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Konwar C, Maini J, Saluja D. Understanding Longevity: SIN-3 and DAF-16 Revealed as Independent Players in Lifespan Regulation. J Gerontol A Biol Sci Med Sci 2024; 79:glae160. [PMID: 38894529 DOI: 10.1093/gerona/glae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Indexed: 06/21/2024] Open
Abstract
Aging is the process of gradual physio-biochemical deterioration. Although aging is inevitable, healthy aging is the key to individual and communal well-being. Therefore, it is essential to understand the regulation of aging. SIN-3/Sin-3 is a unique regulatory protein that regulates aging without DNA-binding activity. It functions by establishing multiple protein interactions. To understand the functional mechanism of this transcriptional regulator, the Caenorhabditis elegans protein interactome was assessed for SIN-3 interactions. DAF-16/FOXO emerged as one of the leading contenders for SIN-3-mediated regulation of aging. This study looks at the concerted role of SIN-3 and DAF-16 proteins in lifespan regulation. Phenotypic profiling for the mutants of these genes shows the functional accord between these 2 proteins with similar functions in stress response and vital biological processes. However, there were no significant physical interactions when checked for protein-protein interaction between SIN-3 and DAF-16 proteins. C. elegans genomics and transcriptomics data also indicated the possibilities of concerted gene regulation. This genetic regulation is more likely related to SIN-3 dominance on DAF-16 function. Overall, SIN-3 and DAF-16 proteins have strong functional interactions that ensure healthy aging. The influence of SIN-3 on DAF-16-mediated stress response is one of their convergence points in longevity regulation.
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Affiliation(s)
- Chandrika Konwar
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Biology and Bioengineering Division, Tianqiao and Chrissy Chen Institute of Neuroscience, California Institute of Technology, Pasadena, California, USA
| | - Jayant Maini
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, IoE, University of Delhi, Delhi, India
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2
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Robert VJ, Caron M, Gely L, Adrait A, Pakulska V, Couté Y, Chevalier M, Riedel CG, Bedet C, Palladino F. SIN-3 acts in distinct complexes to regulate the germline transcriptional program in Caenorhabditis elegans. Development 2023; 150:dev201755. [PMID: 38771303 PMCID: PMC10617626 DOI: 10.1242/dev.201755] [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: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
The transcriptional co-regulator SIN3 influences gene expression through multiple interactions that include histone deacetylases. Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability and autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here, we show that loss of SIN-3, the single SIN3 homolog in Caenorhabditis elegans, results in maternal-effect sterility associated with de-regulation of the germline transcriptome, including de-silencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific histone deacetylases and show that they differentially contribute to fertility. Single-cell, single-molecule fluorescence in situ hybridization reveals that in sin-3 mutants the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells, suggesting a role for SIN-3 in its silencing. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN-3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins.
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Affiliation(s)
- Valerie J. Robert
- 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, 69007 Lyon, France
| | - 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, 69007 Lyon, France
| | - Loic Gely
- 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, 69007 Lyon, France
| | - Annie Adrait
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Victoria Pakulska
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Manon Chevalier
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Christian G. Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Cecile 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, 69007 Lyon, France
| | - 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, 69007 Lyon, France
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SIN-3 functions through multi-protein interaction to regulate apoptosis, autophagy, and longevity in Caenorhabditis elegans. Sci Rep 2022; 12:10560. [PMID: 35732652 PMCID: PMC9217932 DOI: 10.1038/s41598-022-13864-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/09/2022] [Indexed: 11/08/2022] Open
Abstract
SIN3/HDAC is a multi-protein complex that acts as a regulatory unit and functions as a co-repressor/co-activator and a general transcription factor. SIN3 acts as a scaffold in the complex, binding directly to HDAC1/2 and other proteins and plays crucial roles in regulating apoptosis, differentiation, cell proliferation, development, and cell cycle. However, its exact mechanism of action remains elusive. Using the Caenorhabditis elegans (C. elegans) model, we can surpass the challenges posed by the functional redundancy of SIN3 isoforms. In this regard, we have previously demonstrated the role of SIN-3 in uncoupling autophagy and longevity in C. elegans. In order to understand the mechanism of action of SIN3 in these processes, we carried out a comparative analysis of the SIN3 protein interactome from model organisms of different phyla. We identified conserved, expanded, and contracted gene classes. The C. elegans SIN-3 interactome -revealed the presence of well-known proteins, such as DAF-16, SIR-2.1, SGK-1, and AKT-1/2, involved in autophagy, apoptosis, and longevity. Overall, our analyses propose potential mechanisms by which SIN3 participates in multiple biological processes and their conservation across species and identifies candidate genes for further experimental analysis.
