1
|
Yamaya K, Wang B, Memar N, Odiba A, Woglar A, Gartner A, Villeneuve A. Disparate roles for C. elegans DNA translocase paralogs RAD-54.L and RAD-54.B in meiotic prophase germ cells. Nucleic Acids Res 2023; 51:9183-9202. [PMID: 37548405 PMCID: PMC10516670 DOI: 10.1093/nar/gkad638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/06/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023] Open
Abstract
RAD54 family DNA translocases partner with RAD51 recombinases to ensure stable genome inheritance, exhibiting biochemical activities both in promoting recombinase removal and in stabilizing recombinase association with DNA. Understanding how such disparate activities of RAD54 paralogs align with their biological roles is an ongoing challenge. Here we investigate the in vivo functions of Caenorhabditis elegans RAD54 paralogs RAD-54.L and RAD-54.B during meiotic prophase, revealing distinct contributions to the dynamics of RAD-51 association with DNA and to the progression of meiotic double-strand break repair (DSBR). While RAD-54.L is essential for RAD-51 removal from meiotic DSBR sites to enable recombination progression, RAD-54.B is largely dispensable for meiotic DSBR. However, RAD-54.B is required to prevent hyperaccumulation of RAD-51 on unbroken DNA during the meiotic sub-stage when DSBs and early recombination intermediates form. Moreover, DSB-independent hyperaccumulation of RAD-51 foci in the absence of RAD-54.B is RAD-54.L-dependent, revealing a hidden activity of RAD-54.L in promoting promiscuous RAD-51 association that is antagonized by RAD-54.B. We propose a model wherein a division of labor among RAD-54 paralogs allows germ cells to ramp up their capacity for efficient homologous recombination that is crucial to successful meiosis while counteracting potentially deleterious effects of unproductive RAD-51 association with unbroken DNA.
Collapse
Affiliation(s)
- Kei Yamaya
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Nadin Memar
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Alexander Woglar
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Swiss Institute for Experimental Cancer Research (ISREC) and School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Anton Gartner
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Anne M Villeneuve
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
2
|
Lascarez-Lagunas LI, Martinez-Garcia M, Nadarajan S, Diaz-Pacheco BN, Berson E, Colaiácovo MP. Chromatin landscape, DSB levels, and cKU-70/80 contribute to patterning of meiotic DSB processing along chromosomes in C. elegans. PLoS Genet 2023; 19:e1010627. [PMID: 36706157 PMCID: PMC9907818 DOI: 10.1371/journal.pgen.1010627] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/08/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Programmed DNA double-strand break (DSB) formation is essential for achieving accurate chromosome segregation during meiosis. DSB repair timing and template choice are tightly regulated. However, little is known about how DSB distribution and the choice of repair pathway are regulated along the length of chromosomes, which has direct effects on the recombination landscape and chromosome remodeling at late prophase I. Here, we use the spatiotemporal resolution of meiosis in the Caenorhabditis elegans germline along with genetic approaches to study distribution of DSB processing and its regulation. High-resolution imaging of computationally straightened chromosomes immunostained for the RAD-51 recombinase marking DSB repair sites reveals that the pattern of RAD-51 foci throughout pachytene resembles crossover distribution in wild type. Specifically, RAD-51 foci occur primarily along the gene-poor distal thirds of the chromosomes in both early and late pachytene, and on both the X and the autosomes. However, this biased off-center distribution can be abrogated by the formation of excess DSBs. Reduced condensin function, but not an increase in total physical axial length, results in a homogeneous distribution of RAD-51 foci, whereas regulation of H3K9 methylation is required for the enrichment of RAD-51 at off-center positions. Finally, the DSB recognition heterodimer cKU-70/80, but not the non-homologous end-joining canonical ligase LIG-4, contributes to the enriched off-center distribution of RAD-51 foci. Taken together, our data supports a model by which regulation of the chromatin landscape, DSB levels, and DSB detection by cKU-70/80 collaborate to promote DSB processing by homologous recombination at off-center regions of the chromosomes in C. elegans.
Collapse
Affiliation(s)
- Laura I. Lascarez-Lagunas
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marina Martinez-Garcia
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Saravanapriah Nadarajan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brianna N. Diaz-Pacheco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Elizaveta Berson
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mónica P. Colaiácovo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
3
|
Carelli FN, Cerrato C, Dong Y, Appert A, Dernburg A, Ahringer J. Widespread transposon co-option in the Caenorhabditis germline regulatory network. SCIENCE ADVANCES 2022; 8:eabo4082. [PMID: 36525485 PMCID: PMC9757741 DOI: 10.1126/sciadv.abo4082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. We show that transposon expansions in Caenorhabditis nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one-third of Caenorhabditis elegans germline-specific promoters have been co-opted from two related miniature inverted repeat transposable elements (TEs), CERP2 and CELE2. These promoters are regulated by HIM-17, a THAP domain-containing transcription factor related to a transposase. Expansion of CERP2 occurred before radiation of the Caenorhabditis genus, as did fixation of mutations in HIM-17 through positive selection, whereas CELE2 expanded only in C. elegans. Through comparative analyses in Caenorhabditis briggsae, we find not only evolutionary conservation of most CERP2 co-opted promoters but also a substantial fraction that are species-specific. Our work reveals the emergence and evolutionary conservation of a novel transcriptional network driven by TE co-option with a major impact on regulatory evolution.
Collapse
Affiliation(s)
- Francesco Nicola Carelli
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alex Appert
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Abby Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
- Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, Berkeley, CA 94720, USA
| | - Julie Ahringer
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Loss, Gain, and Retention: Mechanisms Driving Late Prophase I Chromosome Remodeling for Accurate Meiotic Chromosome Segregation. Genes (Basel) 2022; 13:genes13030546. [PMID: 35328099 PMCID: PMC8949218 DOI: 10.3390/genes13030546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
To generate gametes, sexually reproducing organisms need to achieve a reduction in ploidy, via meiosis. Several mechanisms are set in place to ensure proper reductional chromosome segregation at the first meiotic division (MI), including chromosome remodeling during late prophase I. Chromosome remodeling after crossover formation involves changes in chromosome condensation and restructuring, resulting in a compact bivalent, with sister kinetochores oriented to opposite poles, whose structure is crucial for localized loss of cohesion and accurate chromosome segregation. Here, we review the general processes involved in late prophase I chromosome remodeling, their regulation, and the strategies devised by different organisms to produce bivalents with configurations that promote accurate segregation.
Collapse
|
5
|
Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
Collapse
Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
| |
Collapse
|