1
|
Dozier J, Villhauer M, Carpenter B. Sterility in the offspring of spr-5; met-2 mutants may be caused by inherited H3K4 methylation and altered germline transcription. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001365. [PMID: 39430681 PMCID: PMC11489868 DOI: 10.17912/micropub.biology.001365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 10/01/2024] [Accepted: 10/03/2024] [Indexed: 10/22/2024]
Abstract
During maternal reprogramming of histone methylation in C. elegans , H3K4me is removed by the histone demethylase, SPR-5 , and H3K9me is subsequently added by the histone methyltransferase, MET-2 . Maternal loss of SPR-5 and MET-2 causes inherited phenotypes, such as sterility, in the progeny. Here, we find that knocking down either the H3K4 methyltransferase SET-2 or the H3K36 methyltransferase MES-4 partially rescues the germline in the progeny of spr-5 ; met-2 mutants, suggesting that the inherited sterility may be caused by inherited H3K4 methylation and altered germline transcription.
Collapse
Affiliation(s)
- Jazmin Dozier
- Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States
| | - Mattie Villhauer
- Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States
| | - Brandon Carpenter
- Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States
| |
Collapse
|
2
|
Bedet C, Quarato P, Palladino F, Cecere G, Robert VJ. The C. elegans SET1 histone methyltransferase SET-2 is not required for transgenerational memory of silencing. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001143. [PMID: 38808193 PMCID: PMC11130714 DOI: 10.17912/micropub.biology.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/22/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
The SET-2 /SET1 histone H3K4 methyltransferase and RNAi pathway components are required to maintain fertility across generations in C. elegans . SET-2 preserves the germline transcriptional program transgenerationally, and RNAi pathways rely on small RNAs to establish and maintain transgenerational gene silencing. We investigated whether the functionality of RNAi-induced transgenerational silencing and the composition of pools of endogenous small RNA are affected by the absence of SET-2 . Our results suggest that defects in RNAi pathways are not responsible for the transcriptional misregulation observed in the absence of SET-2 .
Collapse
Affiliation(s)
- Cécile Bedet
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, Paris, France
- Current address: San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Palladino
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, Paris, France
| | - Valérie J Robert
- Ecole Normale Supérieure de Lyon, Laboratory of Biology and Modeling of the Cell, CNRS UMR5239, Inserm U1293, University Claude Bernard Lyon 1, 69007 Lyon, France Auvergne-Rhône-Alpes, France
| |
Collapse
|
3
|
Ding Y, Zhang C, Zuo Q, Jin K, Li B. lncCPSET1 acts as a scaffold for MLL2/COMPASS to regulate Bmp4 and promote the formation of chicken primordial germ cells. Mol Genet Genomics 2024; 299:41. [PMID: 38551742 DOI: 10.1007/s00438-024-02127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
Primordial germ cells (PGCs) are the ancestors of female and male germ cells. Recent studies have shown that long non-coding RNA (lncRNA) and histone methylation are key epigenetic factors affecting PGC formation; however, their joint regulatory mechanisms have rarely been studied. Here, we explored the mechanism by which lncCPSET1 and H3K4me2 synergistically regulate the formation of chicken PGCs for the first time. Combined with chromatin immunoprecipitation (CHIP) sequencing and RNA-seq of PGCs transfected with the lncCPSET1 overexpression vector, GO annotation and KEGG enrichment analysis revealed that Wnt and TGF-β signaling pathways were significantly enriched, and Fzd2, Id1, Id4, and Bmp4 were identified as candidate genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that ASH2L, DPY30, WDR5, and RBBP5 overexpression significantly increased the expression of Bmp4, which was up-regulated after lncCPSET1 overexpression as well. It indicated that Bmp4 is a target gene co-regulated by lncCPSET1 and MLL2/COMPASS. Interestingly, co-immunoprecipitation results showed that ASH2L, DPY30 and WDR5 combined and RBBP5 weakly combined with DPY30 and WDR5. lncCPSET1 overexpression significantly increased Dpy30 expression and co-immunoprecipitation showed that interference/overexpression of lncCPSET1 did not affect the binding between the proteins in the complexes, but interference with lncCPSET1 inhibited DPY30 expression, which was confirmed by RNA immunoprecipitation that lncCPSET1 binds to DPY30. Additionally, CHIP-qPCR results showed that DPY30 enriched in the Bmp4 promoter region promoted its transcription, thus promoting the formation of PGCs. This study demonstrated that lncCPSET1 and H3K4me2 synergistically promote PGC formation, providing a reference for the study of the regulatory mechanisms between lncRNA and histone methylation, as well as a molecular basis for elucidating the formation mechanism of PGCs in chickens.
Collapse
Affiliation(s)
- Ying Ding
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chen Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- RNA Medicine Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
| | - Qisheng Zuo
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kai Jin
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China.
| |
Collapse
|
4
|
Özcan I, Tursun B. Identifying Molecular Roadblocks for Transcription Factor-Induced Cellular Reprogramming In Vivo by Using C. elegans as a Model Organism. J Dev Biol 2023; 11:37. [PMID: 37754839 PMCID: PMC10531806 DOI: 10.3390/jdb11030037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Generating specialized cell types via cellular transcription factor (TF)-mediated reprogramming has gained high interest in regenerative medicine due to its therapeutic potential to repair tissues and organs damaged by diseases or trauma. Organ dysfunction or improper tissue functioning might be restored by producing functional cells via direct reprogramming, also known as transdifferentiation. Regeneration by converting the identity of available cells in vivo to the desired cell fate could be a strategy for future cell replacement therapies. However, the generation of specific cell types via reprogramming is often restricted due to cell fate-safeguarding mechanisms that limit or even block the reprogramming of the starting cell type. Nevertheless, efficient reprogramming to generate homogeneous cell populations with the required cell type's proper molecular and functional identity is critical. Incomplete reprogramming will lack therapeutic potential and can be detrimental as partially reprogrammed cells may acquire undesired properties and develop into tumors. Identifying and evaluating molecular barriers will improve reprogramming efficiency to reliably establish the target cell identity. In this review, we summarize how using the nematode C. elegans as an in vivo model organism identified molecular barriers of TF-mediated reprogramming. Notably, many identified molecular factors have a high degree of conservation and were subsequently shown to block TF-induced reprogramming of mammalian cells.
Collapse
Affiliation(s)
- Ismail Özcan
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
| | - Baris Tursun
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
| |
Collapse
|
5
|
Godbole AA, Gopalan S, Nguyen TK, Munden AL, Lui DS, Fanelli MJ, Vo P, Lewis CA, Spinelli JB, Fazzio TG, Walker AK. S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress. eLife 2023; 12:e79511. [PMID: 36756948 PMCID: PMC9984191 DOI: 10.7554/elife.79511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Methylation is a widely occurring modification that requires the methyl donor S-adenosylmethionine (SAM) and acts in regulation of gene expression and other processes. SAM is synthesized from methionine, which is imported or generated through the 1-carbon cycle (1 CC). Alterations in 1 CC function have clear effects on lifespan and stress responses, but the wide distribution of this modification has made identification of specific mechanistic links difficult. Exploiting a dynamic stress-induced transcription model, we find that two SAM synthases in Caenorhabditis elegans, SAMS-1 and SAMS-4, contribute differently to modification of H3K4me3, gene expression and survival. We find that sams-4 enhances H3K4me3 in heat shocked animals lacking sams-1, however, sams-1 cannot compensate for sams-4, which is required to survive heat stress. This suggests that the regulatory functions of SAM depend on its enzymatic source and that provisioning of SAM may be an important regulatory step linking 1 CC function to phenotypes in aging and stress.
Collapse
Affiliation(s)
- Adwait A Godbole
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Sneha Gopalan
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
| | - Thien-Kim Nguyen
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Alexander L Munden
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Dominique S Lui
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Matthew J Fanelli
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Paula Vo
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Caroline A Lewis
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
| | - Jessica B Spinelli
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
| | - Thomas G Fazzio
- Cancer Center, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
| | - Amy K Walker
- Program in Molecular Medicine, UMASS Chan Medical SchoolWorcesterUnited States
- Department of Molecular, Cell, and Cancer Biology, UMASS Chan Medical SchoolWorcesterUnited States
| |
Collapse
|
6
|
Ellis RE. Sex Determination in Nematode Germ Cells. Sex Dev 2022:1-18. [PMID: 35172320 PMCID: PMC9378769 DOI: 10.1159/000520872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Animal germ cells differentiate as sperm or as oocytes. These sexual fates are controlled by complex regulatory pathways to ensure that the proper gametes are made at the appropriate times. SUMMARY Nematodes like Caenorhabditis elegans and its close relatives are ideal models for studying how this regulation works, because the XX animals are self-fertile hermaphrodites that produce both sperm and oocytes. In these worms, germ cells use the same signal transduction pathway that functions in somatic cells. This pathway determines the activity of the transcription factor TRA-1, a Gli protein that can repress male genes. However, the pathway is extensively modified in germ cells, largely by the action of translational regulators like the PUF proteins. Many of these modifications play critical roles in allowing the XX hermaphrodites to make sperm in an otherwise female body. Finally, TRA-1 cooperates with chromatin regulators in the germ line to control the activity of fog-1 and fog-3, which are essential for spermatogenesis. FOG-1 and FOG-3 work together to determine germ cell fates by blocking the translation of oogenic transcripts. Key Messages: Although there is great diversity in how germ cell fates are controlled in other animals, many of the key nematode genes are conserved, and the critical role of translational regulators may be universal.
