1
|
Su R, Zhou M, Lin J, Shan G, Huang C. A circular RNA-gawky-chromatin regulatory axis modulates stress-induced transcription. Nucleic Acids Res 2024; 52:3702-3721. [PMID: 38416578 PMCID: PMC11039993 DOI: 10.1093/nar/gkae157] [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: 11/22/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
In response to heavy metal stress, the RNA-binding protein (RBP) gawky translocates into the nucleus and acts as a chromatin-interacting factor to activate the transcription of many stress-responsive genes. However, the upstream regulators of gawky-mediated transcription and their mechanistic details remain unknown. Here, we identified a class of metal-responsive element-containing circRNAs (MRE circRNAs) which specifically interact with gawky during copper stress. Using classic stress-responsive genes as a readout (Drosophila MT), we found that overexpression of MRE circRNAs led to a significant repression in stress-induced transcription. Mechanistically, MRE circRNAs promote the dissociation of gawky from chromatin and increase its aberrant cytoplasmic accumulation, which ultimately impedes the loading of RNA polymerase II to the active gene loci. The MRE motif serves as an important RNA regulon for maintaining the circRNA-gawky interaction, loss of which impaired the inhibitory effects of MRE circRNAs on gawky. Through RNA-seq analyses, we then identified over 500 additional stress-responsive genes whose induced transcription was attenuated upon MRE circRNA overexpression. Finally, we uncovered the physiological relevance of MRE circRNA-mediated regulation in cellular defense against copper overloading. Taken together, this study proposes that the circRNA-RBP-chromatin axis may represent a fundamental regulatory network for gene expression in eukaryotic cells.
Collapse
Affiliation(s)
- Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Min Zhou
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| |
Collapse
|
2
|
Liu Y, Bai S, Li X, Jin C, Wang Z, Zhai J, Li W, Li H, Liu J, Zhang Q. Chronic low salinity stress rescued masculinization effect in farmed Cynoglossus semilaevis population. MARINE POLLUTION BULLETIN 2024; 200:116074. [PMID: 38290369 DOI: 10.1016/j.marpolbul.2024.116074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Salinity, being an indispensable abiotic factor crucial for the survival of marine organisms, has demonstrated diverse alterations globally in response to the current trend of global warming. In this study, the effect of chronic low salinity stress on teleosts' sex differentiation was investigated using Cynoglossus semilaevis, an economically important fish with both genetic and environmental sex determination system. The cultivation experiment was conducted employing artificially simulated seawater of 20 ppt and ambient sea water of 30 ppt to rear juveniles C. semilaevis. Throughout the experiment, the growth performance was assessed and the histology of gonadal development was examined, a significantly lower masculinization rate was observed in LS group. To gain further insights, transcriptome analysis was conducted using raw reads obtained from 53 libraries derived from gonads of 55 days post fertilization (dpf) and 100 dpf juveniles in both LS and CT groups. GO/KEGG enrichment were further proceeded, Terms and pathways involved in reproduction ability, germ cell proliferation, immune function, steroid metabolism etc., were illuminated and a possible crosstalk between HPI and HPG axis was proposed. WGCNA was conducted and two hub genes, hspb8-like and Histone H2A.V were exhibited to be of great significance in the changes of masculinization rate. Our findings provided solid reference for sex differentiation study of GSD + ESD species in a constantly changing ocean environment, as well as practice guiding significance for the environmental management for the culture of C. semilaevis.
Collapse
Affiliation(s)
- Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Shujun Bai
- Laboratory of Fisheries Oceanography, College of Fisheries, Ocean University of China, Qingdao, China
| | - Xiaoqi Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Chaofan Jin
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Zhigang Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Jieming Zhai
- Laizhou Mingbo Aquatic Co., Ltd., Laizhou, China
| | - Wensheng Li
- Laizhou Mingbo Aquatic Co., Ltd., Laizhou, China
| | - Hengde Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Hainan Yazhou Bay Seed Laboratory, Sanya, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
3
|
Prozzillo Y, Fattorini G, Ferreri D, Leo M, Dimitri P, Messina G. Knockdown of DOM/Tip60 Complex Subunits Impairs Male Meiosis of Drosophila melanogaster. Cells 2023; 12:1348. [PMID: 37408183 DOI: 10.3390/cells12101348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/22/2023] [Accepted: 05/02/2023] [Indexed: 07/07/2023] Open
Abstract
ATP-dependent chromatin remodeling complexes are involved in nucleosome sliding and eviction and/or the incorporation of histone variants into chromatin to facilitate several cellular and biological processes, including DNA transcription, replication and repair. The DOM/TIP60 chromatin remodeling complex of Drosophila melanogaster contains 18 subunits, including the DOMINO (DOM), an ATPase that catalyzes the exchange of the canonical H2A with its variant (H2A.V), and TIP60, a lysine-acetyltransferase that acetylates H4, H2A and H2A.V histones. In recent decades, experimental evidence has shown that ATP-dependent chromatin remodeling factors, in addition to their role in chromatin organization, have a functional relevance in cell division. In particular, emerging studies suggested the direct roles of ATP-dependent chromatin remodeling complex subunits in controlling mitosis and cytokinesis in both humans and D. melanogaster. However, little is known about their possible involvement during meiosis. The results of this work show that the knockdown of 12 of DOM/TIP60 complex subunits generates cell division defects that, in turn, cause total/partial sterility in Drosophila males, providing new insights into the functions of chromatin remodelers in cell division control during gametogenesis.
Collapse
Affiliation(s)
- Yuri Prozzillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Gaia Fattorini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), Sapienza University of Rome, 00185 Rome, Italy
| | - Diego Ferreri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Manuela Leo
- Department of Sciences and Technologies, University of Sannio, 82100 Benevento, Italy
| | - Patrizio Dimitri
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Giovanni Messina
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
- Pasteur Institute, Fondazione Cenci-Bolognetti, 00161 Rome, Italy
- Department of Biotechnology and Biosciences, Milano-Bicocca University, 20126 Milan, Italy
| |
Collapse
|
4
|
Escobedo SE, McGovern SE, Jauregui-Lozano JP, Stanhope SC, Anik P, Singhal K, DeBernardis R, Weake VM. Targeted RNAi screen identifies transcriptional mechanisms that prevent premature degeneration of adult photoreceptors. FRONTIERS IN EPIGENETICS AND EPIGENOMICS 2023; 1:1187980. [PMID: 37901602 PMCID: PMC10603763 DOI: 10.3389/freae.2023.1187980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to identify the transcriptional mechanisms that are necessary to maintain photoreceptor viability and function during aging. To do this, we performed a targeted photoreceptor-specific RNAi screen in Drosophila to identify transcriptional regulators whose knockdown results in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of transcription factors, chromatin remodelers, and histone modifiers, we identified 18 high-confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. These 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show similar changes in gene expression to those observed in photoreceptors with advanced age. Together, our data suggest that dysregulation of factors involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate but might also contribute to an increased risk of retinal degeneration.