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Katsanos D, Ferrando-Marco M, Razzaq I, Aughey G, Southall TD, Barkoulas M. Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. Development 2021; 148:dev199452. [PMID: 34397094 PMCID: PMC7613258 DOI: 10.1242/dev.199452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
Abstract
The epidermis of Caenorhabditis elegans is an essential tissue for survival because it contributes to the formation of the cuticle barrier as well as facilitating developmental progression and animal growth. Most of the epidermis consists of the hyp7 hypodermal syncytium, the nuclei of which are largely generated by the seam cells, which exhibit stem cell-like behaviour during development. How seam cell progenitors differ transcriptionally from the differentiated hypodermis is poorly understood. Here, we introduce Targeted DamID (TaDa) in C. elegans as a method for identifying genes expressed within a tissue of interest without cell isolation. We show that TaDa signal enrichment profiles can be used to identify genes transcribed in the epidermis and use this method to resolve differences in gene expression between the seam cells and the hypodermis. Finally, we predict and functionally validate new transcription and chromatin factors acting in seam cell development. These findings provide insights into cell type-specific gene expression profiles likely associated with epidermal cell fate patterning.
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Affiliation(s)
- Dimitris Katsanos
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Mar Ferrando-Marco
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Iqrah Razzaq
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tony D. Southall
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Michalis Barkoulas
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Kubota Y, Ohnishi Y, Hamasaki T, Yasui G, Ota N, Kitagawa H, Esaki A, Fahmi M, Ito M. Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development. Genes Genomics 2021; 43:553-565. [PMID: 33740234 PMCID: PMC8110489 DOI: 10.1007/s13258-021-01076-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Histone deacetylase (HDAC)-1, a Class-I HDAC family member, forms three types of complexes, the nucleosome remodeling deacetylase, Sin3, and CoREST complexes with the specific corepressor components chromodomain-helicase-DNA-binding protein 3 (Mi2/CHD-3), Sin3, and REST corepressor 1 (RCOR1), respectively, in humans. OBJECTIVE To elucidate the functional relationships among the three transcriptional corepressors during embryogenesis. METHODS The activities of HDA-1, LET-418, SIN-3, and SPR-1, the homologs of HDAC-1, Mi2, Sin3, and RCOR1 in Caenorhabditis elegans during embryogenesis were investigated through measurement of relative mRNA expression levels and embryonic lethality given either gene knockdown or deletion. Additionally, the terminal phenotypes of each knockdown and mutant embryo were observed using a differential-interference contrast microscope. Finally, the functional relationships among the three corepressors were examined through genetic interactions and transcriptome analyses. RESULTS Here, we report that each of the corepressors LET-418, SIN-3, and SPR-1 are expressed and have essential roles in C. elegans embryonic development. Our terminal phenotype observations of single mutants further implied that LET-418, SIN-3, and SPR-1 play similar roles in promoting advancement to the middle and late embryonic stages. Combined analysis of genetic interactions and gene ontology of these corepressors indicate a prominent overlapping role among SIN-3, SPR-1, and LET-418 and between SIN-3 and SPR-1. CONCLUSION Our findings suggest that the class-I HDAC-1 corepressors LET-418, SIN-3, and SPR-1 may cooperatively regulate the expression levels of some genes during C. elegans embryogenesis or may have some similar roles but functioning independently within a specific cell.
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Affiliation(s)
- Yukihiro Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yuto Ohnishi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tasuku Hamasaki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Gen Yasui
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Natsumi Ota
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hiromu Kitagawa
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Arashi Esaki
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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6
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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: 6.6] [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.
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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
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Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. eLife 2019; 8:e46703. [PMID: 31386623 PMCID: PMC6684318 DOI: 10.7554/elife.46703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular differentiation requires both activation of target cell transcriptional programs and repression of non-target cell programs. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages from previously differentiated epithelial cells, including a neuron generated by a developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single-cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. ZTF-11 functions together with the MuvB corepressor complex to suppress the activation of non-neuronal genes in neurons. These results dovetail with the ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.
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Affiliation(s)
- Joo Lee
- Department of BiochemistryStanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Caitlin A Taylor
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Ao Shen
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | | | - Allison Chen
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Yang K Xiang
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | - Zhirong Bao
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
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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: 0.8] [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.
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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
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Hajduskova M, Baytek G, Kolundzic E, Gosdschan A, Kazmierczak M, Ofenbauer A, Beato Del Rosal ML, Herzog S, Ul Fatima N, Mertins P, Seelk-Müthel S, Tursun B. MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans. Genetics 2019; 211:121-139. [PMID: 30425042 PMCID: PMC6325694 DOI: 10.1534/genetics.118.301674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin regulators play important roles in the safeguarding of cell identities by opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming barriers in living organisms needs improvement as most studies use tissue culture. We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene on chromosome 15) and is required during germline development in C. elegans However, MRG-1's function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions. Conserved chromatin regulators may have similar functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human cells.