Collapse
Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey, USA
| |
Collapse
|
7
|
Caron M, Gely L, Garvis S, Adrait A, Couté Y, Palladino F, Fabrizio P. Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans. Life Sci Alliance 2021; 5:5/3/e202101140. [PMID: 34893559 PMCID: PMC8675910 DOI: 10.26508/lsa.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/06/2023] Open
Abstract
Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans SET1 homolog. We show that set-2(syb2085) animals retain the ability to form COMPASS, but have a marked global loss of H3K4 di- and trimethylation (H3K4me2/3). Reduced H3K4 methylation was accompanied by loss of fertility, as expected; however, in contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks the SET1/COMPASS chromatin-targeting component. These results challenge previously held views and establish that WT H3K4me2/3 levels are essential for normal lifespan in C. elegans.
Collapse
Affiliation(s)
- Matthieu Caron
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Loïc Gely
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Steven Garvis
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Annie Adrait
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Yohann Couté
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Francesca Palladino
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Paola Fabrizio
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| |
Collapse
|
8
|
Özdemir I, Steiner FA. Transmission of chromatin states across generations in C. elegans. Semin Cell Dev Biol 2021; 127:133-141. [PMID: 34823984 DOI: 10.1016/j.semcdb.2021.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Epigenetic inheritance refers to the transmission of phenotypes across generations without affecting the genomic DNA sequence. Even though it has been documented in many species in fungi, animals and plants, the mechanisms underlying epigenetic inheritance are not fully uncovered. Epialleles, the heritable units of epigenetic information, can take the form of several biomolecules, including histones and their post-translational modifications (PTMs). Here, we review the recent advances in the understanding of the transmission of histone variants and histone PTM patterns across generations in C. elegans. We provide a general overview of the intergenerational and transgenerational inheritance of histone PTMs and their modifiers and discuss the interplay among different histone PTMs. We also evaluate soma-germ line communication and its impact on the inheritance of epigenetic traits.
Collapse
Affiliation(s)
- Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland.
| |
Collapse
|
9
|
Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
Collapse
Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| |
Collapse
|
10
|
Nono M, Kishimoto S, Sato-Carlton A, Carlton PM, Nishida E, Uno M. Intestine-to-Germline Transmission of Epigenetic Information Intergenerationally Ensures Systemic Stress Resistance in C. elegans. Cell Rep 2021; 30:3207-3217.e4. [PMID: 32160530 DOI: 10.1016/j.celrep.2020.02.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 01/29/2023] Open
Abstract
Changes in epigenetic states affect organismal homeostasis, including stress resistance. However, the mechanisms coordinating epigenetic states and systemic stress resistance remain largely unknown. Here, we identify the intestine-to-germline communication of epigenetic states, which intergenerationally enhances stress resistance in C. elegans. The alterations in epigenetic states by deficiency of the histone H3K4me3 modifier ASH-2 in the intestine or germline increase organismal stress resistance, which is abrogated by knockdown of the H3K4 demethylase RBR-2. Remarkably, the increase in stress resistance induced by ASH-2 deficiency in the intestine is abrogated by RBR-2 knockdown in the germline, suggesting the intestine-to-germline transmission of epigenetic information. This communication from intestine to germline in the parental generation increases stress resistance in the next generation. Moreover, the intertissue communication is mediated partly by transcriptional regulation of F08F1.3. These results reveal that intertissue communication of epigenetic information provides mechanisms for intergenerational regulation of systemic stress resistance.
Collapse
Affiliation(s)
- Masanori Nono
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Saya Kishimoto
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Aya Sato-Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Peter Mark Carlton
- Laboratory of Chromosome Function and Inheritance, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Laboratory of Chromosome Function and Inheritance, Radiation Biology Center, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Nishida
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| | - Masaharu Uno
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
| |
Collapse
|
11
|
Kazmierczak M, Farré i Díaz C, Ofenbauer A, Herzog S, Tursun B. The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans. Nucleic Acids Res 2021; 49:e22. [PMID: 33290523 PMCID: PMC7913679 DOI: 10.1093/nar/gkaa1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 12/05/2022] Open
Abstract
Multiple gene activities control complex biological processes such as cell fate specification during development and cellular reprogramming. Investigating the manifold gene functions in biological systems requires also simultaneous depletion of two or more gene activities. RNA interference-mediated knockdown (RNAi) is commonly used in Caenorhabditis elegans to assess essential genes, which otherwise lead to lethality or developmental arrest upon full knockout. RNAi application is straightforward by feeding worms with RNAi plasmid-containing bacteria. However, the general approach of mixing bacterial RNAi clones to deplete two genes simultaneously often yields poor results. To address this issue, we developed a bacterial conjugation-mediated double RNAi technique 'CONJUDOR'. It allows combining RNAi bacteria for robust double RNAi with high-throughput. To demonstrate the power of CONJUDOR for large scale double RNAi screens we conjugated RNAi against the histone chaperone gene lin-53 with more than 700 other chromatin factor genes. Thereby, we identified the Set1/MLL methyltransferase complex member RBBP-5 as a novel germ cell reprogramming barrier. Our findings demonstrate that CONJUDOR increases efficiency and versatility of RNAi screens to examine interconnected biological processes in C. elegans with high-throughput.
Collapse
Affiliation(s)
- Marlon Kazmierczak
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Carlota Farré i Díaz
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Andreas Ofenbauer
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sergej Herzog
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| |
Collapse
|
12
|
How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans? Biochem Soc Trans 2021; 48:1019-1034. [PMID: 32539084 DOI: 10.1042/bst20190944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
Abstract
Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.
Collapse
|
13
|
Padalino G, Chalmers IW, Brancale A, Hoffmann KF. Identification of 6-(piperazin-1-yl)-1,3,5-triazine as a chemical scaffold with broad anti-schistosomal activities. Wellcome Open Res 2020; 5:169. [PMID: 32904763 PMCID: PMC7459852 DOI: 10.12688/wellcomeopenres.16069.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Schistosomiasis, caused by infection with blood fluke schistosomes, is a neglected tropical disease of considerable importance in resource-poor communities throughout the developing world. In the absence of an immunoprophylactic vaccine and due to over-reliance on a single chemotherapy (praziquantel), schistosomiasis control is at risk should drug insensitive schistosomes develop. In this context, application of in silico virtual screening on validated schistosome targets has proven successful in the identification of novel small molecules with anti-schistosomal activity. Methods: Focusing on the Schistosoma mansoni histone methylation machinery, we herein have used RNA interference (RNAi), ELISA-mediated detection of H3K4 methylation, homology modelling and in silico virtual screening to identify a small collection of small molecules for anti-schistosomal testing. A combination of low to high-throughput whole organism assays were subsequently used to assess these compounds' activities on miracidia to sporocyst transformation, schistosomula phenotype/motility metrics and adult worm motility/oviposition readouts. Results: RNAi-mediated knockdown of smp_138030/smmll-1 (encoding a histone methyltransferase, HMT) in adult worms (~60%) reduced parasite motility and egg production. Moreover, in silico docking of compounds into Smp_138030/SmMLL-1's homology model highlighted competitive substrate pocket inhibitors, some of which demonstrated significant activity on miracidia, schistosomula and adult worm lifecycle stages together with variable effects on HepG2 cells. Particularly, the effect of compounds containing a 6-(piperazin-1-yl)-1,3,5-triazine core on adult schistosomes recapitulated the results of the smp_138030/smmll-1 RNAi screens. Conclusions: The biological data and the structure-activity relationship presented in this study define the 6-(piperazin-1-yl)-1,3,5-triazine core as a promising starting point in ongoing efforts to develop new urgently needed schistosomicides.