Collapse
Affiliation(s)
- Spencer E. Escobedo
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Sarah E. McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sarah C. Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Paul Anik
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kratika Singhal
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ryan DeBernardis
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Vikki M. Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
5
|
Simmons JR, An R, Amankwaa B, Zayac S, Kemp J, Labrador M. Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila. PLoS Genet 2022; 18:e1010396. [PMID: 36197938 PMCID: PMC9576066 DOI: 10.1371/journal.pgen.1010396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/17/2022] [Accepted: 08/24/2022] [Indexed: 11/27/2022] Open
Abstract
Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
Collapse
Affiliation(s)
- James R. Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Shannon Zayac
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Justin Kemp
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
6
|
Feng Y, Zhang Y, Lin Z, Ye X, Lin X, Lv L, Lin Y, Sun S, Qi Y, Lin X. Chromatin remodeler Dmp18 regulates apoptosis by controlling H2Av incorporation in Drosophila imaginal disc development. PLoS Genet 2022; 18:e1010395. [PMID: 36166470 PMCID: PMC9514664 DOI: 10.1371/journal.pgen.1010395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Programmed Cell Death (PCD) or apoptosis is a highly conserved biological process and plays essential roles both in the development and stress context. In Drosophila, expression of pro-apoptotic genes, including reaper (rpr), head involution defective (hid), grim, and sickle (skl), is sufficient to induce cell death. Here, we demonstrate that the chromatin remodeler Dmp18, the homolog of mammalian Znhit1, plays a crucial role in regulating apoptosis in eye and wing development. We showed that loss of Dmp18 disrupted eye and wing development, up-regulated transcription of pro-apoptotic genes, and induced apoptosis. Inhibition of apoptosis suppressed the eye defects caused by Dmp18 deletion. Furthermore, loss of Dmp18 disrupted H2Av incorporation into chromatin, promoted H3K4me3, but reduced H3K27me3 modifications on the TSS regions of pro-apoptotic genes. These results indicate that Dmp18 negatively regulates apoptosis by mediating H2Av incorporation and histone H3 modifications at pro-apoptotic gene loci for transcriptional regulation. Our study uncovers the role of Dmp18 in regulating apoptosis in Drosophila eye and wing development and provides insights into chromatin remodeling regulating apoptosis at the epigenetic levels.
Collapse
Affiliation(s)
- Ying Feng
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- * E-mail: (YF); (YQ); (XL)
| | - Yan Zhang
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhiqing Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaolei Ye
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xue Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lixiu Lv
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (YF); (YQ); (XL)
| | - Xinhua Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai, China
- * E-mail: (YF); (YQ); (XL)
| |
Collapse
|
7
|
Wichmann J, Pitt C, Eccles S, Garnham AL, Li-Wai-Suen CSN, May R, Allan E, Wilcox S, Herold MJ, Smyth GK, Monahan BJ, Thomas T, Voss AK. Loss of TIP60 (KAT5) abolishes H2AZ lysine 7 acetylation and causes p53, INK4A, and ARF-independent cell cycle arrest. Cell Death Dis 2022; 13:627. [PMID: 35853868 PMCID: PMC9296491 DOI: 10.1038/s41419-022-05055-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
Abstract
Histone acetylation is essential for initiating and maintaining a permissive chromatin conformation and gene transcription. Dysregulation of histone acetylation can contribute to tumorigenesis and metastasis. Using inducible cre-recombinase and CRISPR/Cas9-mediated deletion, we investigated the roles of the histone lysine acetyltransferase TIP60 (KAT5/HTATIP) in human cells, mouse cells, and mouse embryos. We found that loss of TIP60 caused complete cell growth arrest. In the absence of TIP60, chromosomes failed to align in a metaphase plate during mitosis. In some TIP60 deleted cells, endoreplication occurred instead. In contrast, cell survival was not affected. Remarkably, the cell growth arrest caused by loss of TIP60 was independent of the tumor suppressors p53, INK4A and ARF. TIP60 was found to be essential for the acetylation of H2AZ, specifically at lysine 7. The mRNA levels of 6236 human and 8238 mouse genes, including many metabolism genes, were dependent on TIP60. Among the top 50 differentially expressed genes, over 90% were downregulated in cells lacking TIP60, supporting a role for TIP60 as a key co-activator of transcription. We propose a primary role of TIP60 in H2AZ lysine 7 acetylation and transcriptional activation, and that this fundamental role is essential for cell proliferation. Growth arrest independent of major tumor suppressors suggests TIP60 as a potential anti-cancer drug target.
Collapse
Affiliation(s)
- Johannes Wichmann
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Catherine Pitt
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Samantha Eccles
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Alexandra L. Garnham
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Connie S. N. Li-Wai-Suen
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Rose May
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Elizabeth Allan
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,Cancer Therapeutics CRC, Parkville, VIC Australia
| | - Stephen Wilcox
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia
| | - Marco J. Herold
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Gordon K. Smyth
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSchool of Mathematics and Statistics, University of Melbourne, Parkville, VIC Australia
| | - Brendon J. Monahan
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia ,Cancer Therapeutics CRC, Parkville, VIC Australia
| | - Tim Thomas
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| | - Anne K. Voss
- grid.1042.70000 0004 0432 4889Walter & Eliza Hall Institute of Medical Research, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC Australia
| |
Collapse
|
8
|
Yang YY, Zheng SY, Fang H, Wu XM, Zhang J, Chang MX. Immunoprotective Effects of Two Histone H2A Variants in the Grass Carp Against Flavobacterium columnare Infection. Front Immunol 2022; 13:939464. [PMID: 35898515 PMCID: PMC9310644 DOI: 10.3389/fimmu.2022.939464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
In teleost fish, the nucleotide polymorphisms of histone H2A significantly affect the resistance or susceptibility of zebrafish to Edwardsiella piscicida infection. Whether histone H2A variants can enhance the resistance of grass carp to Flavobacterium columnare infection remains unclear. Here, the effects of 7 previously obtained variants (gcH2A-1~gcH2A-7) and 5 novel histone H2A variants (gcH2A-11, gcH2A-13~gcH2A-16) in response to F. columnare infection were investigated. It was found that these histone H2A variants could be divided into type I and II. Among them, 5 histone H2A variants had no any effects on the F. columnare infection, however 7 histone H2A variants had antibacterial activity against F. columnare infection. The gcH2A-4 and gcH2A-11, whose antibacterial activity was the strongest in type I and II histone H2A variants respectively, were picked out for yeast expression. Transcriptome data for the samples from the intestines of grass carp immunized with the engineered Saccharomyces cerevisiae expressing PYD1, gcH2A-4 or gcH2A-11 revealed that 5 and 12 immune-related signaling pathways were significantly enriched by gcH2A-4 or gcH2A-11, respectively. For the engineered S. cerevisiae expressing gcH2A-4, NOD-like receptor and Toll-like receptor signaling pathways were enriched for up-regulated DEGs. Besides NOD-like receptor and Toll-like receptor signaling pathways, the engineered S. cerevisiae expressing gcH2A-11 also activated Cytosolic DNA-sensing pathway, RIG-I-like receptor signaling pathway and C-type lectin receptor signaling pathway. Furthermore, grass carp were immunized with the engineered S. cerevisiae expressing PYD1, gcH2A-4 or gcH2A-11 for 1 month and challenged with F. columnare. These grass carp immunized with gcH2A-4 or gcH2A-11 showed lower mortality and fewer numbers of F. columnare than did the control group. All these results suggest that gcH2A-4 and gcH2A-11 play important roles in evoking the innate immune responses and enhancing disease resistance of grass carp against F. columnare infection.
