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SUMOylation of the chromodomain factor MRG-1 in C. elegans affects chromatin-regulatory dynamics. Biotechniques 2022; 73:5-17. [PMID: 35698829 DOI: 10.2144/btn-2021-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenetic mechanisms control chromatin accessibility and gene expression to ensure proper cell fate specification. Histone proteins are integral chromatin components, and their modification promotes gene expression regulation. Specific proteins recognize modified histones such as the chromodomain protein MRG-1. MRG-1 is the Caenorhabditis elegans ortholog of mammalian MRG15, which is involved in DNA repair. MRG-1 binds methylated histone H3 and is important for germline maturation and safeguarding. To elucidate interacting proteins that modulate MRG-1 activity, we performed in-depth protein-protein interaction analysis using immunoprecipitations coupled with mass spectrometry. We detected strong association with the Small ubiquitin-like modifier SUMO, and found that MRG-1 is post-translationally modified by SUMO. SUMOylation affects chromatin-binding dynamics of MRG-1, suggesting an epigenetic regulation pathway, which may be conserved.
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2
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DasGupta A, Lee TL, Li C, Saltzman AL. Emerging Roles for Chromo Domain Proteins in Genome Organization and Cell Fate in C. elegans. Front Cell Dev Biol 2020; 8:590195. [PMID: 33195254 PMCID: PMC7649781 DOI: 10.3389/fcell.2020.590195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022] Open
Abstract
In most eukaryotes, the genome is packaged with histones and other proteins to form chromatin. One of the major mechanisms for chromatin regulation is through post-translational modification of histone proteins. Recognition of these modifications by effector proteins, often dubbed histone “readers,” provides a link between the chromatin landscape and gene regulation. The diversity of histone reader proteins for each modification provides an added layer of regulatory complexity. In this review, we will focus on the roles of chromatin organization modifier (chromo) domain containing proteins in the model nematode, Caenorhabditis elegans. An amenability to genetic and cell biological approaches, well-studied development and a short life cycle make C. elegans a powerful system to investigate the diversity of chromo domain protein functions in metazoans. We will highlight recent insights into the roles of chromo domain proteins in the regulation of heterochromatin and the spatial conformation of the genome as well as their functions in cell fate, fertility, small RNA pathways and transgenerational epigenetic inheritance. The spectrum of different chromatin readers may represent a layer of regulation that integrates chromatin landscape, genome organization and gene expression.
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Affiliation(s)
- Abhimanyu DasGupta
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Arneet L Saltzman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
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3
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Mixing and Matching Chromosomes during Female Meiosis. Cells 2020; 9:cells9030696. [PMID: 32178277 PMCID: PMC7140621 DOI: 10.3390/cells9030696] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 01/17/2023] Open
Abstract
Meiosis is a key event in the manufacturing of an oocyte. During this process, the oocyte creates a set of unique chromosomes by recombining paternal and maternal copies of homologous chromosomes, and by eliminating one set of chromosomes to become haploid. While meiosis is conserved among sexually reproducing eukaryotes, there is a bewildering diversity of strategies among species, and sometimes within sexes of the same species, to achieve proper segregation of chromosomes. Here, we review the very first steps of meiosis in females, when the maternal and paternal copies of each homologous chromosomes have to move, find each other and pair. We explore the similarities and differences observed in C. elegans, Drosophila, zebrafish and mouse females.
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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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5
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Turcotte CA, Sloat SA, Rigothi JA, Rosenkranse E, Northrup AL, Andrews NP, Checchi PM. Maintenance of Genome Integrity by Mi2 Homologs CHD-3 and LET-418 in Caenorhabditis elegans. Genetics 2018; 208:991-1007. [PMID: 29339410 PMCID: PMC5844346 DOI: 10.1534/genetics.118.300686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination depends upon the tightly coordinated regulation of chromosome dynamics and is essential for the production of haploid gametes. Central to this process is the formation and repair of meiotic double-stranded breaks (DSBs), which must take place within the constraints of a specialized chromatin architecture. Here, we demonstrate a role for the nucleosome remodeling and deacetylase (NuRD) complex in orchestrating meiotic chromosome dynamics in Caenorhabditis elegans Our data reveal that the conserved Mi2 homologs Chromodomain helicase DNA-binding protein (CHD-3) and its paralog LET-418 facilitate meiotic progression by ensuring faithful repair of DSBs through homologous recombination. We discovered that loss of either CHD-3 or LET-418 results in elevated p53-dependent germ line apoptosis, which relies on the activation of the conserved checkpoint kinase CHK-1 Consistent with these findings, chd-3 and let-418 mutants produce a reduced number of offspring, indicating a role for Mi2 in forming viable gametes. When Mi2 function is compromised, persisting recombination intermediates are detected in late pachytene nuclei, indicating a failure in the timely repair of DSBs. Intriguingly, our data indicate that in Mi2 mutant germ lines, a subset of DSBs are repaired by nonhomologous end joining, which manifests as chromosomal fusions. We find that meiotic defects are exacerbated in Mi2 mutants lacking CKU-80, as evidenced by increased recombination intermediates, corpses, and defects in chromosomal integrity. Taken together, our findings support a model wherein the C. elegans Mi2 complex maintains genomic integrity through reinforcement of a chromatin landscape suitable for homology-driven repair mechanisms.