Collapse
Affiliation(s)
- Gilda Padalino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| |
Collapse
|
14
|
Robert VJ, Knutson AK, Rechtsteiner A, Garvis S, Yvert G, Strome S, Palladino F. Caenorhabditis elegans SET1/COMPASS Maintains Germline Identity by Preventing Transcriptional Deregulation Across Generations. Front Cell Dev Biol 2020; 8:561791. [PMID: 33072747 PMCID: PMC7536326 DOI: 10.3389/fcell.2020.561791] [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: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin regulators contribute to the maintenance of the germline transcriptional program. In the absence of SET-2, the Caenorhabditis elegans homolog of the SET1/COMPASS H3 Lys4 (H3K4) methyltransferase, animals show transgenerational loss of germline identity, leading to sterility. To identify transcriptional signatures associated with progressive loss of fertility, we performed expression profiling of set-2 mutant germlines across generations. We identify a subset of genes whose misexpression is first observed in early generations, a step we refer to as priming; their misexpression then further progresses in late generations, as animals reach sterility. Analysis of misregulated genes shows that down-regulation of germline genes, expression of somatic transcriptional programs, and desilencing of the X-chromosome are concurrent events leading to loss of germline identity in both early and late generations. Upregulation of transcription factor LIN-15B, the C/EBP homolog CEBP-1, and TGF-β pathway components strongly contribute to loss of fertility, and RNAi inactivation of cebp-1 and TGF-β/Smad signaling delays the onset of sterility, showing they individually contribute to maintenance of germ cell identity. Our approach therefore identifies genes and pathways whose misexpression actively contributes to the loss of germ cell fate. More generally, our data shows how loss of a chromatin regulator in one generation leads to transcriptional changes that are amplified over subsequent generations, ultimately leading to loss of appropriate cell fate.
Collapse
Affiliation(s)
- Valérie J Robert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Andrew K Knutson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Steven Garvis
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| |
Collapse
|
15
|
Wang S, Meyer DH, Schumacher B. H3K4me2 regulates the recovery of protein biosynthesis and homeostasis following DNA damage. Nat Struct Mol Biol 2020; 27:1165-1177. [DOI: 10.1038/s41594-020-00513-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/02/2020] [Indexed: 01/08/2023]
|
16
|
ul Fatima N, Tursun B. Conversion of Germ Cells to Somatic Cell Types in C. elegans. J Dev Biol 2020; 8:E24. [PMID: 33036439 PMCID: PMC7712076 DOI: 10.3390/jdb8040024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
The potential of a cell to produce all types of differentiated cells in an organism is termed totipotency. Totipotency is an essential property of germ cells, which constitute the germline and pass on the parental genetic material to the progeny. The potential of germ cells to give rise to a whole organism has been the subject of intense research for decades and remains important in order to better understand the molecular mechanisms underlying totipotency. A better understanding of the principles of totipotency in germ cells could also help to generate this potential in somatic cell lineages. Strategies such as transcription factor-mediated reprogramming of differentiated cells to stem cell-like states could benefit from this knowledge. Ensuring pluripotency or even totipotency of reprogrammed stem cells are critical improvements for future regenerative medicine applications. The C. elegans germline provides a unique possibility to study molecular mechanisms that maintain totipotency and the germ cell fate with its unique property of giving rise to meiotic cells Studies that focused on these aspects led to the identification of prominent chromatin-repressing factors such as the C. elegans members of the Polycomb Repressive Complex 2 (PRC2). In this review, we summarize different factors that were recently identified, which use molecular mechanisms such as control of protein translation or chromatin repression to ensure maintenance of totipotency and the germline fate. Additionally, we focus on recently identified factors involved in preventing transcription-factor-mediated conversion of germ cells to somatic lineages. These so-called reprogramming barriers have been shown in some instances to be conserved with regard to their function as a cell fate safeguarding factor in mammals. Overall, continued studies assessing the different aspects of molecular pathways involved in maintaining the germ cell fate in C. elegans may provide more insight into cell fate safeguarding mechanisms also in other species.
Collapse
Affiliation(s)
- Nida ul Fatima
- Berlin Institute of Medical Systems Biology, 10115 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Baris Tursun
- Berlin Institute of Medical Systems Biology, 10115 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| |
Collapse
|
17
|
Herbette M, Robert V, Bailly A, Gely L, Feil R, Llères D, Palladino F. A Role for Caenorhabditis elegans COMPASS in Germline Chromatin Organization. Cells 2020; 9:cells9092049. [PMID: 32911802 PMCID: PMC7565041 DOI: 10.3390/cells9092049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
Deposition of histone H3 lysine 4 (H3K4) methylation at promoters is catalyzed by the SET1/COMPASS complex and is associated with context-dependent effects on gene expression and local changes in chromatin organization. The role of SET1/COMPASS in shaping chromosome architecture has not been investigated. Here we used Caenorhabditis elegans to address this question through a live imaging approach and genetic analysis. Using quantitative FRET (Förster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) on germ cells expressing histones eGFP-H2B and mCherry-H2B, we find that SET1/COMPASS influences meiotic chromosome organization, with marked effects on the close proximity between nucleosomes. We further show that inactivation of set-2, encoding the C. elegans SET1 homologue, or CFP-1, encoding the chromatin targeting subunit of COMPASS, enhances germline chromosome organization defects and sterility of condensin-II depleted animals. set-2 loss also aggravates germline defects resulting from conditional inactivation of topoisomerase II, another structural component of chromosomes. Expression profiling of set-2 mutant germlines revealed only minor transcriptional changes, suggesting that the observed effects are at least partly independent of transcription. Altogether, our results are consistent with a role for SET1/COMPASS in shaping meiotic chromosomes in C. elegans, together with the non-histone proteins condensin-II and topoisomerase. Given the high degree of conservation, our findings expand the range of functions attributed to COMPASS and suggest a broader role in genome organization in different species.
Collapse
Affiliation(s)
- Marion Herbette
- Laboratory of Biology and Modeling of the Cell (LBMC), CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (V.R.); (L.G.)
| | - Valérie Robert
- Laboratory of Biology and Modeling of the Cell (LBMC), CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (V.R.); (L.G.)
| | - Aymeric Bailly
- Centre de Recherche en Biologie cellulaire de Montpellier, CRBM, CNRS, University of Montpellier, 34090 Montpellier, France;
| | - Loïc Gely
- Laboratory of Biology and Modeling of the Cell (LBMC), CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (V.R.); (L.G.)
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, 34090 Montpellier, France; (R.F.); (D.L.)
| | - David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, University of Montpellier, 34090 Montpellier, France; (R.F.); (D.L.)
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell (LBMC), CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon, 69007 Lyon, France; (M.H.); (V.R.); (L.G.)
- Correspondence: ; Tel.: +33-047-2728-126
| |
Collapse
|
18
|
Abay-Nørgaard S, Attianese B, Boreggio L, Salcini AE. Regulators of H3K4 methylation mutated in neurodevelopmental disorders control axon guidance in Caenorhabditis elegans. Development 2020; 147:dev.190637. [PMID: 32675280 PMCID: PMC7420840 DOI: 10.1242/dev.190637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Abstract
Post-translational histone modifications regulate chromatin compaction and gene expression to control many aspects of development. Mutations in genes encoding regulators of H3K4 methylation are causally associated with neurodevelopmental disorders characterized by intellectual disability and deficits in motor functions. However, it remains unclear how H3K4 methylation influences nervous system development and contributes to the aetiology of disease. Here, we show that the catalytic activity of set-2, the Caenorhabditis elegans homologue of the H3K4 methyltransferase KMT2F/G (SETD1A/B) genes, controls embryonic transcription of neuronal genes and is required for establishing proper axon guidance, and for neuronal functions related to locomotion and learning. Moreover, we uncover a striking correlation between components of the H3K4 regulatory machinery mutated in neurodevelopmental disorders and the process of axon guidance in C. elegans. Thus, our study supports an epigenetic-based model for the aetiology of neurodevelopmental disorders, based on an aberrant axon guidance process originating from deregulated H3K4 methylation. Summary: Analysis of mutants lacking many known H3K4 regulators reveals the role of H3K4 methylation in C. elegans neuronal functions and suggests that aberrant axon guidance is a shared trait in neurodevelopmental diseases.
Collapse
Affiliation(s)
- Steffen Abay-Nørgaard
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Benedetta Attianese
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Laura Boreggio
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- BRIC, University of Copenhagen, Biotech Research and Innovation Centre, Ole Maaloes vej 5, 2200, Copenhagen, Denmark
| |
Collapse
|
19
|
Rogers AK, Phillips CM. RNAi pathways repress reprogramming of C. elegans germ cells during heat stress. Nucleic Acids Res 2020; 48:4256-4273. [PMID: 32187370 PMCID: PMC7192617 DOI: 10.1093/nar/gkaa174] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023] Open
Abstract
Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these cell fate decisions is an active area of investigation. Here we show that RNAi pathways play a key role in maintaining germline gene expression and totipotency after heat stress. By examining transcriptional changes that occur in mut-16 mutants, lacking a key protein in the RNAi pathway, at elevated temperature we found that genes normally expressed in the soma are mis-expressed in germ cells. Furthermore, these genes displayed increased chromatin accessibility in the germlines of mut-16 mutants at elevated temperature. These findings indicate that the RNAi pathway plays a key role in preventing aberrant expression of somatic genes in the germline during heat stress. This regulation occurs in part through the maintenance of germline chromatin, likely acting through the nuclear RNAi pathway. Identification of new pathways governing germ cell reprogramming is critical to understanding how cells maintain proper gene expression and may provide key insights into how cell identity is lost in some germ cell tumors.
