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: 12/10/2019] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a Schizosaccharomyces pombe inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.
Collapse
Affiliation(s)
- Gergana Shipkovenska
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Alexander Durango
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Marian Kalocsay
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, United States
| |
Collapse
|
44
|
Marayati BF, Tucker JF, De La Cerda DA, Hou TC, Chen R, Sugiyama T, Pease JB, Zhang K. The Catalytic-Dependent and -Independent Roles of Lsd1 and Lsd2 Lysine Demethylases in Heterochromatin Formation in Schizosaccharomyces pombe. Cells 2020; 9:E955. [PMID: 32295063 PMCID: PMC7226997 DOI: 10.3390/cells9040955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/30/2022] Open
Abstract
In eukaryotes, heterochromatin plays a critical role in organismal development and cell fate acquisition, through regulating gene expression. The evolutionarily conserved lysine-specific demethylases, Lsd1 and Lsd2, remove mono- and dimethylation on histone H3, serving complex roles in gene expression. In the fission yeast Schizosaccharomyces pombe, null mutations of Lsd1 and Lsd2 result in either severe growth defects or inviability, while catalytic inactivation causes minimal defects, indicating that Lsd1 and Lsd2 have essential functions beyond their known demethylase activity. Here, we show that catalytic mutants of Lsd1 or Lsd2 partially assemble functional heterochromatin at centromeres in RNAi-deficient cells, while the C-terminal truncated alleles of Lsd1 or Lsd2 exacerbate heterochromatin formation at all major heterochromatic regions, suggesting that Lsd1 and Lsd2 repress heterochromatic transcripts through mechanisms both dependent on and independent of their catalytic activities. Lsd1 and Lsd2 are also involved in the establishment and maintenance of heterochromatin. At constitutive heterochromatic regions, Lsd1 and Lsd2 regulate one another and cooperate with other histone modifiers, including the class II HDAC Clr3 and the Sirtuin family protein Sir2 for gene silencing, but not with the class I HDAC Clr6. Our findings explore the roles of lysine-specific demethylases in epigenetic gene silencing at heterochromatic regions.
Collapse
Affiliation(s)
- Bahjat F. Marayati
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - James F. Tucker
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - David A. De La Cerda
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Tien-Chi Hou
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Rong Chen
- Physiology and pharmacology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China;
| | - James B. Pease
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| | - Ke Zhang
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC 27109, USA; (B.F.M.); (J.F.T.); (D.A.D.L.C.); (T.-C.H.); (J.B.P.)
| |
Collapse
|
45
|
Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin. Sci Rep 2020; 10:6055. [PMID: 32269268 PMCID: PMC7142091 DOI: 10.1038/s41598-020-63209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/26/2020] [Indexed: 01/24/2023] Open
Abstract
Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.
Collapse
|
46
|
Taglini F, Chapman E, van Nues R, Theron E, Bayne EH. Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast. Nucleic Acids Res 2020; 48:1239-1253. [PMID: 31822915 PMCID: PMC7026591 DOI: 10.1093/nar/gkz1157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/12/2019] [Accepted: 11/28/2019] [Indexed: 01/04/2023] Open
Abstract
Constitutive domains of repressive heterochromatin are maintained within the fission yeast genome through self-reinforcing mechanisms involving histone methylation and small RNAs. Non-coding RNAs generated from heterochromatic regions are processed into small RNAs by the RNA interference pathway, and are subject to silencing through both transcriptional and post-transcriptional mechanisms. While the pathways involved in maintenance of the repressive heterochromatin state are reasonably well understood, less is known about the requirements for its establishment. Here, we describe a novel role for the post-transcriptional regulatory factor Mkt1 in establishment of heterochromatin at pericentromeres in fission yeast. Loss of Mkt1 does not affect maintenance of existing heterochromatin, but does affect its recovery following depletion, as well as de novo establishment of heterochromatin on a mini-chromosome. Pathway dissection revealed that Mkt1 is required for RNAi-mediated post-transcriptional silencing, downstream of small RNA production. Mkt1 physically associates with pericentromeric transcripts, and is additionally required for maintenance of silencing and heterochromatin at centromeres when transcriptional silencing is impaired. Our findings provide new insight into the mechanism of RNAi-mediated post-transcriptional silencing in fission yeast, and unveil an important role for post-transcriptional silencing in establishment of heterochromatin that is dispensable when full transcriptional silencing is imposed.
