Biology subjects

Cohen, P. E.

Publications and source records attributed to Cohen, P. E..

14 recordsLinked to original sources

bioRxiv2025

Argonaute proteins regulate the timing of the spermatogenic transcriptional program

Argonaute proteins are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we show that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes where they are required for transcriptional silencing of XY-linked genes, known as Meiotic Sex Chromosome Inactivation (MSCI). Using an Ago413-/- mouse, we show that AGO3 and AGO4 are key regulators of spermatogenesis, orchestrating expression of meiosis-related genes during prophase I while maintaining silencing of spermiogenesis genes. Premature overexpression of spermiogenesis genes during prophase I in Ago413-/- mice results in subfertility, altered sperm morphology and reduced fertilization capability. We also identify BRG1, a BAF complex subunit, as an AGO3 interactor. Loss of AGO3 and AGO4 results in increased BRG1 in spermatocytes, suggesting that AGO3 aids in removing BRG1 from the XY chromatin to achieve MSCI and demonstrating a meiotic role for AGO3 in transcriptional control through the chromatin remodeling machinery.

developmental biology↗

bioRxiv2023

The DNA helicase FANCJ (BRIP1) functions in Double Strand Break repair processing, but not crossover formation during Prophase I of meiosis in male mice

During meiotic prophase I, recombination between homologous parental chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs), each of which must be repaired with absolute fidelity to ensure genome stability of the germline. One outcome of these DSB events is the formation of Crossovers (COs), the sites of physical DNA exchange between homologs that are critical to ensure the correct segregation of parental chromosomes. However, COs account for only a small ([~]10%) proportion of all DSB repair events; the remaining 90% are repaired as non-crossovers (NCOs), most by synthesis dependent strand annealing. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers. The number and positioning of COs is exquisitely controlled via mechanisms that remain poorly understood, but which undoubtedly require the coordinated action of multiple repair pathways downstream of the initiating DSB. In a previous report we found evidence suggesting that the DNA helicase and Fanconi Anemia repair protein, FANCJ (BRIP1/BACH1), functions to regulate meiotic recombination in mouse. A gene-trap disruption of Fancj showed an elevated number of MLH1 foci and COs. FANCJ is known to interact with numerous DNA repair proteins in somatic cell repair contexts, including MLH1, BLM, BRCA1, and TOPBP1, and we hypothesized that FANCJ regulates CO formation through a direct interaction with MLH1 to suppress the major CO pathway. To further elucidate the function of FANCJ in meiosis, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, a mutant line lacking the MLH1 interaction site and the N-terminal region of the Helicase domain, and a C-terminal 6xHIS-HA dual-tagged allele of Fancj. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, while Fanconi-like phenotypes are observed within the somatic cell lineages of the full deletion Fancj line, none of the Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I of meiosis. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 during late prophase I. Instead, FANCJ forms discrete foci along the chromosome cores beginning in early meiotic prophase I, occasionally co-localizing with MSH4, and then becomes densely localized on unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Strikingly, this localization strongly overlaps with BRCA1 and TOPBP1. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data suggest a role for FANCJ in early DSB repair events, and possibly in the formation of NCOs, but they rule out a role for FANCJ in MLH1-mediated CO events. Thus, the role of FANCJ in meiotic cells involves different pathways and different interactors to those described in somatic cell lineages.

genetics↗

bioRxiv2023

Cyclin N-terminal domain-containing 1 (CNTD1) is critical for crossover designation during meiotic prophase I and for maintenance of ovarian reserve in mammalian oocytes