Collapse
Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
20
|
Padalino G, Chalmers IW, Brancale A, Hoffmann KF. Identification of 6-(piperazin-1-yl)-1,3,5-triazine as a chemical scaffold with broad anti-schistosomal activities. Wellcome Open Res 2020; 5:169. [PMID: 32904763 PMCID: PMC7459852 DOI: 10.12688/wellcomeopenres.16069.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Schistosomiasis, caused by infection with blood fluke schistosomes, is a neglected tropical disease of considerable importance in resource-poor communities throughout the developing world. In the absence of an immunoprophylactic vaccine and due to over-reliance on a single chemotherapy (praziquantel), schistosomiasis control is at risk should drug insensitive schistosomes develop. In this context, application of in silico virtual screening on validated schistosome targets has proven successful in the identification of novel small molecules with anti-schistosomal activity. Methods: Focusing on the Schistosoma mansoni histone methylation machinery, we herein have used RNA interference (RNAi), ELISA-mediated detection of H3K4 methylation, homology modelling and in silico virtual screening to identify a small collection of small molecules for anti-schistosomal testing. A combination of low to high-throughput whole organism assays were subsequently used to assess these compounds' activities on miracidia to sporocyst transformation, schistosomula phenotype/motility metrics and adult worm motility/oviposition readouts. Results: RNAi-mediated knockdown of smp_138030/smmll-1 (encoding a histone methyltransferase, HMT) in adult worms (~60%) reduced parasite motility and egg production. Moreover, in silico docking of compounds into Smp_138030/SmMLL-1's homology model highlighted competitive substrate pocket inhibitors, some of which demonstrated significant activity on miracidia, schistosomula and adult worm lifecycle stages together with variable effects on HepG2 cells. Particularly, the effect of compounds containing a 6-(piperazin-1-yl)-1,3,5-triazine core on adult schistosomes recapitulated the results of the smp_138030/smmll-1 RNAi screens. Conclusions: The biological data and the structure-activity relationship presented in this study define the 6-(piperazin-1-yl)-1,3,5-triazine core as a promising starting point in ongoing efforts to develop new urgently needed schistosomicides.
Collapse
Affiliation(s)
- Gilda Padalino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, Wales, CF10 3NB, UK
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3DA, UK
| |
Collapse
|
21
|
Zraly CB, Zakkar A, Perez JH, Ng J, White KP, Slattery M, Dingwall AK. The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. Nucleic Acids Res 2020; 48:3476-3495. [PMID: 32052053 PMCID: PMC7144903 DOI: 10.1093/nar/gkaa082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi depletion of the Cmi (also known as Lpt) subunit that contains the chromatin binding PHD finger domains attenuates enhancer functions, but unexpectedly results in inappropriate enhancer activation during stages when hormone responsive enhancers are poised, revealing critical epigenetic roles involved in both the activation and repression of enhancers depending on developmental context. Cmi is necessary for robust H3K4 monomethylation and H3K27 acetylation that mark active enhancers, but not for the chromatin binding of Trr, the MLR methyltransferase. Our data reveal two likely major regulatory modes of MLR function, contributions to enhancer commissioning in early embryogenesis and bookmarking enhancers to enable rapid transcriptional re-activation at subsequent developmental stages.
Collapse
Affiliation(s)
- Claudia B Zraly
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abdul Zakkar
- Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - John Hertenstein Perez
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jeffrey Ng
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Biology, Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.,Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Andrew K Dingwall
- Department of Cancer Biology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.,Department of Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
22
|
Kranz A, Anastassiadis K. The role of SETD1A and SETD1B in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194578. [PMID: 32389824 DOI: 10.1016/j.bbagrm.2020.194578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/16/2020] [Accepted: 05/03/2020] [Indexed: 12/13/2022]
Abstract
The Trithorax-related Set1 H3K4 methyltransferases are conserved from yeast to human. In yeast loss of Set1 causes pleiotropic effects but is compatible with life. In contrast, both mammalian Set1 orthologs: SETD1A and SETD1B are essential for embryonic development, however they have distinct functions. SETD1A is required shortly after epiblast formation whereas SETD1B becomes indispensible during early organogenesis. In adult mice both SETD1A and SETD1B regulate hematopoiesis differently: SETD1A is required for the establishment of definitive hematopoiesis whereas SETD1B is important for the maintenance of long-term hematopoietic stem cells. Both are implicated in different diseases with accumulating evidence for the association of SETD1A variants in neurological disorders and SETD1B variants with cancer. Why the two paralogs cannot or only partially compensate for the loss of each other is part of the puzzle that we try to sort out in this review.
Collapse
Affiliation(s)
- Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany.
| |
Collapse
|
23
|
Lee TWS, David HS, Engstrom AK, Carpenter BS, Katz DJ. Repressive H3K9me2 protects lifespan against the transgenerational burden of COMPASS activity in C. elegans. eLife 2019; 8:e48498. [PMID: 31815663 PMCID: PMC7299346 DOI: 10.7554/elife.48498] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/06/2019] [Indexed: 12/17/2022] Open
Abstract
In Caenorhabditis elegans, mutations in WDR-5 and other components of the COMPASS H3K4 methyltransferase complex extend lifespan and enable its inheritance. Here, we show that wdr-5 mutant longevity is itself a transgenerational trait that corresponds with a global enrichment of the heterochromatin factor H3K9me2 over twenty generations. In addition, we find that the transgenerational aspects of wdr-5 mutant longevity require the H3K9me2 methyltransferase MET-2, and can be recapitulated by removal of the putative H3K9me2 demethylase JHDM-1. Finally, we show that the transgenerational acquisition of longevity in jhdm-1 mutants is associated with accumulating genomic H3K9me2 that is inherited by their long-lived wild-type descendants at a subset of loci. These results suggest that heterochromatin facilitates the transgenerational establishment and inheritance of a complex trait. Based on these results, we propose that transcription-coupled H3K4me via COMPASS limits lifespan by encroaching upon domains of heterochromatin in the genome.
Collapse
Affiliation(s)
- Teresa Wei-sy Lee
- Department of Cell BiologyEmory University School of MedicineAtlantaUnited States
| | - Heidi Shira David
- Department of Cell BiologyEmory University School of MedicineAtlantaUnited States
| | | | | | - David John Katz
- Department of Cell BiologyEmory University School of MedicineAtlantaUnited States
| |
Collapse
|
24
|
Bazopoulou D, Knoefler D, Zheng Y, Ulrich K, Oleson BJ, Xie L, Kim M, Kaufmann A, Lee YT, Dou Y, Chen Y, Quan S, Jakob U. Developmental ROS individualizes organismal stress resistance and lifespan. Nature 2019; 576:301-305. [PMID: 31801997 PMCID: PMC7039399 DOI: 10.1038/s41586-019-1814-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
A central aspect of aging research concerns the question of when individuality in lifespan arises1. Here we show that a transient increase in reactive oxygen species (ROS), which occurs naturally during early development in a subpopulation of synchronized Caenorhabditis elegans, sets processes in motion that increase stress resistance, improve redox homeostasis and ultimately prolong lifespan in those animals. We find that these effects are linked to the global ROS-mediated decrease in developmental histone H3K4me3 levels. Studies in HeLa cells confirmed that global H3K4me3 levels are ROS-sensitive and that depletion of H3K4me3 levels increases stress resistance in mammalian cell cultures. In vitro studies identified SET1/MLL histone methyltransferases as redox sensitive units of the H3K4-trimethylating complex of proteins (COMPASS). Our findings implicate a link between early-life events, ROS-sensitive epigenetic marks, stress resistance and lifespan.
Collapse
Affiliation(s)
- Daphne Bazopoulou
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniela Knoefler
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yongxin Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, China
| | - Kathrin Ulrich
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Bryndon J Oleson
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lihan Xie
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Minwook Kim
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anke Kaufmann
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Young-Tae Lee
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, China
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
25
|
Beurton F, Stempor P, Caron M, Appert A, Dong Y, Chen RAJ, Cluet D, Couté Y, Herbette M, Huang N, Polveche H, Spichty M, Bedet C, Ahringer J, Palladino F. Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. Nucleic Acids Res 2019; 47:11164-11180. [PMID: 31602465 PMCID: PMC6868398 DOI: 10.1093/nar/gkz880] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022] Open
Abstract
The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.