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Affiliation(s)
- Martina Hajduskova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Gülkiz Baytek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Ena Kolundzic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Alexander Gosdschan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Marlon Kazmierczak
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Andreas Ofenbauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Maria Lena Beato Del Rosal
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Sergej Herzog
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Nida Ul Fatima
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefanie Seelk-Müthel
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Baris Tursun
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
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10
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Pandey R, Sharma M, Saluja D. SIN-3 as a key determinant of lifespan and its sex dependent differential role on healthspan in C aenorhabditis elegans. Aging (Albany NY) 2018; 10:3910-3937. [PMID: 30541942 PMCID: PMC6326684 DOI: 10.18632/aging.101682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 11/22/2018] [Indexed: 01/14/2023]
Abstract
Aging/senescence includes not just decline in lifespan but also etiologies of age associated morbidities which are inadequately understood. Extensive research has been undertaken to delineate the pathways and generate mutants with extended lifespan. However, little is known about the health status of these long lived mutants in the background of important genetic perturbations. Caenorhabditis elegans is one of the leading in vivo model organisms to study aging. Deletion of SIN-3, a transcription coregulator in C. elegans has been shown to reduce the lifespan of the mutant worms by half as compared to the wild-type and isogenic controls. The current study focuses on the effect of SIN-3 deletion on the healthspan of the worms. We find that not only are sin-3 mutants more susceptible to stress, but the overall stress intolerance and physiological decline is sex dependent. The severity of the phenotype is more pronounced in hermaphrodites as compared to the males carrying the same mutation with respect to the controls. The results further suggest that genetic perturbation along with the gender play an important role in determining the lifespan, healthspan and overall fitness of an organism.
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Affiliation(s)
- Renu Pandey
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi -07, India
| | - Meenakshi Sharma
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi -07, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi -07, India
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Tsang SW, Guo Y, Chan LH, Huang Y, Chow KL. Generation and characterization of pathogenic Mab21l2(R51C) mouse model. Genesis 2018; 56:e23261. [PMID: 30375740 DOI: 10.1002/dvg.23261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
MAB21L2(R51C) is one of the five documented MAB21L2 mutations in human patients with bilateral eye malformations identified via whole exome sequencing. In addition to the eye abnormality, patients with MAB21L2 R51C/+ mutation also have skeletal dysplasia and intellectual disability. To evaluate the pathology of this mutant allele systematically in understanding the functional role of MAB21L2 in human development, we introduce the R51C mutation into the mouse genome by CRISPR/Cas9 system to generate a mouse model for detailed characterization. The Mab21l2 R51C/+ mice have eyeless phenotype and skeletal abnormalities. Micro-computed tomography (micro-CT) analysis showed the Mab21l2 R51C/+ mice have no eye balls but with two abnormal tissues underneath the brain. Histological analysis revealed that the early eye development in the mutant embryos is interrupted. In addition, Mab21l2 R51C/+ mice also have joint fusion phenotype; the humerus is fused with radius, whereas femur is fused with tibia. Limbs in the mutant animals are distinctly shorter than the wild type; and deltoid tuberosities in humeri are absent in these Mab21l2 R51C/+ mice. In summary, we showed that our Mab21l2 R51C/+ mutant mice have recapitulated the pathological features in eye and bone of human patients. Further analyses of the mutant phenotype with molecular markers will provide insight on how MAB21L2 guides the optic differentiation and skeletogenesis, revealing specific underlying pathogenic mechanism of the MAB21L2(R51C) mutation.