Collapse
Affiliation(s)
- Yuan Yuan Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Si Yao Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hong Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Man Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Xian Chang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Ming Xian Chang,
| |
Collapse
|
9
|
Osakabe A, Molaro A. Histone renegades: Unusual H2A histone variants in plants and animals. Semin Cell Dev Biol 2022; 135:35-42. [PMID: 35570098 DOI: 10.1016/j.semcdb.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/27/2022]
Abstract
H2A variants are histones that carry out specialized nucleosome function during the eukaryote genome packaging. Most genes encoding H2A histone variants arose in the distant past, and have highly conserved domains and structures. Yet, novel H2A variants have continued to arise throughout the radiation of eukaryotes and disturbed the apparent tranquility of nucleosomes. These species-specific H2A variants contributed to the functional diversification of nucleosomes through changes in both their structure and expression patterns. In this short review, we discuss the evolutionary trajectories of these histone renegades in plants and animal genomes.
Collapse
Affiliation(s)
- Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Antoine Molaro
- Genetics, Reproduction & Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
| |
Collapse
|
10
|
Liu Y, Bai S, Wang Y, Li X, Qu J, Han M, Zhai J, Li W, Liu J, Zhang Q. Intensive masculinization caused by chronic heat stress in juvenile Cynoglossus semilaevis: Growth performance, gonadal histology and gene responses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113250. [PMID: 35121259 DOI: 10.1016/j.ecoenv.2022.113250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The sea temperature has been observed to chronically increase during the past decades, leaving unpredictable influences to the marine biological resources. Thus, it is of vital significance to study the biological responses of ocean inhabited organisms with the artificially stimulated heat stress environment. Cynoglossus semilaevis provides us with an ideal model to study the influence of chronic heat stress on the sexual differentiation in marine teleosts for its genetic sex determination (GSD) + environmental effected (EE) sex determination system. In this study, the comparative experiment was conducted employing heated seawater (HT group) and ambient seawater (CT group) to cultivate juvenile C. semilaevis respectively. Significant differences were exhibited in growth performance and a delayed germ cell development effect was found in pseudomales formed under chronic heat stress. Using transcriptome analysis, the transcription profile of 55 days post fertilization (dpf) and 100 dpf juveniles' gonads were studied. A total of 47 libraries were constructed with an average mapping rate of 94.63% after assembling. GO and KEGG enrichment were proceeded using DEGs screened out between (1) pseudomale gonads at 55 dpf and 100 dpf in HT and CT group (2) pseudomale and female gonads at 55 dpf and 100 dpf in HT and CT group. Terms and pathways involved in steroid stimulation, reproduction ability, germ cell proliferation et al. were shed light on. The expression pattern of 29 DEGs including amh, hsp90b1, pgr et al. were also provided to supplement the results of functional enrichment. Weighted gene co-expression networks analysis (WGCNA) was constructed and hspb8-like, histone H2A.V were exhibited to play vital roles in the heat-induced masculinization. Our findings facilitate the understanding for transcriptional variations in intensive masculinization cause by chronic heat stress of C. semilaevis and provide referable study of the influences on the teleosts in elevated sea temperature.
Collapse
Affiliation(s)
- Yuxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Shujun Bai
- Laboratory of Fisheries Oceanography, College of Fisheries, Ocean University of China, Qingdao, China
| | - Yujue Wang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Xiaoqi Li
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Jiangbo Qu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Miao Han
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Jieming Zhai
- Laizhou Mingbo Aquatic Co., Ltd., Laizhou, China
| | - Wensheng Li
- Laizhou Mingbo Aquatic Co., Ltd., Laizhou, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao, Shandong, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.
| |
Collapse
|
11
|
What makes a histone variant a variant: Changing H2A to become H2A.Z. PLoS Genet 2021; 17:e1009950. [PMID: 34871303 PMCID: PMC8675926 DOI: 10.1371/journal.pgen.1009950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/16/2021] [Accepted: 11/16/2021] [Indexed: 01/01/2023] Open
Abstract
Chromatin structure and underlying DNA accessibility is modulated by the incorporation of histone variants. H2A.Z, a variant of the H2A core histone family, plays a distinct and essential role in a diverse set of biological functions including gene regulation and maintenance of heterochromatin-euchromatin boundaries. Although it is currently unclear how the replacement of H2A with H2A.Z can regulate gene expression, the variance in their amino acid sequence likely contributes to their functional differences. To tease apart regions of H2A.Z that confer its unique identity, a set of plasmids expressing H2A-H2A.Z hybrids from the native H2A.Z promoter were examined for their ability to recapitulate H2A.Z function. First, we found that the H2A.Z M6 region was necessary and sufficient for interaction with the SWR1-C chromatin remodeler. Remarkably, the combination of only 9 amino acid changes, the H2A.Z M6 region, K79 and L81 (two amino acids in the α2-helix), were sufficient to fully rescue growth phenotypes of the htz1Δ mutant. Furthermore, combining three unique H2A.Z regions (K79 and L81, M6, C-terminal tail) was sufficient for expression of H2A.Z-dependent heterochromatin-proximal genes and GAL1 derepression. Surprisingly, hybrid constructs that restored the transcription of H2A.Z-dependent genes, did not fully recapitulate patterns of H2A.Z-specific enrichment at the tested loci. This suggested that H2A.Z function in transcription regulation may be at least partially independent of its specific localization in chromatin. Together, this work has identified three regions that can confer specific H2A.Z-identity to replicative H2A, furthering our understanding of what makes a histone variant a variant. Chromatin structure in eukaryotes is integral to all aspects of genome function. Many essential biological processes depend on chromatin remodeling for regulating access to DNA such as transcription, replication, and DNA repair. One highly conserved method of chromatin remodeling is the replacement of the replicative histones with a histone variant. Unlike replicative histones, which are distributed equally in chromatin during DNA replication, histone variants can be transcribed and deposited throughout the cell cycle at specific locations. Once incorporated, small differences in a histone variant’s protein sequence and structure can result in unique chromatin neighbourhoods with distinct character and function from the replicative histone. Therefore, to better understand the role of a histone variant, it is important to define how its protein sequence contributes to its unique identity. Here, using a hybrid gene approach in budding yeast, we systematically determine which amino acids contribute to H2A.Z unique identity as a histone variant.
Collapse
|
12
|
Histone variant H2A.Z regulates zygotic genome activation. Nat Commun 2021; 12:7002. [PMID: 34853314 PMCID: PMC8636486 DOI: 10.1038/s41467-021-27125-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z. H2A.Z enrichment precedes ZGA and RNA Polymerase II loading onto chromatin. In vivo knockdown of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that H2A.Z is essential for the de novo establishment of transcriptional programs during ZGA via chromatin reorganization. During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.
Collapse
|
13
|
Llorens-Giralt P, Camilleri-Robles C, Corominas M, Climent-Cantó P. Chromatin Organization and Function in Drosophila. Cells 2021; 10:cells10092362. [PMID: 34572010 PMCID: PMC8465611 DOI: 10.3390/cells10092362] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic genomes are packaged into high-order chromatin structures organized in discrete territories inside the cell nucleus, which is surrounded by the nuclear envelope acting as a barrier. This chromatin organization is complex and dynamic and, thus, determining the spatial and temporal distribution and folding of chromosomes within the nucleus is critical for understanding the role of chromatin topology in genome function. Primarily focusing on the regulation of gene expression, we review here how the genome of Drosophila melanogaster is organized into the cell nucleus, from small scale histone–DNA interactions to chromosome and lamina interactions in the nuclear space.