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Affiliation(s)
| | - Solomon A Sloat
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | - Julia A Rigothi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | | | | | | | - Paula M Checchi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
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6
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Sung M, Kawasaki I, Shim YH. Depletion of cdc-25.3, a Caenorhabditis elegans orthologue of cdc25, increases physiological germline apoptosis. FEBS Lett 2017. [PMID: 28627101 DOI: 10.1002/1873-3468.12717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In Caenorhabditis elegans hermaphrodites, physiological germline apoptosis is higher in cdc-25.3 mutants than in wild-type. The elevated germline apoptosis in cdc-25.3 mutants seems to be induced by accumulation of double-stranded DNA breaks (DSBs). Both DNA damage and synapsis checkpoint genes are required to increase the germline apoptosis. Notably, the number of germ cells that lose P-granule components, PGL-1 and PGL-3, increase in cdc-25.3 mutants, and the increase in germline apoptosis requires the activity of SIR-2.1, a Sirtuin orthologue. These results suggest that elevation of germline apoptosis in cdc-25.3 mutants is induced by accumulation of DSBs, leading to a loss of PGL-1 and PGL-3 in germ cells, which promotes cytoplasmic translocation of SIR-2.1, and finally activates the core apoptotic machinery.
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Affiliation(s)
- Minhee Sung
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Ichiro Kawasaki
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Yhong-Hee Shim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
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Wang X, Yang C. Programmed cell death and clearance of cell corpses in Caenorhabditis elegans. Cell Mol Life Sci 2016; 73:2221-36. [PMID: 27048817 PMCID: PMC11108496 DOI: 10.1007/s00018-016-2196-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 01/01/2023]
Abstract
Programmed cell death is critical to the development of diverse animal species from C. elegans to humans. In C. elegans, the cell death program has three genetically distinguishable phases. During the cell suicide phase, the core cell death machinery is activated through a protein interaction cascade. This activates the caspase CED-3, which promotes numerous pro-apoptotic activities including DNA degradation and exposure of the phosphatidylserine "eat me" signal on the cell corpse surface. Specification of the cell death fate involves transcriptional activation of the cell death initiator EGL-1 or the caspase CED-3 by coordinated actions of specific transcription factors in distinct cell types. In the cell corpse clearance stage, recognition of cell corpses by phagocytes triggers several signaling pathways to induce phagocytosis of apoptotic cell corpses. Cell corpse-enclosing phagosomes ultimately fuse with lysosomes for digestion of phagosomal contents. This article summarizes our current knowledge about programmed cell death and clearance of cell corpses in C. elegans.
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Affiliation(s)
- Xiaochen Wang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China.
| | - Chonglin Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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Mei F, Chen PF, Dombecki CR, Aljabban I, Nabeshima K. A Defective Meiotic Outcome of a Failure in Homologous Pairing and Synapsis Is Masked by Meiotic Quality Control. PLoS One 2015; 10:e0134871. [PMID: 26247362 PMCID: PMC4527744 DOI: 10.1371/journal.pone.0134871] [Citation(s) in RCA: 3] [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: 02/23/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
Successful gamete production is ensured by meiotic quality control, a process in which germ cells that fail in bivalent chromosome formation are eliminated during meiotic prophase. To date, numerous meiotic mutants have been isolated in a variety of model organisms, using defects associated with a failure in bivalent formation as hallmarks of the mutant. Presumably, the meiotic quality control mechanism in those mutants is overwhelmed. In these mutants, all germ cells fail in bivalent formation, and a subset of cells seem to survive the elimination process and develop into gametes. It is possible that mutants that are partially defective in bivalent formation were missed in past genetic screens, because no evident meiotic defects associated with failure in bivalent formation would have been detectable. Meiotic quality control effectively eliminates most failed germ cells, leaving predominately successful ones. Here, we provide evidence supporting this possibility. The Caenorhabditis elegans mrg-1 loss-of-function mutant does not appear to be defective in bivalent formation in diakinesis oocytes. However, defects in homologous chromosome pairing and synapsis during the preceding meiotic prophase, prerequisites for successful bivalent formation, were observed in most, but not all, germ cells. Failed bivalent formation in the oocytes became evident once meiotic quality control was abrogated in the mrg-1 mutant. Both double-strand break repair and synapsis checkpoints are partly responsible for eliminating failed germ cells in the mrg-1 mutant. Interestingly, removal of both checkpoint activities from the mrg-1 mutant is not sufficient to completely suppress the increased germline apoptosis, suggesting the presence of a novel meiotic checkpoint mechanism.