Collapse
Affiliation(s)
- Flore Beurton
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ron A-j Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marion Herbette
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hélène Polveche
- INSERM UMR 861, I-STEM, 28, Rue Henri Desbruères, 91100 Corbeil-Essonnes, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| |
Collapse
|
26
|
Pokhrel B, Chen Y, Biro JJ. CFP-1 interacts with HDAC1/2 complexes in C. elegans development. FEBS J 2019; 286:2490-2504. [PMID: 30941832 DOI: 10.1111/febs.14833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/31/2019] [Accepted: 04/01/2019] [Indexed: 01/27/2023]
Abstract
CXXC finger binding protein 1 (CFP-1) is an evolutionarily conserved protein that binds to non-methylated CpG-rich promoters in mammals and Caenorhabditis elegans. This conserved epigenetic regulator is part of the COMPASS complex that contains the H3K4me3 methyltransferase SET1 in mammals and SET-2 in C. elegans. Previous studies have indicated the importance of CFP1 in embryonic stem cell differentiation and cell fate specification. However, neither the function nor the mechanism of action of CFP1 is well understood at the organismal level. Here, we have used cfp-1(tm6369) and set-2(bn129) C. elegans mutants to investigate the function of CFP-1 in gene induction and development. We have characterised C. elegansCOMPASS mutants cfp-1(tm6369) and set-2(bn129) and found that both cfp-1 and set-2 play an important role in the regulation of fertility and development of the organism. Furthermore, we found that both cfp-1 and set-2 are required for H3K4 trimethylation and play a repressive role in the expression of heat shock and salt-inducible genes. Interestingly, we found that cfp-1 but not set-2 genetically interacts with histone deacetylase (HDAC1/2) complexes to regulate fertility, suggesting a function of CFP-1 outside of the COMPASS complex. Additionally, we found that cfp-1 and set-2 independently regulate fertility and development of the organism. Our results suggest that CFP-1 genetically interacts with HDAC1/2 complexes to regulate fertility, independent of its function within the COMPASS complex. We propose that CFP-1 could cooperate with the COMPASS complex and/or HDAC1/2 in a context-dependent manner.
Collapse
Affiliation(s)
- Bharat Pokhrel
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Yannic Chen
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Jonathan Joseph Biro
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
| |
Collapse
|
27
|
Ding W, Higgins DP, Yadav DK, Godbole AA, Pukkila-Worley R, Walker AK. Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine. PLoS Genet 2018; 14:e1007812. [PMID: 30485261 PMCID: PMC6287882 DOI: 10.1371/journal.pgen.1007812] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/10/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022] Open
Abstract
S-adenosylmethionine (SAM) is a donor which provides the methyl groups for histone or nucleic acid modification and phosphatidylcholine production. SAM is hypothesized to link metabolism and chromatin modification, however, its role in acute gene regulation is poorly understood. We recently found that Caenorhabditis elegans with reduced SAM had deficiencies in H3K4 trimethylation (H3K4me3) at pathogen-response genes, decreasing their expression and limiting pathogen resistance. We hypothesized that SAM may be generally required for stress-responsive transcription. Here, using genetic assays, we show that transcriptional responses to bacterial or xenotoxic stress fail in C. elegans with low SAM, but that expression of heat shock genes are unaffected. We also found that two H3K4 methyltransferases, set-2/SET1 and set-16/MLL, had differential responses to survival during stress. set-2/SET1 is specifically required in bacterial responses, whereas set-16/MLL is universally required. These results define a role for SAM in the acute stress-responsive gene expression. Finally, we find that modification of metabolic gene expression correlates with enhanced survival during stress.
Collapse
Affiliation(s)
- Wei Ding
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Daniel P. Higgins
- Department of Computer Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Dilip K. Yadav
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Adwait A. Godbole
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, UMASS Medical School, Worcester, MA, United States of America
| | - Amy K. Walker
- Program in Molecular Medicine, UMASS Medical School, Worcester, MA, United States of America
| |
Collapse
|
28
|
Saltzman AL, Soo MW, Aram R, Lee JT. Multiple Histone Methyl-Lysine Readers Ensure Robust Development and Germline Immortality in Caenorhabditis elegans. Genetics 2018; 210:907-923. [PMID: 30185429 PMCID: PMC6218232 DOI: 10.1534/genetics.118.301518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/23/2018] [Indexed: 11/18/2022] Open
Abstract
Chromatin modifications, including methylation of histone H3 at lysine 27 (H3K27me) by the Polycomb group proteins, play a broadly conserved role in the maintenance of cell fate. Diverse chromatin organization modifier (chromo) domain proteins act as "readers" of histone methylation states. However, understanding the functional relationships among chromo domains and their roles in the inheritance of gene expression patterns remains challenging. Here, we identify two chromo-domain proteins, CEC-1 and CEC-6, as potential readers of H3K27me in Caenorhabditis elegans, where they have divergent expression patterns and contribute to distinct phenotypes. Both cec-1 and cec-6 genetically interact with another chromo-domain gene, cec-3, a reader of H3K9 methylation. Combined loss of cec-1 and cec-3 leads to developmental defects in the adult that result in decreased fitness. Furthermore, loss of cec-6 and cec-3 surprisingly leads to a progressive loss of fertility across generations, a "mortal germline" phenotype. Our results provide evidence of functional compensation between H3K27me and H3K9me heterochromatin pathways, and show that histone methylation readers contribute to both somatic development and transgenerational fitness.
Collapse
Affiliation(s)
- Arneet L Saltzman
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Mark W Soo
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Reta Aram
- Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3G5, Canada
| | - Jeannie T Lee
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
29
|
Tabuchi TM, Rechtsteiner A, Jeffers TE, Egelhofer TA, Murphy CT, Strome S. Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis. Nat Commun 2018; 9:4310. [PMID: 30333496 PMCID: PMC6193031 DOI: 10.1038/s41467-018-06236-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 08/15/2018] [Indexed: 12/21/2022] Open
Abstract
Paternal contributions to epigenetic inheritance are not well understood. Paternal contributions via marked nucleosomes are particularly understudied, in part because sperm in some organisms replace the majority of nucleosome packaging with protamine packaging. Here we report that in Caenorhabditis elegans sperm, the genome is packaged in nucleosomes and carries a histone-based epigenetic memory of genes expressed during spermatogenesis, which unexpectedly include genes well known for their expression during oogenesis. In sperm, genes with spermatogenesis-restricted expression are uniquely marked with both active and repressive marks, which may reflect a sperm-specific chromatin signature. We further demonstrate that epigenetic information provided by sperm is important and in fact sufficient to guide proper germ cell development in offspring. This study establishes one mode of paternal epigenetic inheritance and offers a potential mechanism for how the life experiences of fathers may impact the development and health of their descendants.
Collapse
Affiliation(s)
- Tomoko M Tabuchi
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Tess E Jeffers
- Department of Molecular Biology and LSI Genomics, Carl Icahn Lab 148, Princeton University, Princeton, NJ, 08545, USA
| | - Thea A Egelhofer
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Coleen T Murphy
- Department of Molecular Biology and LSI Genomics, Carl Icahn Lab 148, Princeton University, Princeton, NJ, 08545, USA
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.
| |
Collapse
|
30
|
Frézal L, Demoinet E, Braendle C, Miska E, Félix MA. Natural Genetic Variation in a Multigenerational Phenotype in C. elegans. Curr Biol 2018; 28:2588-2596.e8. [PMID: 30078564 PMCID: PMC6984962 DOI: 10.1016/j.cub.2018.05.091] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/16/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
Although heredity mostly relies on the transmission of DNA sequence, additional molecular and cellular features are heritable across several generations. In the nematode Caenorhabditis elegans, insights into such unconventional inheritance result from two lines of work. First, the mortal germline (Mrt) phenotype was defined as a multigenerational phenotype whereby a selfing lineage becomes sterile after several generations, implying multigenerational memory [1, 2]. Second, certain RNAi effects are heritable over several generations in the absence of the initial trigger [3-5]. Both lines of work converged when the subset of Mrt mutants that are heat sensitive were found to closely correspond to mutants defective in the RNAi-inheritance machinery, including histone modifiers [6-9]. Here, we report the surprising finding that several C. elegans wild isolates display a heat-sensitive mortal germline phenotype in laboratory conditions: upon chronic exposure to higher temperatures, such as 25°C, lines reproducibly become sterile after several generations. This phenomenon is reversible, as it can be suppressed by temperature alternations at each generation, suggesting a non-genetic basis for the sterility. We tested whether natural variation in the temperature-induced Mrt phenotype was of genetic nature by building recombinant inbred lines between the isolates MY10 (Mrt) and JU1395 (non-Mrt). Using bulk segregant analysis, we detected two quantitative trait loci. After further recombinant mapping and genome editing, we identified the major causal locus as a polymorphism in the set-24 gene, encoding a SET- and SPK-domain protein. We conclude that C. elegans natural populations may harbor natural genetic variation in epigenetic inheritance phenomena.