Collapse
|
14
|
Tang R, Huang W, Guan J, Liu Q, Beerntsen BT, Ling E. Drosophila H2Av negatively regulates the activity of the IMD pathway via facilitating Relish SUMOylation. PLoS Genet 2021; 17:e1009718. [PMID: 34370736 PMCID: PMC8376203 DOI: 10.1371/journal.pgen.1009718] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/19/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Insects depend on the innate immune response for defense against a wide array of pathogens. Central to Drosophila immunity are antimicrobial peptides (AMPs), released into circulation when pathogens trigger either of the two widely studied signal pathways, Toll or IMD. The Toll pathway responds to infection by Gram-positive bacteria and fungi while the IMD pathway is activated by Gram-negative bacteria. During activation of the IMD pathway, the NF-κB-like transcription factor Relish is phosphorylated and then cleaved, which is crucial for IMD-dependent AMP gene induction. Here we show that loss-of-function mutants of the unconventional histone variant H2Av upregulate IMD-dependent AMP gene induction in germ-free Drosophila larvae and adults. After careful dissection of the IMD pathway, we found that Relish has an epistatic relationship with H2Av. In the H2Av mutant larvae, SUMOylation is down-regulated, suggesting a possible role of SUMOylation in the immune phenotype. Eventually we demonstrated that Relish is mostly SUMOylated on amino acid K823. Loss of the potential SUMOylation site leads to significant auto-activation of Relish in vivo. Further work indicated that H2Av regulates Relish SUMOylation after physically interacting with Su(var)2-10, the E3 component of the SUMOylation pathway. Biochemical analysis suggested that SUMOylation of Relish prevents its cleavage and activation. Our findings suggest a new mechanism by which H2Av can negatively regulate, and thus prevent spontaneous activation of IMD-dependent AMP production, through facilitating SUMOylation of the NF-κB like transcription factor Relish. Toll and IMD signaling pathways should be involved in the production of antimicrobial peptides in animals upon infection. Immunity responses are energy consuming. Thus, these two pathways are fine-tuned. Animal H2A variant histones are involved in many physiological functions. In Drosophila, the production of antibacterial peptides is out of control in the mutant of H2A variant (H2Av810). After careful examination, we found that Relish, the transcription factor of the IMD pathway, was activated in this mutant. Eventually we demonstrate that Relish can be SUMOylated with the involvement of H2Av. Loss of the main SUMOylation site in Relish induces it to auto-activate following over-expression. Therefore, H2Av is a negative regulator of the IMD signaling pathway by maintaining the normal level of Relish SUMOylation in Drosophila.
Collapse
Affiliation(s)
- Ruijuan Tang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wuren Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jingmin Guan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qiuning Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetland, Yancheng Teachers University, Yancheng, China
| | - Brenda T. Beerntsen
- Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Erjun Ling
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
15
|
Hsu CL, Chong SY, Lin CY, Kao CF. Histone dynamics during DNA replication stress. J Biomed Sci 2021; 28:48. [PMID: 34144707 PMCID: PMC8214274 DOI: 10.1186/s12929-021-00743-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/08/2021] [Indexed: 01/20/2023] Open
Abstract
Accurate and complete replication of the genome is essential not only for genome stability but also for cell viability. However, cells face constant threats to the replication process, such as spontaneous DNA modifications and DNA lesions from endogenous and external sources. Any obstacle that slows down replication forks or perturbs replication dynamics is generally considered to be a form of replication stress, and the past decade has seen numerous advances in our understanding of how cells respond to and resolve such challenges. Furthermore, recent studies have also uncovered links between defects in replication stress responses and genome instability or various diseases, such as cancer. Because replication stress takes place in the context of chromatin, histone dynamics play key roles in modulating fork progression and replication stress responses. Here, we summarize the current understanding of histone dynamics in replication stress, highlighting recent advances in the characterization of fork-protective mechanisms.
Collapse
Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin Yen Chong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
16
|
Schmücker A, Lei B, Lorković ZJ, Capella M, Braun S, Bourguet P, Mathieu O, Mechtler K, Berger F. Crosstalk between H2A variant-specific modifications impacts vital cell functions. PLoS Genet 2021; 17:e1009601. [PMID: 34086674 PMCID: PMC8208582 DOI: 10.1371/journal.pgen.1009601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/16/2021] [Accepted: 05/14/2021] [Indexed: 12/15/2022] Open
Abstract
Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phosphorylates the KSPK motif of H2A.W but only in absence of an SQ motif. Phosphomimicry of KSPK prevented DNA damage response by the SQ motif of the hybrid H2A.W/X variant. In a synthetic yeast expressing the hybrid H2A.W/X variant, phosphorylation of KSPK prevented binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and impaired response to DNA damage. Our findings illustrate that PTMs mediate interference between the function of H2A variant specific C-terminal motifs. Such interference could explain the mutual exclusion of motifs that led to evolution of H2A variants.
Collapse
Affiliation(s)
- Anna Schmücker
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Bingkun Lei
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Zdravko J. Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Matías Capella
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Sigurd Braun
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
- International Max Planck Research School for Molecular and Cellular Life Sciences, Planegg-Martinsried, Germany
| | - Pierre Bourguet
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- CNRS, Université Clermont Auvergne, Inserm, Génétique Reproduction et Développement, Clermont-Ferrand, France
| | - Olivier Mathieu
- CNRS, Université Clermont Auvergne, Inserm, Génétique Reproduction et Développement, Clermont-Ferrand, France
| | - Karl Mechtler
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| |
Collapse
|
17
|
In Vivo Silencing of Genes Coding for dTip60 Chromatin Remodeling Complex Subunits Affects Polytene Chromosome Organization and Proper Development in Drosophila melanogaster. Int J Mol Sci 2021; 22:ijms22094525. [PMID: 33926075 PMCID: PMC8123692 DOI: 10.3390/ijms22094525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/17/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin organization is developmentally regulated by epigenetic changes mediated by histone-modifying enzymes and chromatin remodeling complexes. In Drosophila melanogaster, the Tip60 chromatin remodeling complex (dTip60) play roles in chromatin regulation, which are shared by evolutionarily-related complexes identified in animal and plants. Recently, it was found that most subunits previously assigned to the dTip60 complex are shared by two related complexes, DOM-A.C and DOM-B.C, defined by DOM-A and DOM-B isoforms, respectively. In this work, we combined classical genetics, cell biology, and reverse genetics approaches to further investigate the biological roles played during Drosophila melanogaster development by a number of subunits originally assigned to the dTip60 complex.
Collapse
|
18
|
Vidaurre V, Chen X. Epigenetic regulation of drosophila germline stem cell maintenance and differentiation. Dev Biol 2021; 473:105-118. [PMID: 33610541 DOI: 10.1016/j.ydbio.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/26/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Gametogenesis is one of the most extreme cellular differentiation processes that takes place in Drosophila male and female germlines. This process begins at the germline stem cell, which undergoes asymmetric cell division (ACD) to produce a self-renewed daughter that preserves its stemness and a differentiating daughter cell that undergoes epigenetic and genomic changes to eventually produce haploid gametes. Research in molecular genetics and cellular biology are beginning to take advantage of the continually advancing genomic tools to understand: (1) how germ cells are able to maintain their identity throughout the adult reproductive lifetime, and (2) undergo differentiation in a balanced manner. In this review, we focus on the epigenetic mechanisms that address these two questions through their regulation of germline-soma communication to ensure germline stem cell identity and activity.