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Affiliation(s)
- Shun-Wa Tsang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yanjiang Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Long-Hei Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yingyu Huang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - King L Chow
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans. Genetics 2018; 210:1329-1337. [PMID: 30287474 DOI: 10.1534/genetics.118.301450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/25/2018] [Indexed: 12/29/2022] Open
Abstract
Animals have evolved critical mechanisms to maintain cellular and organismal proteostasis during development, disease, and exposure to environmental stressors. The Unfolded Protein Response (UPR) is a conserved pathway that senses and responds to the accumulation of misfolded proteins in the endoplasmic reticulum (ER) lumen. We have previously demonstrated that the IRE-1-XBP-1 branch of the UPR is required to maintain Caenorhabditis elegans ER homeostasis during larval development in the presence of pathogenic Pseudomonas aeruginosa In this study, we identify loss-of-function mutations in four conserved transcriptional regulators that suppress the larval lethality of xbp-1 mutant animals caused by immune activation in response to infection by pathogenic bacteria: FKH-9, a forkhead family transcription factor; ARID-1, an ARID/Bright domain-containing transcription factor; HCF-1, a transcriptional regulator that associates with histone modifying enzymes; and SIN-3, a subunit of a histone deacetylase complex. Further characterization of FKH-9 suggests that loss of FKH-9 enhances resistance to the ER toxin tunicamycin and results in enhanced ER-associated degradation (ERAD). Increased ERAD activity of fkh-9 loss-of-function mutants is accompanied by a diminished capacity to degrade cytosolic proteasomal substrates and a corresponding increased sensitivity to the proteasomal inhibitor bortezomib. Our data underscore how the balance between ER and cytosolic proteostasis can be influenced by compensatory activation of ERAD during the physiological ER stress of infection and immune activation.
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Sharma M, Pandey R, Saluja D. ROS is the major player in regulating altered autophagy and lifespan in sin-3 mutants of C. elegans. Autophagy 2018; 14:1239-1255. [PMID: 29912629 PMCID: PMC6103711 DOI: 10.1080/15548627.2018.1474312] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 04/25/2018] [Accepted: 05/02/2018] [Indexed: 12/14/2022] Open
Abstract
SIN3, a transcriptional corepressor has been implicated in varied functions both as transcription activator and repressor. Recent studies associated Sin3 with the macroautophagic/autophagic process as a negative regulator of Atg8 and Atg32. Though the role of SIN3 in autophagy is being explored, little is known about the overall effect of SIN3 deletion on the survival of an organism. In this study using a Caenorhabditis elegans sin-3(tm1279);him-5(e1490) strain, we demonstrate that under in vivo conditions SIN-3 differentially modulates autophagy and lifespan. We provide evidence that the enhanced autophagy and decreased lifespan observed in sin-3 deletion mutants is dependent on ROS and intracellular oxidative stress. Inability of the mutant worms to maintain redox balance along with dysregulation of enzymatic antioxidants, depletion of GSH and NADP reserves and elevation of ROS markers compromises the longevity of the worms. It is possible that the enhanced autophagic process observed in sin-3(tm1279);him-5(e1490) worms is required to compensate for oxidative stress generated in these worms. ABBREVIATIONS cat: catalase; DCFDA: 2',7'-dichlorodihydrofluoroscein diacetate; GSH: reduced glutathione; GSSG: oxidized glutathione; H2O2: hydrogen peroxide; HDAC: Histone deacetylase; HID: HDAC interacting domain; him-5: high incidence of males; HLH-30: Helix Loop Helix-30; HNE: 4-hydroxyl-2-noneal; LIPL: LIPase Like; MDA: malondialdehyde; NGM: nematode growth medium; PAH: paired amphipathic α-helix; PE: phosphatidylethanolamine; RFU: relative fluorescence unit; ROS: reactive oxygen species; sin-3/SIN3: yeast Switch Independent; SOD: superoxide dismutase; NADP: nicotinamide adenine dinucleotide phosphate; SQST-1: SeQueSTosome related-1; ATG: AuTophaGy related.
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Affiliation(s)
- Meenakshi Sharma
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - Renu Pandey
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
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Chaubal A, Pile LA. Same agent, different messages: insight into transcriptional regulation by SIN3 isoforms. Epigenetics Chromatin 2018; 11:17. [PMID: 29665841 PMCID: PMC5902990 DOI: 10.1186/s13072-018-0188-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
SIN3 is a global transcriptional coregulator that governs expression of a large repertoire of gene targets. It is an important player in gene regulation, which can repress or activate diverse gene targets in a context-dependent manner. SIN3 is required for several vital biological processes such as cell proliferation, energy metabolism, organ development, and cellular senescence. The functional flexibility of SIN3 arises from its ability to interact with a large variety of partners through protein interaction domains that are conserved across species, ranging from yeast to mammals. Several isoforms of SIN3 are present in these different species that can perform common and specialized functions through interactions with distinct enzymes and DNA-binding partners. Although SIN3 has been well studied due to its wide-ranging functions and highly conserved interaction domains, precise roles of individual SIN3 isoforms have received less attention. In this review, we discuss the differences in structure and function of distinct SIN3 isoforms and provide possible avenues to understand the complete picture of regulation by SIN3.