Collapse
Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France; Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | | | | | - Eric Miska
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, INSERM, École Normale Supérieure, Paris Sciences et Lettres, Paris, France.
| |
Collapse
|
31
|
Abstract
The eukaryotic epigenome has an instrumental role in determining and maintaining cell identity and function. Epigenetic components such as DNA methylation, histone tail modifications, chromatin accessibility, and DNA architecture are tightly correlated with central cellular processes, while their dysregulation manifests in aberrant gene expression and disease. The ability to specifically edit the epigenome holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes. Genome engineering technologies use highly specific DNA-targeting tools to precisely deposit epigenetic changes in a locus-specific manner, creating diverse epigenome editing platforms. This review summarizes these technologies and insights from recent studies, describes the complex relationship between epigenetic components and gene regulation, and highlights caveats and promises of the emerging field of epigenome editing, including applications for translational purposes, such as epigenetic therapy and regenerative medicine.
Collapse
Affiliation(s)
- Liad Holtzman
- Department of Biomedical Engineering and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; ,
| | - Charles A Gersbach
- Department of Biomedical Engineering and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; , .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| |
Collapse
|
32
|
Wang W, Chaturbedi A, Wang M, An S, Santhi Velayudhan S, Lee SS. SET-9 and SET-26 are H3K4me3 readers and play critical roles in germline development and longevity. eLife 2018; 7:34970. [PMID: 29714684 PMCID: PMC6010342 DOI: 10.7554/elife.34970] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/30/2018] [Indexed: 12/25/2022] Open
Abstract
C. elegans SET-9 and SET-26 are highly homologous paralogs that share redundant functions in germline development, but SET-26 alone plays a key role in longevity and heat stress response. Whereas SET-26 is broadly expressed, SET-9 is only detectable in the germline, which likely accounts for their different biological roles. SET-9 and SET-26 bind to H3K4me3 with adjacent acetylation marks in vitro and in vivo. In the soma, SET-26 acts through DAF-16 to modulate longevity. In the germline, SET-9 and SET-26 restrict H3K4me3 domains around SET-9 and SET-26 binding sites, and regulate the expression of specific target genes, with critical consequence on germline development. SET-9 and SET-26 are highly conserved and our findings provide new insights into the functions of these H3K4me3 readers in germline development and longevity. Cells keep their DNA organized by wrapping it around groups of proteins called histones. These structures not only keep the genetic code tidy, they also affect how and when a cell uses its genes. This is because small chemical groups that are added to histones, such as a methyl group added to the fourth position of histone H3 (known as H3K4me3), affect which proteins can access the surrounding genes. This in turn determines whether those genes are likely to be on or off. Many proteins help to regulate histone modifications, including proteins that add or remove the specific chemical groups. Enzymes that add a methyl group to histone usually contain a region called SET; while proteins containing a structure called a PHD finger can recognize histone modifications and help to amplify the signal to switch a gene on or off. SET-9 and SET-26 are two proteins containing both SET regions and PHD fingers. Found in the worm Caenorhabditis elegans, these proteins are 97% identical. Changes in histone modifications can affect the lifespan of these worms, and the number of offspring they produce. Recent work revealed that loss of SET-9 and SET-26 makes the worms live longer. Now, Wang et al. use gene editing to better understand how these proteins have their effects. Experiments with worms lacking the gene for SET-9 or SET-26 or both revealed that, despite looking almost identical, SET-9 and SET-26 have different roles. Every cell in the worm makes SET-26 protein and getting rid of it increases their lifespan by affecting the activity of a protein called DAF-16. But, only the cells in the reproductive system make SET-9, and both proteins play a role in fertility. A technique called ChIP-seq revealed where each protein attached to the genome. The PHD fingers of SET-9 and SET-26 bound to around half of the possible H3K4me3 modification sites. Not all the possible sites actually had a methyl group attached, and the pattern of binding matched the pattern of modifications. This indicates that the two proteins arrive only once the positions already have their methyl groups. Getting rid of the SET-9 and SET-26 proteins increased the number of H3K4me3 sites with methyl groups attached. This suggests that the role of SET-9 and SET-26 is to stop the spread of H3K4me3 modifications, controlling the use of certain genes. In mammals, the proteins SETD5 and MLL5 likely do the job of SET-9 and SET-26. Understanding how they work in worms could further our understanding of fertility and ageing in humans.
Collapse
Affiliation(s)
- Wenke Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Minghui Wang
- Computational Biology Service Unit, Cornell University, Ithaca, United States
| | - Serim An
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | | | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| |
Collapse
|
33
|
Ding B, Cao Z, Hong R, Li H, Zuo X, Luo L, Li Y, Huang W, Li W, Zhang K, Zhang Y. WDR5 in porcine preimplantation embryos: expression, regulation of epigenetic modifications and requirement for early development†. Biol Reprod 2018; 96:758-771. [PMID: 28379447 DOI: 10.1093/biolre/iox020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/29/2017] [Indexed: 11/12/2022] Open
Abstract
WD repeat-containing protein 5 (WDR5), a member of conserved WD40 protein family, is an essential component of the mixed lineage leukemia (MLL) complexes, which are crucial for numerous key biological processes including methylation of histone H3 lysine 4 (H3K4), self-renewal of embryonic stem cells, and formation of induced pluripotent stem cells. The expression pattern and functional role of WDR5 during porcine preimplantation embryonic development, however, remain unknown. Our results showed that the transcripts and protein of WDR5 exhibited stage-specific expression pattern in porcine early embryos. Moreover, blastocyst rate and total cell number per blastocyst were reduced by RNAi-mediated silencing of WDR5 or pharmacological inhibition of WDR5. Knockdown of WDR5 also disturbed the expression of several pluripotency genes. Interestingly, tri-methylation of H3K4 (H3K4me3) level was dramatically increased by WDR5 depletion. Further analysis revealed that loss of MLL3 phenocopied WDR5 knockdown, triggering increased H3K4me3 level. Simultaneously, WDR5 depletion significantly decreased the levels of histone H4 lysine 16 acetylation (H4K16ac) and its writer males absent on the first (MOF). Last but not least, WDR5 knockdown induced DNA damage and DNA repair defects during porcine preimplantation development. Taken together, results of described studies establish that WDR5 plays a significant role in porcine preimplantation embryos probably through regulating key epigenetic modifications and genome integrity.
Collapse
Affiliation(s)
- Biao Ding
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.,Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Zubing Cao
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Renyun Hong
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Hui Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaoyuan Zuo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Lei Luo
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Yunsheng Li
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Weiping Huang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Wenyong Li
- Key Laboratory of Embryo Development and Reproduction Regulation of Anhui Province, College of Biological and Food Engineering, Fuyang Normal University, Fuyang, Anhui, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| |
Collapse
|
34
|
Herbette M, Mercier M, Michal F, Cluet D, Burny C, Yvert G, Robert V, Palladino F. The C. elegans SET-2/SET1 histone H3 Lys4 (H3K4) methyltransferase preserves genome stability in the germline. DNA Repair (Amst) 2017; 57:139-150. [DOI: 10.1016/j.dnarep.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
|
35
|
Albritton SE, Kranz AL, Winterkorn LH, Street LA, Ercan S. Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. eLife 2017; 6. [PMID: 28562241 PMCID: PMC5451215 DOI: 10.7554/elife.23645] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/02/2017] [Indexed: 12/17/2022] Open
Abstract
In many organisms, it remains unclear how X chromosomes are specified for dosage compensation, since DNA sequence motifs shown to be important for dosage compensation complex (DCC) recruitment are themselves not X-specific. Here, we addressed this problem in C. elegans. We found that the DCC recruiter, SDC-2, is required to maintain open chromatin at a small number of primary DCC recruitment sites, whose sequence and genomic context are X-specific. Along the X, primary recruitment sites are interspersed with secondary sites, whose function is X-dependent. A secondary site can ectopically recruit the DCC when additional recruitment sites are inserted either in tandem or at a distance (>30 kb). Deletion of a recruitment site on the X results in reduced DCC binding across several megabases surrounded by topologically associating domain (TAD) boundaries. Our work elucidates that hierarchy and long-distance cooperativity between gene-regulatory elements target a single chromosome for regulation. DOI:http://dx.doi.org/10.7554/eLife.23645.001 The DNA inside living cells is organized in structures called chromosomes. In many animals, females have two X chromosomes, whereas males have only one. To ensure that females do not end up with a double dose of the proteins encoded by the genes on the X chromosome, animals use a process called dosage compensation to correct this imbalance. The mechanisms underlying this process vary between species, but they typically involve a regulatory complex that binds to the X chromosomes of one sex to modify gene expression. Caenorhabditis elegans, for example, is a species of nematode worm in which individuals with two X chromosomes are hermaphrodites and those with one X chromosome are males. In C. elegans, a regulatory complex, called the dosage compensation complex, attaches to both X chromosomes of a hermaphrodite, and reduces the expression of the genes on each by half to match the level seen in the males. Previous research has shown that short DNA sequences, known as motifs, recruit the dosage compensation complex to the X chromosomes. However, these sequences are also found on the other chromosomes and, until now, it was not known why the complex was only recruited to the X chromosomes. Albritton et al. now show the X chromosomes have a ‘hierarchical’ recruitment system. A few sites on the X chromosomes contain clusters of a specific DNA motif, which initiate the process and attract the dosage compensation complex more strongly than other sites. These ‘strong’ recruitment sites are placed across the length of the X chromosomes and cooperate with several ‘weaker’ ones located in between. This way, multiple recruitment sites can cooperate over a long distance, while non-sex chromosomes, which have only one or two stronger recruitment sites, do not have thisadvantage. Hierarchy and cooperativity may be general features of gene expression, in which proteins are targeted to chromosomes without the need for having specific motifs at every recruitment site. The way DNA sequences are distributed across the genome may give us clues about their role. Thus, knowing how genomes are structured will help us identify disrupted areas in diseases such as cancer. DOI:http://dx.doi.org/10.7554/eLife.23645.002
Collapse
Affiliation(s)
- Sarah Elizabeth Albritton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Anna-Lena Kranz
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Lara Heermans Winterkorn
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Lena Annika Street
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| | - Sevinc Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, United States
| |
Collapse
|
36
|
A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2017; 7:343-353. [PMID: 28007841 PMCID: PMC5295584 DOI: 10.1534/g3.116.037747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mi2 proteins are evolutionarily conserved, ATP-dependent chromatin remodelers of the CHD family that play key roles in stem cell differentiation and reprogramming. In Caenorhabditis elegans, the let-418 gene encodes one of the two Mi2 homologs, which is part of at least two chromatin complexes, namely the Nucleosome Remodeling and histone Deacetylase (NuRD) complex and the MEC complex, and functions in larval development, vulval morphogenesis, lifespan regulation, and cell fate determination. To explore the mechanisms involved in the action of LET-418/Mi2, we performed a genome-wide RNA interference (RNAi) screen for suppressors of early larval arrest associated with let-418 mutations. We identified 29 suppressor genes, of which 24 encode chromatin regulators, mostly orthologs of proteins present in transcriptional activator complexes. The remaining five genes vary broadly in their predicted functions. All suppressor genes could suppress multiple aspects of the let-418 phenotype, including developmental arrest and ectopic expression of germline genes in the soma. Analysis of available transcriptomic data and quantitative PCR revealed that LET-418 and the suppressors of early larval arrest are regulating common target genes. These suppressors might represent direct competitors of LET-418 complexes for chromatin regulation of crucial genes involved in the transition to postembryonic development.