Collapse
Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA.
| |
Collapse
|
19
|
Scacchetti A, Becker PB. Variation on a theme: Evolutionary strategies for H2A.Z exchange by SWR1-type remodelers. Curr Opin Cell Biol 2020; 70:1-9. [PMID: 33217681 DOI: 10.1016/j.ceb.2020.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023]
Abstract
Histone variants are a universal means to alter the biochemical properties of nucleosomes, implementing local changes in chromatin structure. H2A.Z, one of the most conserved histone variants, is incorporated into chromatin by SWR1-type nucleosome remodelers. Here, we summarize recent advances toward understanding the transcription-regulatory roles of H2A.Z and of the remodeling enzymes that govern its dynamic chromatin incorporation. Tight transcriptional control guaranteed by H2A.Z nucleosomes depends on the context provided by other histone variants or chromatin modifications, such as histone acetylation. The functional cooperation of SWR1-type remodelers with NuA4 histone acetyltransferase complexes, a recurring theme during evolution, is structurally implemented by species-specific strategies.
Collapse
Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.
| |
Collapse
|
20
|
Scacchetti A, Becker PB. Loss of nucleosome remodelers CHRAC/ACF does not sensitize early Drosophila embryos to X-rays. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000287. [PMID: 32760884 PMCID: PMC7396160 DOI: 10.17912/micropub.biology.000287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University, Munich, Germany
| | - Peter B. Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University, Munich, Germany,
Correspondence to: Peter B. Becker ()
| |
Collapse
|
21
|
Scacchetti A, Schauer T, Reim A, Apostolou Z, Campos Sparr A, Krause S, Heun P, Wierer M, Becker PB. Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms. eLife 2020; 9:e56325. [PMID: 32432549 PMCID: PMC7239659 DOI: 10.7554/elife.56325] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/23/2020] [Indexed: 12/11/2022] Open
Abstract
Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.
Collapse
Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Tamas Schauer
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Zivkos Apostolou
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Aline Campos Sparr
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Patrick Heun
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| |
Collapse
|
22
|
Gaub A, Sheikh BN, Basilicata MF, Vincent M, Nizon M, Colson C, Bird MJ, Bradner JE, Thevenon J, Boutros M, Akhtar A. Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation. Nat Commun 2020; 11:2243. [PMID: 32382029 PMCID: PMC7206058 DOI: 10.1038/s41467-020-16103-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional networks underlying their expression remain poorly understood. The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator. It is essential in Drosophila, and haploinsufficiency of the human KANSL1 subunit results in the Koolen-de Vries syndrome. Here, we perform a genome-wide RNAi screen and identify the BET protein BRD4 as an evolutionary conserved co-factor of the NSL complex. Using Drosophila and mouse embryonic stem cells, we characterise a recruitment hierarchy, where NSL-deposited histone acetylation enables BRD4 recruitment for transcription of constitutively active genes. Transcriptome analyses in Koolen-de Vries patient-derived fibroblasts reveals perturbations with a cellular homeostasis signature that are evoked by the NSL complex/BRD4 axis. We propose that BRD4 represents a conserved bridge between the NSL complex and transcription activation, and provide a new perspective in the understanding of their functions in healthy and diseased states.
Collapse
Affiliation(s)
- Aline Gaub
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France
| | - Cindy Colson
- Service Génétique, Génétique Clinique, CHU, Avenue Georges Clemenceau CS 30001, 14033, Caen, France.,Normandy University, UNICAEN, BIOTARGEN, Esplanade de la Paix CS 14032, 14032, Caen, France
| | - Matthew J Bird
- Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - James E Bradner
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Julien Thevenon
- CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Allée des Alpes, 38700, La Tronche Grenoble, France
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
| |
Collapse
|
23
|
Bayer FE, Deichsel S, Mahl P, Nagel AC. Drosophila Xrcc2 regulates DNA double-strand repair in somatic cells. DNA Repair (Amst) 2020; 88:102807. [PMID: 32006716 DOI: 10.1016/j.dnarep.2020.102807] [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: 09/12/2019] [Revised: 01/07/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
Abstract
Genomic integrity is challenged by endo- and exogenous assaults that are combated by highly conserved DNA repair mechanisms. Repair of DNA double-strand breaks (DSBs) is of particular importance, as DSBs inflict chromosome breaks that are the basis of genomic instability. High fidelity recombination repair of DSBs relies on the Rad51 recombinase, aided by several Rad51 paralogs. Despite their significant contribution to DSB repair, the individual roles for Rad51 paralogs are incompletely understood. Drosophila serves as a metazoan model for DNA damage repair at the organismal level. Yet, only two out of four Rad51 paralogs have been studied so far and both are restricted to meiotic recombination repair. Using CRISPR/Cas9 technology, we have generated the first X-ray repair cross complementing 2 (xrcc2) null mutant in Drosophila. Like any other Drosophila Rad51 homologue, loss of xrcc2 does not affect fly development. We found that Drosophila xrcc2 - despite a specific expression in ovaries - is not essential for meiotic DSB repair, but supports the process. In contrast, xrcc2 is required for mitotic DNA damage repair: the mutants are highly sensitive towards various genotoxic stressors, including ionizing radiation, which significantly increase mortality. Moreover, loss of xrcc2 provokes chromosome aberrations in mitotic larval neuroblasts under unstressed conditions and enduring chromosomal breaks as well as persistent repair foci after irradiation exposure. Together these results demonstrate that xrcc2 plays a crucial role in combating genotoxic insult by controlling DSB repair in somatic cells of Drosophila.
Collapse
Affiliation(s)
- Fabienne E Bayer
- Institute of Biology, Department of Genetics (190g), University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany
| | - Sebastian Deichsel
- Institute of Biology, Department of Genetics (190g), University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany
| | - Pascal Mahl
- Institute of Biology, Department of Genetics (190g), University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany
| | - Anja C Nagel
- Institute of Biology, Department of Genetics (190g), University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany.
| |
Collapse
|
24
|
Harpprecht L, Baldi S, Schauer T, Schmidt A, Bange T, Robles MS, Kremmer E, Imhof A, Becker PB. A Drosophila cell-free system that senses DNA breaks and triggers phosphorylation signalling. Nucleic Acids Res 2019; 47:7444-7459. [PMID: 31147711 PMCID: PMC6698661 DOI: 10.1093/nar/gkz473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 11/23/2022] Open
Abstract
Preblastoderm Drosophila embryo development is characterized by fast cycles of nuclear divisions. Extracts from these embryos can be used to reconstitute complex chromatin with high efficiency. We now discovered that this chromatin assembly system contains activities that recognize unprotected DNA ends and signal DNA damage through phosphorylation. DNA ends are initially bound by Ku and MRN complexes. Within minutes, the phosphorylation of H2A.V (homologous to γH2A.X) initiates from DNA breaks and spreads over tens of thousands DNA base pairs. The γH2A.V phosphorylation remains tightly associated with the damaged DNA and does not spread to undamaged DNA in the same reaction. This first observation of long-range γH2A.X spreading along damaged chromatin in an in vitro system provides a unique opportunity for mechanistic dissection. Upon further incubation, DNA ends are rendered single-stranded and bound by the RPA complex. Phosphoproteome analyses reveal damage-dependent phosphorylation of numerous DNA-end-associated proteins including Ku70, RPA2, CHRAC16, the exonuclease Rrp1 and the telomer capping complex. Phosphorylation of spindle assembly checkpoint components and of microtubule-associated proteins required for centrosome integrity suggests this cell-free system recapitulates processes involved in the regulated elimination of fatally damaged syncytial nuclei.