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Affiliation(s)
- Frank Mei
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter F. Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Carolyn R. Dombecki
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Imad Aljabban
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kentaro Nabeshima
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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9
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Gupta P, Leahul L, Wang X, Wang C, Bakos B, Jasper K, Hansen D. Proteasome regulation of the chromodomain protein MRG-1 controls the balance between proliferative fate and differentiation in the C. elegans germ line. Development 2015; 142:291-302. [PMID: 25564623 DOI: 10.1242/dev.115147] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The level of stem cell proliferation must be tightly controlled for proper development and tissue homeostasis. Multiple levels of gene regulation are often employed to regulate stem cell proliferation to ensure that the amount of proliferation is aligned with the needs of the tissue. Here we focus on proteasome-mediated protein degradation as a means of regulating the activities of proteins involved in controlling the stem cell proliferative fate in the C. elegans germ line. We identify five potential E3 ubiquitin ligases, including the RFP-1 RING finger protein, as being involved in regulating proliferative fate. RFP-1 binds to MRG-1, a homologue of the mammalian chromodomain-containing protein MRG15 (MORF4L1), which has been implicated in promoting the proliferation of neural precursor cells. We find that C. elegans with reduced proteasome activity, or that lack RFP-1 expression, have increased levels of MRG-1 and a shift towards increased proliferation in sensitized genetic backgrounds. Likewise, reduction of MRG-1 partially suppresses stem cell overproliferation. MRG-1 levels are controlled independently of the spatially regulated GLP-1/Notch signalling pathway, which is the primary signal controlling the extent of stem cell proliferation in the C. elegans germ line. We propose a model in which MRG-1 levels are controlled, at least in part, by the proteasome, and that the levels of MRG-1 set a threshold upon which other spatially regulated factors act in order to control the balance between the proliferative fate and differentiation in the C. elegans germ line.
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Affiliation(s)
- Pratyush Gupta
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Lindsay Leahul
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Xin Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Chris Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Brendan Bakos
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Katie Jasper
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
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Lamelza P, Bhalla N. Histone methyltransferases MES-4 and MET-1 promote meiotic checkpoint activation in Caenorhabditis elegans. PLoS Genet 2012; 8:e1003089. [PMID: 23166523 PMCID: PMC3499413 DOI: 10.1371/journal.pgen.1003089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/28/2012] [Indexed: 11/18/2022] Open
Abstract
Chromosomes that fail to synapse during meiosis become enriched for chromatin marks associated with heterochromatin assembly. This response, called meiotic silencing of unsynapsed or unpaired chromatin (MSUC), is conserved from fungi to mammals. In Caenorhabditis elegans, unsynapsed chromosomes also activate a meiotic checkpoint that monitors synapsis. The synapsis checkpoint signal is dependent on cis-acting loci called Pairing Centers (PCs). How PCs signal to activate the synapsis checkpoint is currently unknown. We show that a chromosomal duplication with PC activity is sufficient to activate the synapsis checkpoint and that it undergoes heterochromatin assembly less readily than a duplication of a non-PC region, suggesting that the chromatin state of these loci is important for checkpoint function. Consistent with this hypothesis, MES-4 and MET-1, chromatin-modifying enzymes associated with transcriptional activity, are required for the synapsis checkpoint. In addition, a duplication with PC activity undergoes heterochromatin assembly when mes-4 activity is reduced. MES-4 function is required specifically for the X chromosome, while MES-4 and MET-1 act redundantly to monitor autosomal synapsis. We propose that MES-4 and MET-1 antagonize heterochromatin assembly at PCs of unsynapsed chromosomes by promoting a transcriptionally permissive chromatin environment that is required for meiotic checkpoint function. Moreover, we suggest that different genetic requirements to monitor the behavior of sex chromosomes and autosomes allow for the lone unsynapsed X present in male germlines to be shielded from inappropriate checkpoint activation.
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Affiliation(s)
| | - Needhi Bhalla
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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