Collapse
|
37
|
Boussaha M, Michot P, Letaief R, Hozé C, Fritz S, Grohs C, Esquerré D, Duchesne A, Philippe R, Blanquet V, Phocas F, Floriot S, Rocha D, Klopp C, Capitan A, Boichard D. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genet Sel Evol 2016; 48:87. [PMID: 27846802 PMCID: PMC5111192 DOI: 10.1186/s12711-016-0268-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. Results In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. Conclusions To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Pauline Michot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Amandine Duchesne
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Philippe
- GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France
| | | | - Florence Phocas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandrine Floriot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| |
Collapse
|
38
|
Ahn JH, Rechsteiner A, Strome S, Kelly WG. A Conserved Nuclear Cyclophilin Is Required for Both RNA Polymerase II Elongation and Co-transcriptional Splicing in Caenorhabditis elegans. PLoS Genet 2016; 12:e1006227. [PMID: 27541139 PMCID: PMC4991786 DOI: 10.1371/journal.pgen.1006227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/08/2016] [Indexed: 01/22/2023] Open
Abstract
The elongation phase of transcription by RNA Polymerase II (Pol II) involves numerous events that are tightly coordinated, including RNA processing, histone modification, and chromatin remodeling. RNA splicing factors are associated with elongating Pol II, and the interdependent coupling of splicing and elongation has been documented in several systems. Here we identify a conserved, multi-domain cyclophilin family member, SIG-7, as an essential factor for both normal transcription elongation and co-transcriptional splicing. In embryos depleted for SIG-7, RNA levels for over a thousand zygotically expressed genes are substantially reduced, Pol II becomes significantly reduced at the 3' end of genes, marks of transcription elongation are reduced, and unspliced mRNAs accumulate. Our findings suggest that SIG-7 plays a central role in both Pol II elongation and co-transcriptional splicing and may provide an important link for their coordination and regulation.
Collapse
Affiliation(s)
- Jeong H. Ahn
- Biology Department, Emory University, Atlanta, Georgia, United States of America
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
| | - Andreas Rechsteiner
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
39
|
Klosin A, Lehner B. Mechanisms, timescales and principles of trans-generational epigenetic inheritance in animals. Curr Opin Genet Dev 2016; 36:41-9. [DOI: 10.1016/j.gde.2016.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/20/2022]
|
40
|
Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Res 2015; 43:9694-710. [PMID: 26476455 PMCID: PMC4787770 DOI: 10.1093/nar/gkv1063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/01/2015] [Indexed: 12/05/2022] Open
Abstract
Genome-wide analyses in Caenorhabditis elegans show that post-translational modifications (PTMs) of histones are evolutionary conserved and distributed along functionally distinct genomic domains. However, a global profile of PTMs and their co-occurrence on the same histone tail has not been described in this organism. We used mass spectrometry based middle-down proteomics to analyze histone H3 N-terminal tails from C. elegans embryos for the presence, the relative abundance and the potential cross-talk of co-existing PTMs. This analysis highlighted that the lysine 23 of histone H3 (H3K23) is extensively modified by methylation and that tri-methylated H3K9 (H3K9me3) is exclusively detected on histone tails with di-methylated H3K23 (H3K23me2). Chromatin immunoprecipitation approaches revealed a positive correlation between H3K23me2 and repressive marks. By immunofluorescence analyses, H3K23me2 appears differentially regulated in germ and somatic cells, in part by the action of the histone demethylase JMJD-1.2. H3K23me2 is enriched in heterochromatic regions, localizing in H3K9me3 and heterochromatin protein like-1 (HPL-1)-positive foci. Biochemical analyses indicated that HPL-1 binds to H3K23me2 and interacts with a conserved CoREST repressive complex. Thus, our study suggests that H3K23me2 defines repressive domains and contributes to organizing the genome in distinct heterochromatic regions during embryogenesis.
Collapse
Affiliation(s)
- Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simone Sidoli
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Carsten Friis
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Jesper Christensen
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark The Danish Stem Cell Centre (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Ole N Jensen
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|
41
|
Ding W, Smulan LJ, Hou NS, Taubert S, Watts JL, Walker AK. s-Adenosylmethionine Levels Govern Innate Immunity through Distinct Methylation-Dependent Pathways. Cell Metab 2015; 22:633-45. [PMID: 26321661 PMCID: PMC4598287 DOI: 10.1016/j.cmet.2015.07.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/29/2015] [Accepted: 07/17/2015] [Indexed: 12/13/2022]
Abstract
s-adenosylmethionine (SAM) is the sole methyl donor modifying histones, nucleic acids, and phospholipids. Its fluctuation affects hepatic phosphatidylcholine (PC) synthesis or may be linked to variations in DNA or histone methylation. Physiologically, low SAM is associated with lipid accumulation, tissue injury, and immune responses in fatty liver disease. However, molecular connections among SAM limitation, methyltransferases, and disease-associated phenotypes are unclear. We find that low SAM can activate or attenuate Caenorhabditis elegans immune responses. Immune pathways are stimulated downstream of PC production on a non-pathogenic diet. In contrast, distinct SAM-dependent mechanisms limit survival on pathogenic Pseudomonas aeruginosa. C. elegans undertakes a broad transcriptional response to pathogens and we find that low SAM restricts H3K4me3 at Pseudomonas-responsive promoters, limiting their expression. Furthermore, this response depends on the H3K4 methyltransferase set-16/MLL. Thus, our studies provide molecular links between SAM and innate immune functions and suggest that SAM depletion may limit stress-induced gene expression.
Collapse
Affiliation(s)
- Wei Ding
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Lorissa J Smulan
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Nicole S Hou
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Stefan Taubert
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Jennifer L Watts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
| | - Amy K Walker
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
42
|
Rankin CH. A review of transgenerational epigenetics for RNAi, longevity, germline maintenance and olfactory imprinting in Caenorhabditis elegans. ACTA ACUST UNITED AC 2015; 218:41-9. [PMID: 25568450 DOI: 10.1242/jeb.108340] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Inheritance of acquired characteristics without changes in DNA sequence has been called transgenerational epigenetics. This review looks at studies that used the model system Caenorhabditis elegans to uncover mechanisms of transgenerational epigenetics in studies of RNA interference, studies of longevity, studies of germline continuity and a study on olfactory imprinting. In each case, researchers have uncovered critical roles for small RNAs and for Argonaute proteins. They have revealed several different genetic pathways that mediate RNA silencing of foreign RNA for a few or for many generations, as well as identifying a related pathway responsible for recognized self-generated RNAs. Together, these studies have greatly advanced our understanding of trangenerational epigenetics.