Collapse
Affiliation(s)
- Lisa Harpprecht
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Sandro Baldi
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Bioinformatics Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas Schmidt
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Protein Analysis Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Tanja Bange
- Institute of Medical Psychology, LMU Munich, 80336 Munich, Germany
| | - Maria S Robles
- Institute of Medical Psychology, LMU Munich, 80336 Munich, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Axel Imhof
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
- Protein Analysis Unit, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, LMU Munich, 81377 Munich, Germany
- To whom correspondence should be addressed. Tel: +49 89 2180 75427; Fax: +49 89 2180 75425;
| |
Collapse
|
25
|
Prozzillo Y, Delle Monache F, Ferreri D, Cuticone S, Dimitri P, Messina G. The True Story of Yeti, the "Abominable" Heterochromatic Gene of Drosophila melanogaster. Front Physiol 2019; 10:1093. [PMID: 31507454 PMCID: PMC6713933 DOI: 10.3389/fphys.2019.01093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/08/2019] [Indexed: 12/21/2022] Open
Abstract
The Drosophila Yeti gene (CG40218) was originally identified by recessive lethal mutation and subsequently mapped to the deep pericentromeric heterochromatin of chromosome 2. Functional studies have shown that Yeti encodes a 241 amino acid protein called YETI belonging to the evolutionarily conserved family of Bucentaur (BCNT) proteins and exhibiting a widespread distribution in animals and plants. Later studies have demonstrated that YETI protein: (i) is able to bind both subunits of the microtubule-based motor kinesin-I; (ii) is required for proper chromosome organization in both mitosis and meiosis divisions; and more recently (iii) is a new subunit of dTip60 chromatin remodeling complex. To date, other functions of YETI counterparts in chicken (CENtromere Protein 29, CENP-29), mouse (Cranio Protein 27, CP27), zebrafish and human (CranioFacial Development Protein 1, CFDP1) have been reported in literature, but the fully understanding of the multifaceted molecular function of this protein family remains still unclear. In this review we comprehensively highlight recent work and provide a more extensive hypothesis suggesting a broader range of YETI protein functions in different cellular processes.
Collapse
Affiliation(s)
- Yuri Prozzillo
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Francesca Delle Monache
- "Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Diego Ferreri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Stefano Cuticone
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Patrizio Dimitri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giovanni Messina
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
26
|
Glastad KM, Hunt BG, Goodisman MAD. Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity. ANNUAL REVIEW OF ENTOMOLOGY 2019; 64:185-203. [PMID: 30285490 DOI: 10.1146/annurev-ento-011118-111914] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.
Collapse
Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, Georgia 30223, USA;
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA;
| |
Collapse
|
27
|
Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
Collapse
|
28
|
Johnson MR, Stephenson RA, Ghaemmaghami S, Welte MA. Developmentally regulated H2Av buffering via dynamic sequestration to lipid droplets in Drosophila embryos. eLife 2018; 7:36021. [PMID: 30044219 PMCID: PMC6089599 DOI: 10.7554/elife.36021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022] Open
Abstract
Regulating nuclear histone balance is essential for survival, yet in early Drosophila melanogaster embryos many regulatory strategies employed in somatic cells are unavailable. Previous work had suggested that lipid droplets (LDs) buffer nuclear accumulation of the histone variant H2Av. Here, we elucidate the buffering mechanism and demonstrate that it is developmentally controlled. Using live imaging, we find that H2Av continuously exchanges between LDs. Our data suggest that the major driving force for H2Av accumulation in nuclei is H2Av abundance in the cytoplasm and that LD binding slows nuclear import kinetically, by limiting this cytoplasmic pool. Nuclear H2Av accumulation is indeed inversely regulated by overall buffering capacity. Histone exchange between LDs abruptly ceases during the midblastula transition, presumably to allow canonical regulatory mechanisms to take over. These findings provide a mechanistic basis for the emerging role of LDs as regulators of protein homeostasis and demonstrate that LDs can control developmental progression.
Collapse
Affiliation(s)
| | | | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, Rochester, United States
| | | |
Collapse
|
29
|
Börner K, Becker PB. Splice variants of the SWR1-type nucleosome remodeling factor Domino have distinct functions during Drosophila melanogaster oogenesis. Development 2017; 143:3154-67. [PMID: 27578180 DOI: 10.1242/dev.139634] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/21/2016] [Indexed: 12/16/2022]
Abstract
SWR1-type nucleosome remodeling factors replace histone H2A by variants to endow chromatin locally with specialized functionality. In Drosophila melanogaster a single H2A variant, H2A.V, combines functions of mammalian H2A.Z and H2A.X in transcription regulation and the DNA damage response. A major role in H2A.V incorporation for the only SWR1-like enzyme in flies, Domino, is assumed but not well documented in vivo. It is also unclear whether the two alternatively spliced isoforms, DOM-A and DOM-B, have redundant or specialized functions. Loss of both DOM isoforms compromises oogenesis, causing female sterility. We systematically explored roles of the two DOM isoforms during oogenesis using a cell type-specific knockdown approach. Despite their ubiquitous expression, DOM-A and DOM-B have non-redundant functions in germline and soma for egg formation. We show that chromatin incorporation of H2A.V in germline and somatic cells depends on DOM-B, whereas global incorporation in endoreplicating germline nurse cells appears to be independent of DOM. By contrast, DOM-A promotes the removal of H2A.V from stage 5 nurse cells. Remarkably, therefore, the two DOM isoforms have distinct functions in cell type-specific development and H2A.V exchange.
Collapse
Affiliation(s)
- Kenneth Börner
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, Großhaderner Strasse 9, 82152 Munich, Germany
| | - Peter B Becker
- Biomedical Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, Großhaderner Strasse 9, 82152 Munich, Germany
| |
Collapse
|
30
|
Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorín F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun 2017; 8:283. [PMID: 28819201 PMCID: PMC5561251 DOI: 10.1038/s41467-017-00338-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/22/2017] [Indexed: 12/01/2022] Open
Abstract
Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops). R-loops accumulation is readily detectable in G1-phase, whereas γH2Av increases mainly during DNA replication. These defects induce JNK-mediated apoptosis and are specific of dH1 depletion since they are not observed when heterochromatin silencing is relieved by HP1a depletion. Altogether, our results suggest that histone H1 prevents R-loops-induced DNA damage in heterochromatin and unveil its essential contribution to maintenance of genome stability.While structural importance of linker histone H1 in packaging eukaryotic genome into chromatin is well known, its biological function remains poorly understood. Here the authors reveal that Drosophila linker histone H1 prevents DNA:RNA hybrids accumulation and genome instability in heterochromatin.