Collapse
Affiliation(s)
- Francesca Taglini
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Elliott Chapman
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rob van Nues
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Emmanuelle Theron
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Elizabeth H Bayne
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
47
|
Liu Y, Zhang M, Xie R, Zhang F, Wang S, Pan X, Wang S, Zhuang Z. The Methyltransferase AflSet1 Is Involved in Fungal Morphogenesis, AFB1 Biosynthesis, and Virulence of Aspergillus flavus. Front Microbiol 2020; 11:234. [PMID: 32132990 PMCID: PMC7040179 DOI: 10.3389/fmicb.2020.00234] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/31/2020] [Indexed: 11/17/2022] Open
Abstract
The filament fungal pathogen, Aspergillus flavus, spreads worldwide and contaminates several important crops. Histone posttranslational modifications are deeply involved in fungal development and virulence, but the biological function of the histone methyltransferase AflSet1 in A. flavus is still unknown. In the study, Aflset1 deletion strain was constructed through homologous recombination, and it was found that AflSet1 up-regulates hyphae growth, and promotes conidiation by sporulation regulation genes: abaA and brlA. It was also found that AflSet1 involves in sclerotia formation and AFB1 biosynthesis via sclerotia related transcriptional factors and orthodox AFB1 synthesis pathway, respectively. Crop models revealed that AflSet1 plays critical roles in colonization and AFB1 production on crop kernels. Lipase activity analysis suggested that AflSet1 affects fungal virulence to crops via digestive enzymes. Stresses tests revealed that AflSet1 is deeply involved in fungal resistance against osmotic, oxidative and cell membrane stress. The preparation of N_SET, SET domain deletion mutants and H988K mutant revealed that both domains play critical roles in fungal development and AFB1 production, and that H988 is very important in executing biological functions on morphogenesis and AFB1 synthesis. Subcellular location analysis revealed that AflSet1 is stably accumulated in nuclei in both spore germination and hyphae growth stages, even under the stress of SDS. Through immunoblot analysis, it was found that AflSet1 methylates H3K4me2 and me3 as well as H3K9me2. This study provides a solid evidence to discover the biological functions of histone methyltransferase in pathogenic fungi.
Collapse
Affiliation(s)
- Yaju Liu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengjuan Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui Xie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
48
|
Newman SA. Cell differentiation: What have we learned in 50 years? J Theor Biol 2020; 485:110031. [DOI: 10.1016/j.jtbi.2019.110031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
|
49
|
Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Mol Cell 2019; 77:51-66.e8. [PMID: 31784357 DOI: 10.1016/j.molcel.2019.10.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/19/2019] [Accepted: 10/11/2019] [Indexed: 12/31/2022]
Abstract
Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.
Collapse
|
50
|
Saha P, Mishra RK. Heterochromatic hues of transcription-the diverse roles of noncoding transcripts from constitutive heterochromatin. FEBS J 2019; 286:4626-4641. [PMID: 31644838 DOI: 10.1111/febs.15104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/19/2019] [Accepted: 10/22/2019] [Indexed: 02/05/2023]
Abstract
Constitutive heterochromatin has been canonically considered as transcriptionally inert chromosomal regions, which silences the repeats and transposable elements (TEs), to preserve genomic integrity. However, several studies from the last few decades show that centromeric and pericentromeric regions also get transcribed and these transcripts are involved in multiple cellular processes. Regulation of such spatially and temporally controlled transcription and their relevance to heterochromatin function have emerged as an active area of research in chromatin biology. Here, we review the myriad of roles of noncoding transcripts from the constitutive heterochromatin in the establishment and maintenance of heterochromatin, kinetochore assembly, germline epigenome maintenance, early development, and diseases. Contrary to general expectations, there are active protein-coding genes in the heterochromatin although the regulatory mechanisms of their expression are largely unknown. We propose plausible hypotheses to explain heterochromatic gene expression using Drosophila melanogaster as a model, and discuss the evolutionary significance of these transcripts in the context of Drosophilid speciation. Such analyses offer insights into the regulatory pathways and functions of heterochromatic transcripts which open new avenues for further investigation.
Collapse
Affiliation(s)
- Parna Saha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|