In meiotic prophase I, hundreds of double-strand breaks (DSBs) are formed throughout the genome. A majority of these breaks are repaired as non-crossovers (NCOs), while a minor subset are repaired as crossovers (CO). COs are essential for the faithful segregation of homologous chromsomes at the end of prophase I and errors in CO designation can result in aneuploidy, germ cell death, birth defects, or infertility. These errors are more evident in female meiosis compared to males and suggests that the events of meiotic prophase I are sexually dimorphic with respect to CO formation, placement, resolution, and/or surveillance. Here, we demonstrate a critical role for Cyclin N-Terminal Domain Containing 1 (CNTD1) protein in ensuring appropriate CO frequency and distribution across the genome during meiosis in females. We find that CNTD1 localizes with the heterodimer, MutL{gamma}, which marks the majority of CO that emerge in pachynema of prophase I, implicating CNTD1 in late-stage CO designation and/or maturation. Accordingly, loss of Cntd1 in oocytes results in failure to load MutL{gamma} and thus results in a catastrophic loss of chiasmata and sterility. Further investigation yielded a distinct phenotype in which the primordial follicles that form upon dictyate arrest are steadily lost from birth onwards, a temporal loss of follicles that is different to that seen in other CO mutants. We find that this follicle loss in Cntd1 mutants is dependent on the checkpoint kinase CHK2. Thus, in females, loss of Cntd1 appears to result in phenotypes that are temporally disconnected from early and late CO mutants such as MutS{gamma} and MutL{gamma}, which show early prophase I disruption and ablation of ovary structure, and no prophase I disruption and an appearance of wildtype ovaries, respectively. These data suggest novel dual roles for CNTD1 in CO designation and faithful progression of oocytes into dictyate arrest at late pachynema, the latter being critical for establishing the ovarian reserve in female mice.

genetics↗

bioRxiv2023

Dynamic regulatory phosphorylation of mouse CDK2 occurs during meiotic prophase I

During prophase I of meiosis, DNA double-strand breaks form throughout the genome, with a subset repairing as crossover events, enabling the accurate segregation of homologous chromosomes during the first meiotic division. The mechanism by which DSBs become selected to repair as crossovers is unknown, although the crossover positioning and levels in each cell indicate it is a highly regulated process. One of the proteins that localises to crossover sites is the serine/threonine cyclin-dependent kinase CDK2. Regulation of CDK2 occurs via phosphorylation at tyrosine 15 (Y15) and threonine 160 (T160) inhibiting and activating the kinase, respectively. In this study we use a combination of immunofluorescence staining on spread spermatocytes and fixed testis sections, and STA-PUT gravitational sedimentation to isolate cells at different developmental stages to further investigate the temporal phospho regulation of CDK2 during prophase I. Western blotting reveals differential levels of the two CDK2 isoforms (CDK233kDa and CDK239kDa) throughout prophase I, with inhibitory phosphorylation of CDK2 at Y15 occurring early in prophase I, localising to telomeres and diminishing as cells enter pachynema. Conversely, the activatory phosphorylation on T160 occurs later, specifically the CDK233kDa isoform, and T160 signal is detected in spermatogonia and pachytene spermatocytes, where it co-localises with the Class I crossover protein MLH3. Taken together, our data reveals intricate control of CDK2 both with regards to levels of the two CDK2 isoforms, and differential regulation via inhibitory and activatory phosphorylation.

cell biology↗

bioRxiv2023

A TOPBP1 Allele Causing Male Infertility Uncouples XY Silencing Dynamics From Sex Body Formation

Meiotic sex chromosome inactivation (MSCI) is a critical feature of meiotic prophase I progression in males. While the ATR kinase and its activator TOPBP1 are key drivers of MSCI within the specialized sex body (SB) domain of the nucleus, how they promote silencing remains unclear given their multifaceted meiotic functions that also include DNA repair, chromosome synapsis and SB formation. Here we report a novel mutant mouse harboring mutations in the TOPBP1-BRCT5 domain. Topbp1B5/B5 males are infertile, with impaired MSCI despite displaying grossly normal events of early prophase I, including synapsis and SB formation. Specific ATR-dependent events are disrupted including phosphorylation and localization of the RNA:DNA helicase Senataxin. Topbp1B5/B5 spermatocytes initiate, but cannot maintain ongoing, MSCI. These findings reveal a non-canonical role for the ATR-TOPBP1 signaling axis in MSCI dynamics at advanced stages in pachynema and establish the first mouse mutant that separates ATR signaling and MSCI from SB formation.