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Affiliation(s)
- Ashlesha Chaubal
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
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15
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Barr MM, García LR, Portman DS. Sexual Dimorphism and Sex Differences in Caenorhabditis elegans Neuronal Development and Behavior. Genetics 2018; 208:909-935. [PMID: 29487147 PMCID: PMC5844341 DOI: 10.1534/genetics.117.300294] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 01/05/2023] Open
Abstract
As fundamental features of nearly all animal species, sexual dimorphisms and sex differences have particular relevance for the development and function of the nervous system. The unique advantages of the nematode Caenorhabditis elegans have allowed the neurobiology of sex to be studied at unprecedented scale, linking ultrastructure, molecular genetics, cell biology, development, neural circuit function, and behavior. Sex differences in the C. elegans nervous system encompass prominent anatomical dimorphisms as well as differences in physiology and connectivity. The influence of sex on behavior is just as diverse, with biological sex programming innate sex-specific behaviors and modifying many other aspects of neural circuit function. The study of these differences has provided important insights into mechanisms of neurogenesis, cell fate specification, and differentiation; synaptogenesis and connectivity; principles of circuit function, plasticity, and behavior; social communication; and many other areas of modern neurobiology.
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Affiliation(s)
- Maureen M Barr
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854-8082
| | - L Rene García
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Douglas S Portman
- Department of Biomedical Genetics, University of Rochester, New York 14642
- Department of Neuroscience, University of Rochester, New York 14642
- Department of Biology, University of Rochester, New York 14642
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Takahashi C, Kusakabe M, Suzuki T, Miyatake K, Nishida E. mab21-l3 regulates cell fate specification of multiciliate cells and ionocytes. Nat Commun 2015; 6:6017. [DOI: 10.1038/ncomms7017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 12/02/2014] [Indexed: 01/26/2023] Open
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Rainger J, Pehlivan D, Johansson S, Bengani H, Sanchez-Pulido L, Williamson KA, Ture M, Barker H, Rosendahl K, Spranger J, Horn D, Meynert A, Floyd JAB, Prescott T, Anderson CA, Rainger JK, Karaca E, Gonzaga-Jauregui C, Jhangiani S, Muzny DM, Seawright A, Soares DC, Kharbanda M, Murday V, Finch A, Gibbs RA, van Heyningen V, Taylor MS, Yakut T, Knappskog PM, Hurles ME, Ponting CP, Lupski JR, Houge G, FitzPatrick DR. Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations. Am J Hum Genet 2014; 94:915-23. [PMID: 24906020 PMCID: PMC4121478 DOI: 10.1016/j.ajhg.2014.05.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/13/2014] [Indexed: 11/28/2022] Open
Abstract
We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated children with bilateral anophthalmia, intellectual disability, and rhizomelic skeletal dysplasia. c.152G>A (p.Arg51His) segregated with autosomal-dominant bilateral colobomatous microphthalmia in a large multiplex family. The fourth heterozygous mutation (c.145G>A [p.Glu49Lys]) affected an amino acid within two residues of Arg51 in an adult male with bilateral colobomata. In a fifth family, a homozygous mutation (c.740G>A [p.Arg247Gln]) altering a different region of the protein was identified in two male siblings with bilateral retinal colobomata. In mouse embryos, Mab21l2 showed strong expression in the developing eye, pharyngeal arches, and limb bud. As predicted by structural homology, wild-type MAB21L2 bound single-stranded RNA, whereas this activity was lost in all altered forms of the protein. MAB21L2 had no detectable nucleotidyltransferase activity in vitro, and its function remains unknown. Induced expression of wild-type MAB21L2 in human embryonic kidney 293 cells increased phospho-ERK (pERK1/2) signaling. Compared to the wild-type and p.Arg247Gln proteins, the proteins with the Glu49 and Arg51 variants had increased stability. Abnormal persistence of pERK1/2 signaling in MAB21L2-expressing cells during development is a plausible pathogenic mechanism for the heterozygous mutations. The phenotype associated with the homozygous mutation might be a consequence of complete loss of MAB21L2 RNA binding, although the cellular function of this interaction remains unknown.
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Affiliation(s)
- Joe Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Stefan Johansson
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Hemant Bengani
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - Kathleen A Williamson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mehmet Ture
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Heather Barker
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Karen Rosendahl
- Paediatric Radiology Department, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Denise Horn
- Institut für Medizinische Genetik, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - James A B Floyd
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Trine Prescott
- Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jacqueline K Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Claudia Gonzaga-Jauregui
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Anne Seawright
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Dinesh C Soares
- Centre for Genomics and Experimental Medicine, Medical Research Council Institute Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mira Kharbanda
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Victoria Murday
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Andrew Finch
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Veronica van Heyningen
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Martin S Taylor
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Tahsin Yakut
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Chris P Ponting
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway
| | - David R FitzPatrick
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK.