Collapse
Affiliation(s)
- Aleix Bayona-Feliu
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
| |
Collapse
|
31
|
Lorković ZJ, Park C, Goiser M, Jiang D, Kurzbauer MT, Schlögelhofer P, Berger F. Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants. Curr Biol 2017; 27:1192-1199. [PMID: 28392109 DOI: 10.1016/j.cub.2017.03.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
Abstract
DNA double-strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1-7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2, 8-14]. However, KAP1 is not conserved in plants and the HP1-related protein Like-HP1 (LHP1) is not localized at constitutive heterochromatin [15], suggesting that in plants, alternative mechanisms could be responsible for repair of DSBs in heterochromatin. In Arabidopsis, constitutive heterochromatin is marked by H3K9 methylation and the plant-specific histone variants H2A.W, which are distinguished by their C-terminal motif KSPKK and required for heterochromatin compaction [16-18]. We report that the Arabidopsis histone variant H2A.W.7 is confined to heterochromatin and carries a SQ motif that is phosphorylated by ATM. In response to DNA damage, phosphorylation of H2A.W.7 takes place in heterochromatin, while H2A.X phosphorylation takes place primarily in euchromatin. We propose that H2A.W.7 evolved in addition to H2A.X to facilitate DNA damage response in highly condensed heterochromatin, thus playing a role similar to KAP1 and HP1 phosphorylation in mammals. These data support the idea of the functional diversification of histone variants and their role in spatial compartmentalization of chromatin-related functions in eukaryotes.
Collapse
Affiliation(s)
- Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chulmin Park
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Danhua Jiang
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Marie-Therese Kurzbauer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
32
|
Messina G, Atterrato MT, Prozzillo Y, Piacentini L, Losada A, Dimitri P. The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization. Sci Rep 2017; 7:45022. [PMID: 28367969 PMCID: PMC5377257 DOI: 10.1038/srep45022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the first in vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
Collapse
Affiliation(s)
- Giovanni Messina
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Maria Teresa Atterrato
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Yuri Prozzillo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Lucia Piacentini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | | | - Patrizio Dimitri
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| |
Collapse
|
33
|
Grigorian M, DeBruhl H, Lipsick JS. The role of variant histone H2AV in Drosophila melanogaster larval hematopoiesis. Development 2017; 144:1441-1449. [PMID: 28242611 DOI: 10.1242/dev.142729] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/20/2017] [Indexed: 11/20/2022]
Abstract
Replication-independent histone variants can replace the canonical replication-dependent histones. Vertebrates have multiple H2A variant histones, including H2AZ and H2AX that are present in most eukaryotes. H2AZ regulates transcriptional activation as well as the maintenance of gene silencing, while H2AX is important in DNA damage repair. The fruit fly Drosophila melanogaster has only one histone H2A variant (H2AV), which is a chimera of H2AZ and H2AX. In this study we found that lack of H2AV led to the formation of black melanotic masses in Drosophila third instar larvae. The formation of these masses was found in conjunction with a loss of the majority of the primary lymph gland lobes. Interestingly, the cells of the posterior signaling center were preserved in these mutants. Reduction of H2AV levels by RNAi knockdown caused a milder phenotype that preserved the lymph gland structure but that included precocious differentiation of the prohemocytes located within the medullary zone and the secondary lobes of the lymph gland. Mutant rescue experiments suggest that the H2AZ-like rather than the H2AX-like function of H2AV is primarily required for normal hematopoiesis.
Collapse
Affiliation(s)
- Melina Grigorian
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5323, USA
| | - Heather DeBruhl
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5323, USA
| | - Joseph S Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5323, USA
| |
Collapse
|
34
|
Messina G, Atterrato MT, Dimitri P. When chromatin organisation floats astray: theSrcapgene and Floating–Harbor syndrome. J Med Genet 2016; 53:793-797. [DOI: 10.1136/jmedgenet-2016-103842] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 01/19/2023]
|
35
|
SMARCAD1 is an ATP-dependent stimulator of nucleosomal H2A acetylation via CBP, resulting in transcriptional regulation. Sci Rep 2016; 6:20179. [PMID: 26888216 PMCID: PMC4757861 DOI: 10.1038/srep20179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/23/2015] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation plays a pivotal role in transcriptional regulation, and ATP-dependent nucleosome remodeling activity is required for optimal transcription from chromatin. While these two activities have been well characterized, how they are coordinated remains to be determined. We discovered ATP-dependent histone H2A acetylation activity in Drosophila nuclear extracts. This activity was column purified and demonstrated to be composed of the enzymatic activities of CREB-binding protein (CBP) and SMARCAD1, which belongs to the Etl1 subfamily of the Snf2 family of helicase-related proteins. SMARCAD1 enhanced acetylation by CBP of H2A K5 and K8 in nucleosomes in an ATP-dependent fashion. Expression array analysis of S2 cells having ectopically expressed SMARCAD1 revealed up-regulated genes. Using native genome templates of these up-regulated genes, we found that SMARCAD1 activates their transcription in vitro. Knockdown analysis of SMARCAD1 and CBP indicated overlapping gene control, and ChIP-seq analysis of these commonly controlled genes showed that CBP is recruited to the promoter prior to SMARCAD1. Moreover, Drosophila genetic experiments demonstrated interaction between SMARCAD1/Etl1 and CBP/nej during development. The interplay between the remodeling activity of SMARCAD1 and histone acetylation by CBP sheds light on the function of chromatin and the genome-integrity network.
Collapse
|
36
|
A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis. Dev Biol 2016; 411:217-230. [PMID: 26851213 DOI: 10.1016/j.ydbio.2016.01.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/11/2015] [Accepted: 01/31/2016] [Indexed: 11/23/2022]
Abstract
The Chromatin Accessibility Complex (CHRAC) consists of the ATPase ISWI, the large ACF1 subunit and a pair of small histone-like proteins, CHRAC-14/16. CHRAC is a prototypical nucleosome sliding factor that mobilizes nucleosomes to improve the regularity and integrity of the chromatin fiber. This may facilitate the formation of repressive chromatin. Expression of the signature subunit ACF1 is restricted during embryonic development, but remains high in primordial germ cells. Therefore, we explored roles for ACF1 during Drosophila oogenesis. ACF1 is expressed in somatic and germline cells, with notable enrichment in germline stem cells and oocytes. The asymmetrical localization of ACF1 to these cells depends on the transport of the Acf1 mRNA by the Bicaudal-D/Egalitarian complex. Loss of ACF1 function in the novel Acf1(7) allele leads to defective egg chambers and their elimination through apoptosis. In addition, we find a variety of unusual 16-cell cyst packaging phenotypes in the previously known Acf1(1) allele, with a striking prevalence of egg chambers with two functional oocytes at opposite poles. Surprisingly, we found that the Acf1(1) deletion--despite disruption of the Acf1 reading frame--expresses low levels of a PHD-bromodomain module from the C-terminus of ACF1 that becomes enriched in oocytes. Expression of this module from the Acf1 genomic locus leads to packaging defects in the absence of functional ACF1, suggesting competitive interactions with unknown target molecules. Remarkably, a two-fold overexpression of CHRAC (ACF1 and CHRAC-16) leads to increased apoptosis and packaging defects. Evidently, finely tuned CHRAC levels are required for proper oogenesis.
Collapse
|
37
|
Abstract
Eyes absent (Eya), a protein conserved from plants to humans and best characterized as a transcriptional coactivator, is also the prototype for a novel class of eukaryotic aspartyl protein tyrosine phosphatases. This minireview discusses recent breakthroughs in elucidating the substrates and cellular events regulated by Eya's tyrosine phosphatase function and highlights some of the complexities, new questions, and surprises that have emerged from efforts to understand how Eya's unusual multifunctionality influences developmental regulation and signaling.
Collapse
|
38
|
Abstract
Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed.