Collapse
Affiliation(s)
- Catharine H Rankin
- Department of Psychology and Brain Research Centre, University of British Columbia, Vancouver, BC, Canada, V6T 2B5
| |
Collapse
|
43
|
The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
Collapse
|
44
|
Hoe M, Nicholas HR. Evidence of a MOF histone acetyltransferase-containing NSL complex in C. elegans. WORM 2014; 3:e982967. [PMID: 26430553 PMCID: PMC4588387 DOI: 10.4161/21624054.2014.982967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 11/19/2022]
Abstract
Regulation of chromatin is a key process in the developmental control of gene expression. Many multi-subunit protein complexes have been found to regulate chromatin through the modification of histone residues. One such complex is the MOF histone acetyltransferase-containing NSL complex. While the composition of the human and Drosophila NSL complexes has been determined and the functions of these complexes investigated, the existence of an equivalent complex in nematodes such as Caenorhabditis elegans has not yet been explored. Here we summarise evidence, from our own work and that of others, that homologues of NSL complex components are found in C. elegans. We review data suggesting that nematode proteins SUMV-1 and SUMV-2 are homologous to NSL2 and NSL3, respectively, and that SUMV-1 and SUMV-2 may form a complex with MYS-2, the worm homolog of MOF. We propose that these interactions suggest the existence of a nematode NSL-like complex and discuss the roles of this putative NSL complex in worms as well as exploring the possibility of crosstalk between NSL and COMPASS complexes via components that are common to both. We present the groundwork from which a full characterization of a nematode NSL complex may begin.
Collapse
Affiliation(s)
- Matthew Hoe
- School of Molecular Bioscience; University of Sydney ; Sydney, Australia
| | - Hannah R Nicholas
- School of Molecular Bioscience; University of Sydney ; Sydney, Australia
| |
Collapse
|
45
|
Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1440-53. [DOI: 10.1016/j.bbagrm.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/22/2023]
|
46
|
Robert VJ, Mercier MG, Bedet C, Janczarski S, Merlet J, Garvis S, Ciosk R, Palladino F. The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the Caenorhabditis elegans germline. Cell Rep 2014; 9:443-50. [PMID: 25310986 DOI: 10.1016/j.celrep.2014.09.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/21/2014] [Accepted: 09/09/2014] [Indexed: 01/17/2023] Open
Abstract
Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes, including Ash2 and Wdr5. Although individual subunits contribute to complex activity, how they influence gene expression in specific tissues remains largely unknown. In Caenorhabditis elegans, SET-2/SET1, WDR-5.1, and ASH-2 are differentially required for germline H3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2, or wdr-5.1, we show that these subunits play unique as well as redundant functions in order to promote expression of germline genes and repress somatic genes. Furthermore, we show that in set-2- and wdr-5.1-deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1 to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency and underline the complexity of the cellular network regulating this process.
Collapse
Affiliation(s)
- Valérie J Robert
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France
| | - Marine G Mercier
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France
| | - Cécile Bedet
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France
| | - Stéphane Janczarski
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France
| | - Jorge Merlet
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Steve Garvis
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Francesca Palladino
- Laboratory of Molecular and Cellular Biology, CNRS, Université de Lyon 1, Ecole Normale Supérieure, 69364 Lyon Cedex 07, France.
| |
Collapse
|
47
|
Chen RAJ, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res 2014; 24:1138-46. [PMID: 24653213 PMCID: PMC4079969 DOI: 10.1101/gr.161992.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/26/2013] [Indexed: 12/20/2022]
Abstract
Most vertebrate promoters lie in unmethylated CpG-dense islands, whereas methylation of the more sparsely distributed CpGs in the remainder of the genome is thought to contribute to transcriptional repression. Nonmethylated CG dinucleotides are recognized by CXXC finger protein 1 (CXXC1, also known as CFP1), which recruits SETD1A (also known as Set1) methyltransferase for trimethylation of histone H3 lysine 4, an active promoter mark. Genomic regions enriched for CpGs are thought to be either absent or irrelevant in invertebrates that lack DNA methylation, such as C. elegans; however, a CXXC1 ortholog (CFP-1) is present. Here we demonstrate that C. elegans CFP-1 targets promoters with high CpG density, and these promoters are marked by high levels of H3K4me3. Furthermore, as for mammalian promoters, high CpG content is associated with nucleosome depletion irrespective of transcriptional activity. We further show that highly occupied target (HOT) regions identified by the binding of a large number of transcription factors are CpG-rich promoters in C. elegans and human genomes, suggesting that the unusually high factor association at HOT regions may be a consequence of CpG-linked chromatin accessibility. Our results indicate that nonmethylated CpG-dense sequence is a conserved genomic signal that promotes an open chromatin state, targeting by a CXXC1 ortholog, and H3K4me3 modification in both C. elegans and human genomes.
Collapse
Affiliation(s)
- Ron A.-J. Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Thomas A. Down
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Eva Zeiser
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Sky K. Feuer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| |
Collapse
|
48
|
SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line. Proc Natl Acad Sci U S A 2014; 111:9509-14. [PMID: 24979765 DOI: 10.1073/pnas.1321843111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Caenorhabditis elegans LSD1 H3K4me2 demethylase SPR-5 reprograms epigenetic transcriptional memory during passage through the germ line. Here we show that mutants in the H3K9me2 methyltransferase, met-2, result in transgenerational epigenetic effects that parallel spr-5 mutants. In addition, we find that spr-5;met-2 double mutants have a synergistic effect on sterility, H3K4me2, and spermatogenesis expression. These results implicate MET-2 as a second histone-modifying enzyme in germ-line reprogramming and suggest a model in which SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state required for the continued immortality of the C. elegans germ line. Without SPR-5 and MET-2, we find that the ability to express spermatogenesis genes is transgenerationally passed on to the somatic cells of the subsequent generation. This indicates that H3K4me2 may act in the maintenance of cell fate. Finally, we demonstrate that reducing H3K4me2 causes a large increase in H3K9me2 added by the SPR-5;MET-2 reprogramming mechanism. This finding suggests a novel histone code interaction in which the input chromatin environment dictates the output chromatin state. Taken together, our results provide evidence for a broader reprogramming mechanism in which multiple enzymes coordinately regulate histone information during passage through the germ line.
Collapse
|
49
|
SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans. Dev Biol 2014; 392:266-82. [PMID: 24882710 DOI: 10.1016/j.ydbio.2014.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 11/22/2022]
Abstract
Chromatin regulators contribute to the developmental control of gene expression. In the nematode Caenorhabditis elegans, the roles of chromatin regulation in development have been explored in several contexts, including vulval differentiation. The synthetic multivulva (synMuv) genes are regulators of vulval development in C. elegans and the proteins encoded by these genes include components of several histone modification and chromatin remodelling complexes. By inhibiting ectopic expression of the epidermal growth factor (LIN-3) in the nematode hypodermis, the synMuv genes prevent inappropriate vulval induction. In a forward genetic screen for modifiers of the expression of a hypodermal reporter gene, we identified a mutation that results in increased expression of the reporter. This mutation also suppresses ectopic vulval induction in synMuv mutants and we have consequently named the affected gene suppressor of synthetic multivulva-1 (sumv-1). We show that SUMV-1 is required in the hypodermis for the synMuv phenotype and that loss of sumv-1 function suppresses ectopic expression of lin-3 in synMuv mutant animals. In yeast two-hybrid assays SUMV-1 physically interacts with SUMV-2, and reduction of sumv-2 function also suppresses the synMuv phenotype. We identified similarities between SUMV-1 and SUMV-2 and mammalian proteins KAT8 NSL2 and KAT8 NSL3, respectively, which are components of the KAT8/MOF histone acetyltransferase complex. Reduction of function of mys-2, which encodes the enzymatic component of the KAT8/MOF complex, also suppresses the synMuv phenotype, and MYS-2 physically interacts with SUMV-2 in yeast two-hybrid assays. Together these observations suggest that SUMV-1 and SUMV-2 may function together with MYS-2 in a nematode KAT8/MOF-like complex to antagonise the activity of the synMuv genes.
Collapse
|
50
|
González-Aguilera C, Palladino F, Askjaer P. C. elegans epigenetic regulation in development and aging. Brief Funct Genomics 2014; 13:223-34. [PMID: 24326118 PMCID: PMC4031453 DOI: 10.1093/bfgp/elt048] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The precise developmental map of the Caenorhabditis elegans cell lineage, as well as a complete genome sequence and feasibility of genetic manipulation make this nematode species highly attractive to study the role of epigenetics during development. Genetic dissection of phenotypical traits, such as formation of egg-laying organs or starvation-resistant dauer larvae, has illustrated how chromatin modifiers may regulate specific cell-fate decisions and behavioral programs. Moreover, the transparent body of C. elegans facilitates non-invasive microscopy to study tissue-specific accumulation of heterochromatin at the nuclear periphery. We also review here recent findings on how small RNA molecules contribute to epigenetic control of gene expression that can be propagated for several generations and eventually determine longevity.
Collapse
|