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Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 2013; 92:237-46. [PMID: 24189169 DOI: 10.1016/j.ejcb.2013.09.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022] Open
Abstract
Sin3, a large acidic protein, shares structural similarity with the helix-loop-helix dimerization domain of proteins of the Myc family of transcription factors. Sin3/HDAC corepressor complex functions in transcriptional regulation of several genes and is therefore implicated in the regulation of key biological processes. Knockdown studies have confirmed the role of Sin3 in cellular proliferation, differentiation, apoptosis and cell cycle regulation, emphasizing Sin3 as an essential regulator of critical cellular events in normal and pathological processes. The present review covers the diverse functions of this master transcriptional regulator as well as illustrates the redundant and distinct functions of its two mammalian isoforms.
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Affiliation(s)
- Rama Kadamb
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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19
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Abstract
Transforming Growth Factor-β (TGF-β) superfamily ligands regulate many aspects of cell identity, function, and survival in multicellular animals. Genes encoding five TGF-β family members are present in the genome of C. elegans. Two of the ligands, DBL-1 and DAF-7, signal through a canonical receptor-Smad signaling pathway; while a third ligand, UNC-129, interacts with a noncanonical signaling pathway. No function has yet been associated with the remaining two ligands. Here we summarize these signaling pathways and their biological functions.
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Affiliation(s)
- Tina L Gumienny
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX 77843, USA
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20
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GEI-8, a homologue of vertebrate nuclear receptor corepressor NCoR/SMRT, regulates gonad development and neuronal functions in Caenorhabditis elegans. PLoS One 2013; 8:e58462. [PMID: 23484030 PMCID: PMC3590189 DOI: 10.1371/journal.pone.0058462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 02/05/2013] [Indexed: 12/29/2022] Open
Abstract
NCoR and SMRT are two paralogous vertebrate proteins that function as corepressors with unliganded nuclear receptors. Although C. elegans has a large number of nuclear receptors, orthologues of the corepressors NCoR and SMRT have not unambiguously been identified in Drosophila or C. elegans. Here, we identify GEI-8 as the closest homologue of NCoR and SMRT in C. elegans and demonstrate that GEI-8 is expressed as at least two isoforms throughout development in multiple tissues, including neurons, muscle and intestinal cells. We demonstrate that a homozygous deletion within the gei-8 coding region, which is predicted to encode a truncated protein lacking the predicted NR domain, results in severe mutant phenotypes with developmental defects, slow movement and growth, arrested gonadogenesis and defects in cholinergic neurotransmission. Whole genome expression analysis by microarrays identified sets of de-regulated genes consistent with both the observed mutant phenotypes and a role of GEI-8 in regulating transcription. Interestingly, the upregulated transcripts included a predicted mitochondrial sulfide:quinine reductase encoded by Y9C9A.16. This locus also contains non-coding, 21-U RNAs of the piRNA class. Inhibition of the expression of the region coding for 21-U RNAs leads to irregular gonadogenesis in the homozygous gei-8 mutants, but not in an otherwise wild-type background, suggesting that GEI-8 may function in concert with the 21-U RNAs to regulate gonadogenesis. Our results confirm that GEI-8 is the orthologue of the vertebrate NCoR/SMRT corepressors and demonstrate important roles for this putative transcriptional corepressor in development and neuronal function.
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Xmab21l3 mediates dorsoventral patterning in Xenopus laevis. Mech Dev 2012; 129:136-46. [PMID: 22609272 DOI: 10.1016/j.mod.2012.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/04/2012] [Accepted: 05/07/2012] [Indexed: 02/05/2023]
Abstract
Specification of the dorsoventral (DV) axis is critical for the subsequent differentiation of regional fate in the primary germ layers of the vertebrate embryo. We have identified a novel factor that is essential for dorsal development in embryos of the frog Xenopus laevis. Misexpression of Xenopus mab21-like 3 (Xmab21l3) dorsalizes gastrula-stage mesoderm and neurula-stage ectoderm, while morpholino-mediated knockdown of Xmab21l3 inhibits dorsal differentiation of these embryonic germ layers. Xmab21l3 is a member of a chordate-specific subclass of a recently characterized gene family, all members of which contain a conserved, but as yet ill-defined, Mab21 domain. Our studies suggest that Xmab21l3 functions to repress ventralizing activity in the early vertebrate embryo, via regulation of BMP/Smad and Ras/ERK signaling.