Collapse
|
39
|
Vernì F, Cenci G. The Drosophila histone variant H2A.V works in concert with HP1 to promote kinetochore-driven microtubule formation. Cell Cycle 2015; 14:577-88. [PMID: 25591068 DOI: 10.4161/15384101.2014.991176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Unlike other organisms that have evolved distinct H2A variants for different functions, Drosophila melanogaster has just one variant which is capable of filling many roles. This protein, H2A.V, combines the features of the conserved variants H2A.Z and H2A.X in transcriptional control/heterochromatin assembly and DNA damage response, respectively. Here we show that mutations in the gene encoding H2A.V affect chromatin compaction and perturb chromosome segregation in Drosophila mitotic cells. A microtubule (MT) regrowth assay after cold exposure revealed that loss of H2A.V impairs the formation of kinetochore-driven (k) fibers, which can account for defects in chromosome segregation. All defects are rescued by a transgene encoding H2A.V that lacks the H2A.X function in the DNA damage response, suggesting that the H2A.Z (but not H2A.X) functionality of H2A.V is required for chromosome segregation. We also found that loss of H2A.V weakens HP1 localization, specifically at the pericentric heterochromatin of metaphase chromosomes. Interestingly, loss of HP1 yielded not only telomeric fusions but also mitotic defects similar to those seen in H2A.V null mutants, suggesting a role for HP1 in chromosome segregation. We also show that H2A.V precipitates HP1 from larval brain extracts indicating that both proteins are part of the same complex. Moreover, we found that the overexpression of HP1 rescues chromosome missegregation and defects in the kinetochore-driven k-fiber regrowth of H2A.V mutants indicating that both phenotypes are influenced by unbalanced levels of HP1. Collectively, our results suggest that H2A.V and HP1 work in concert to ensure kinetochore-driven MT growth.
Collapse
Affiliation(s)
- Fiammetta Vernì
- a Dipartimento di Biologia e Biotecnologie "C. Darwin" ; Sapienza Università di Roma ; Roma , Italy
| | | |
Collapse
|
40
|
Melters DP, Nye J, Zhao H, Dalal Y. Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes (Basel) 2015; 6:751-76. [PMID: 26262644 PMCID: PMC4584328 DOI: 10.3390/genes6030751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 01/30/2023] Open
Abstract
Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.
Collapse
Affiliation(s)
- Daniël P Melters
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Haiqing Zhao
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| |
Collapse
|
41
|
Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
Collapse
Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
| | | |
Collapse
|
42
|
Abstract
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.
Collapse
Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - M Mitchell Smith
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
| |
Collapse
|
43
|
Messina G, Celauro E, Atterrato MT, Giordano E, Iwashita S, Dimitri P. The Bucentaur (BCNT) protein family: a long-neglected class of essential proteins required for chromatin/chromosome organization and function. Chromosoma 2014; 124:153-62. [DOI: 10.1007/s00412-014-0503-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/05/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
|
44
|
Li Z, Johnson MR, Ke Z, Chen L, Welte MA. Drosophila lipid droplets buffer the H2Av supply to protect early embryonic development. Curr Biol 2014; 24:1485-91. [PMID: 24930966 DOI: 10.1016/j.cub.2014.05.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/31/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
Abstract
Assembly of DNA into chromatin requires a delicate balancing act, as both dearth and excess of histones severely disrupt chromatin function [1-3]. In particular, cells need to carefully control histone stoichiometry: if different types of histones are incorporated into chromatin in an imbalanced manner, it can lead to altered gene expression, mitotic errors, and death [4-6]. Both the balance between individual core histones and the balance between core histones and histone variants are critical [5, 7]. Here, we find that in early Drosophila embryos, histone balance in the nuclei is regulated by lipid droplets, cytoplasmic fat-storage organelles [8]. Lipid droplets were previously known to function in long-term histone storage: newly laid embryos contain large amounts of excess histones generated during oogenesis [9], and the maternal supplies of core histone H2A and the histone variant H2Av are anchored to lipid droplets via the novel protein Jabba [3]. We find that in these embryos, synthesis of new H2A and H2Av is imbalanced, and that newly produced H2Av can be recruited to lipid droplets. When droplet sequestration is disrupted by mutating Jabba, embryos display an elevated H2Av/H2A ratio in nuclei as well as mitotic defects, reduced viability, and hypersensitivity to H2Av overexpression. We propose that in Drosophila embryos, lipid droplets serve as a histone buffer, not only storing maternal histones to support the early cell cycles but also transiently sequestering H2Av produced in excess and thus ensuring proper histone balance in the nucleus.
Collapse
Affiliation(s)
- Zhihuan Li
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Matthew R Johnson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhonghe Ke
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lili Chen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| |
Collapse
|
45
|
Zhuang Q, Smallman H, Lambert SJ, Sodngam SS, Reynolds CD, Evans K, Dickman MJ, Baldwin JP, Wood CM. Cofractionation of HMGB proteins with histone dimers. Anal Biochem 2014; 447:98-106. [PMID: 24239809 DOI: 10.1016/j.ab.2013.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 10/26/2022]
Abstract
An effective and flexible method is presented that can be used to investigate cofractionation of groups of nuclear proteins. The method was used to analyze chromatin-related proteins, of which high-mobility group B (HMGB) proteins consistently cofractionated by cation-exchange chromatography with the histone dimer (H2A-H2B). This led to the hypothesis that the two form a complex, further suggested by gel filtration, in which the HMGBs with core histones eluted as a defined high-molecular-weight peak. A necessary requirement for further studying protein interactions is that the constituents are of the highest possible purity and the pure histone dimers and tetramers used in this study were derived from pure histone octamers with their native marks. There is a growing interest in protein-protein interactions and an increasing focus on protein-interaction domains: most frequently, pull-down assays are used to examine these. The technology presented here can provide an effective system that complements pull-down assays.
Collapse
Affiliation(s)
- Qinqin Zhuang
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Hugh Smallman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Stanley J Lambert
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Sirirath S Sodngam
- Natural Products Research Unit, Centre of Excellence for Innovation in Chemistry (PERCH-CIC), Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Colin D Reynolds
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Katie Evans
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Mark J Dickman
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - John P Baldwin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Christopher M Wood
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
| |
Collapse
|
46
|
Morillo Prado JR, Srinivasan S, Fuller MT. The histone variant His2Av is required for adult stem cell maintenance in the Drosophila testis. PLoS Genet 2013; 9:e1003903. [PMID: 24244183 PMCID: PMC3820763 DOI: 10.1371/journal.pgen.1003903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 09/08/2013] [Indexed: 12/19/2022] Open
Abstract
Many tissues are sustained by adult stem cells, which replace lost cells by differentiation and maintain their own population through self-renewal. The mechanisms through which adult stem cells maintain their identity are thus important for tissue homeostasis and repair throughout life. Here, we show that a histone variant, His2Av, is required cell autonomously for maintenance of germline and cyst stem cells in the Drosophila testis. The ATP-dependent chromatin-remodeling factor Domino is also required in this tissue for adult stem cell maintenance possibly by regulating the incorporation of His2Av into chromatin. Interestingly, although expression of His2Av was ubiquitous, its function was dispensable for germline and cyst cell differentiation, suggesting a specific role for this non-canonical histone in maintaining the stem cell state in these lineages.
Collapse
Affiliation(s)
- Jose Rafael Morillo Prado
- Department of Developmental Biology, Stanford University, School of Medicine Stanford, California, United States of America
| | | | | |
Collapse
|