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22
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Checchi PM, Engebrecht J. Caenorhabditis elegans histone methyltransferase MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation. PLoS Genet 2011; 7:e1002267. [PMID: 21909284 PMCID: PMC3164706 DOI: 10.1371/journal.pgen.1002267] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/12/2011] [Indexed: 11/23/2022] Open
Abstract
Meiosis is a specialized form of cellular division that results in the precise halving of the genome to produce gametes for sexual reproduction. Checkpoints function during meiosis to detect errors and subsequently to activate a signaling cascade that prevents the formation of aneuploid gametes. Indeed, asynapsis of a homologous chromosome pair elicits a checkpoint response that can in turn trigger germline apoptosis. In a heterogametic germ line, however, sex chromosomes proceed through meiosis with unsynapsed regions and are not recognized by checkpoint machinery. We conducted a directed RNAi screen in Caenorhabditis elegans to identify regulatory factors that prevent recognition of heteromorphic sex chromosomes as unpaired and uncovered a role for the SET domain histone H3 lysine 9 histone methyltransferase (HMTase) MET-2 and two additional HMTases in shielding the male X from checkpoint machinery. We found that MET-2 also mediates the transcriptional silencing program of meiotic sex chromosome inactivation (MSCI) but not meiotic silencing of unsynapsed chromatin (MSUC), suggesting that these processes are distinct. Further, MSCI and checkpoint shielding can be uncoupled, as double-strand breaks targeted to an unpaired, transcriptionally silenced extra-chromosomal array induce checkpoint activation in germ lines depleted for met-2. In summary, our data uncover a mechanism by which repressive chromatin architecture enables checkpoint proteins to distinguish between the partnerless male X chromosome and asynapsed chromosomes thereby shielding the lone X from inappropriate activation of an apoptotic program. Meiosis results in the generation of non-identical haploid gametes and maintenance of chromosome number during sexual reproduction. Precise meiotic chromosome segregation is essential for life, and in humans errors in this process contribute to aneuploidy or failure in meiosis, which manifests as spontaneous abortions or infertility. Cellular surveillance pathways monitor the steps of meiosis; and, if homologous chromosomes fail to pair and recombine, checkpoint machinery responds by eliciting signals to induce apoptosis. However, in many species males possess a single X chromosome that is transcriptionally silenced, accumulates repressive histone marks, and is not recognized as partnerless by meiotic checkpoints. Here, we used C. elegans to investigate how the male X is precluded from checkpoint signaling and uncovered a role for conserved chromatin-remodeling proteins that block checkpoints and mediate meiotic silencing. Our data elucidate the molecular mechanisms by which chromatin architecture influences both transcriptional silencing and checkpoint response to breaks on unpaired sex chromosomes, and we propose a model by which repressive chromatin modifiers directly block meiotic checkpoints from accessing the male X chromosome.
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Affiliation(s)
- Paula M. Checchi
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
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23
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Kim BG, Park YJ, Libermann TA, Cho JY. PTH regulates myleoid ELF-1-like factor (MEF)-induced MAB-21-like-1 (MAB21L1) expression through the JNK1 pathway. J Cell Biochem 2011; 112:2051-61. [DOI: 10.1002/jcb.23124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Cederlund ML, Vendrell V, Morrissey ME, Yin J, Gaora PÓ, Smyth VA, Higgins DG, Kennedy BN. mab21l2 transgenics reveal novel expression patterns of mab21l1 and mab21l2, and conserved promoter regulation without sequence conservation. Dev Dyn 2011; 240:745-54. [PMID: 21360786 DOI: 10.1002/dvdy.22573] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2010] [Indexed: 11/10/2022] Open
Abstract
mab21l1 and mab21l2 paralogs have widespread and dynamic expression patterns during vertebrate development. Both genes are expressed in the developing eye, midbrain, neural tube, and branchial arches. Our goal was to identify promoter regions with activity in mab21l2 expression domains. Assays of mab21l2 promoter-EGFP constructs in zebrafish embryos confirm that constructs containing 7.2 or 4.9 kb of mab21l2 promoter region are sufficient to drive expression in known (e.g., tectum, branchial arches) and unexpected domains (e.g., lens and retinal amacrine cells). A comparative analysis identifies complementary and novel expression domains of endogenous mab21l2 (e.g., lens and ventral iridocorneal canal) and mab21l1 (e.g., retinal amacrine and ganglion cells). Interestingly, therefore, despite the absence of conserved non-coding elements, a 4.9-kb mab21l2 promoter is sufficient to recapitulate expression in tissues unique to mab21l1 or mab21l2.
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Affiliation(s)
- Maria L Cederlund
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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Tsang WH, Shek KF, Lee TY, Chow KL. An evolutionarily conserved nested gene pair - Mab21 and Lrba/Nbea in metazoan. Genomics 2009; 94:177-87. [PMID: 19482073 DOI: 10.1016/j.ygeno.2009.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 05/23/2009] [Accepted: 05/26/2009] [Indexed: 11/30/2022]
Abstract
The embedding of one gene in another as a nested gene pair is a unique phenomenon of gene clustering in the metazoan genome. A gene-centric paralogous genomic sequence comparison strategy was used in this study to align these paralogous nested pairs, Mab21l2-Lrba and Mab21l1-Nbea, to identify the associated paralogous non-coding elements (pNEs) they shared. A majority of these pNEs in the Mab21l2-Lrba locus display tissue-specific enhancer activities recapitulating the expression profiles of Mab21l2 and Mab21l1. Since these enhancers are spread into the introns of Lrba, dissociation of the two genes will likely disrupt the function of at least one of them. Phylogenetic analysis of this complex locus in different species suggests that Mab21 was probably locked in the Lrba/Nbea intron in the ancestral metazoan species, in which the cis-elements uncovered in this study may act as a selective force to prevent the dissociation of this gene pair in vertebrates.
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Affiliation(s)
- W H Tsang
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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26
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Cunliffe VT. Eloquent silence: developmental functions of Class I histone deacetylases. Curr Opin Genet Dev 2008; 18:404-10. [PMID: 18929655 PMCID: PMC2671034 DOI: 10.1016/j.gde.2008.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 09/16/2008] [Accepted: 10/02/2008] [Indexed: 11/10/2022]
Abstract
Histone deacetylases (HDACs) are essential catalytic components of the transcription silencing machinery and they play important roles in the programming of multicellular development. HDACs are present within multisubunit protein complexes, other components of which govern HDAC target gene specificity by controlling interactions with sequence-specific DNA-binding proteins. Here, I review the different developmental roles of the Sin3, NuRD, CoREST and NCoR/SMRT Class I HDAC complexes. With their distinct subunit composition, these versatile molecular devices function in many different settings, to promote axis specification and tissue patterning, to maintain stem cell pluripotency, facilitate self-renewal, guide lineage commitment and drive cell differentiation.
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Affiliation(s)
- Vincent T Cunliffe
- MRC Centre for Developmental and Biomedical Genetics and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.
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Gao SB, Hua X, Jin GH. Menin regulates endocrine diseases by controlling histone modification and gene transcription. ANNALES D'ENDOCRINOLOGIE 2008; 69:426-32. [PMID: 18752793 DOI: 10.1016/j.ando.2008.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Multiple endocrine neoplasia type 1 (MEN1), a human familial tumor syndrome, results from mutations in the Men1 gene. Although much progress has been made in demonstrating the definitive role for menin in suppressing tumorigenesis in endocrine organs, the molecular pathways responsible for menin action in normal tissues and tumors remain poorly defined. Here, we review the recent progress on the molecular functions of menin in controlling cell proliferation, apoptosis, and DNA repair. The majority of these functions are largely executed by menin-mediated influencing of histone modifications and chromatin structure. These findings lead to a new model of understanding menin's tumor-suppressing function, providing insights into understanding of how menin regulates cell proliferation and the development of endocrine tumors. The new knowledge could also be translated into new strategies to improve therapeutic interventions against MEN1 and other endocrine diseases including diabetes.
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Affiliation(s)
- S B Gao
- Department of Basic Medical Sciences, Xiamen University Medical College, No. 168, Daxue Road, Xiamen 361005, Fujian Province, PR China
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Keeping things quiet: roles of NuRD and Sin3 co-repressor complexes during mammalian development. Int J Biochem Cell Biol 2008; 41:108-16. [PMID: 18775506 DOI: 10.1016/j.biocel.2008.07.022] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 01/05/2023]
Abstract
Gene inactivation studies of mammalian histone and DNA-modifying proteins have demonstrated a role for many such proteins in embryonic development. Post-implantation embryonic lethality implies a role for epigenetic factors in differentiation and in development of specific lineages or tissues. However a handful of chromatin-modifying enzymes have been found to be required in pre- or peri-implantation embryos. This is significant as implantation is the time when inner cell mass cells of the blastocyst exit pluripotency and begin to commit to form the various lineages that will eventually form the adult animal. These observations indicate a critical role for chromatin-modifying proteins in the earliest lineage decisions of mammalian development, and/or in the formation of the first embryonic cell types. Recent work has shown that the two major class I histone deacetylase-containing co-repressor complexes, the NuRD and Sin3 complexes, are both required at peri-implantation stages of mouse development, demonstrating the importance of histone deacetylation in cell fate decisions. Over the past 10 years both genetic and biochemical studies have revealed surprisingly divergent roles for these two co-repressors in mammalian cells. In this review we will summarise the evidence that the two major class I histone deacetylase complexes in mammalian cells, the NuRD and Sin3 complexes, play important roles in distinct aspects of embryonic development.
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