cell biology↗

bioRxiv2021

Genetic Dissection of the RNA Polymerase II Transcription Cycle

How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.

genomics↗

bioRxiv2021

Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis

DNA damage response mechanisms have meiotic roles that ensure successful gamete formation. While completion of meiotic double-strand break (DSB) repair requires the canonical RAD9A-RAD1-HUS1 (9A-1-1) complex, mammalian meiocytes also express RAD9A and HUS1 paralogs, RAD9B and HUS1B, predicted to form alternative 9-1-1 complexes. The RAD1 subunit is shared by all predicted 9-1-1 complexes and localizes to meiotic chromosomes even in the absence of HUS1 and RAD9A. Here we report that testis-specific RAD1 disruption resulted in impaired DSB repair, germ cell depletion and infertility. Unlike Hus1 or Rad9a disruption, Rad1 loss also caused defects in homolog synapsis, ATR signaling and meiotic sex chromosome inactivation. Comprehensive testis phosphoproteomics revealed that RAD1 and ATR coordinately regulate numerous proteins involved in DSB repair, meiotic silencing, synaptonemal complex formation, and cohesion. Together, these results establish critical roles for both canonical and alternative 9-1-1 complexes in meiotic ATR activation and successful prophase I completion.

genetics↗

bioRxiv2020

Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain, which can be excluded via MLH3 splice redirection to suppress expansion

Somatic expansion of the CAG repeat tract that causes Huntingtons disease (HD) is thought to contribute to the rate of disease pathogenesis. Therefore, factors influencing repeat expansion are potential therapeutic targets. Genes in the DNA mismatch repair pathway are critical drivers of somatic expansion in HD mouse models. Here, we have tested, using genetic and pharmacological approaches, the role of the endonuclease domain of the mismatch repair protein MLH3 in somatic CAG expansion in HD mice and patient cells. A point mutation in the MLH3 endonuclease domain completely eliminated CAG expansion in the brain and peripheral tissues of a HD knock-in mouse model (HttQ111). To test whether the MLH3 endonuclease could be manipulated pharmacologically, we delivered splice switching oligonucleotides in mice to redirect Mlh3 splicing to exclude the endonuclease domain. Splice redirection to an isoform lacking the endonuclease domain was associated with reduced CAG expansion. Finally, CAG expansion in HD patient-derived primary fibroblasts was also significantly reduced by redirecting MLH3 splicing to the endogenous endonuclease domain-lacking isoform. These data indicate the potential of targeting the MLH3 endonuclease domain to slow somatic CAG repeat expansion in HD, a therapeutic strategy that may be applicable across multiple repeat expansion disorders.

genetics↗

bioRxiv2019

Cyclin N-Terminal Domain-Containing 1 (CNTD1) coordinates meiotic crossover formation with cell cycle progression in a cyclin-independent manner

During meiotic prophase I, programmed DNA double-strand breaks repair as non-crossover or crossover events, the latter predominantly occurring via the Class I crossover pathway and requiring the cyclin family member CNTD1. Using an epitope-tagged Cntd1 allele, we show that mouse CNTD1 exists in vivo as a short isoform that lacks the predicted N-terminal cyclin domain and does not bind cyclin-dependent kinases. Instead, we find that CNTD1 associates with Replication Factor C to drive crossover formation and the Skp1-Cullin1-F-Box complex to regulate ubiquitination and subsequent degradation of the WEE1 kinase, thereby indirectly modulating cell cycle progression. We propose that these interactions enable CNTD1 to orchestrate the steps of prophase I and coordinate crossover formation with cellular division.

cell biology↗

bioRxiv2019

Mutation of the ATPase domain of MutS homolog-5 (MSH5) reveals a requirement for a functional MutSγ complex for all crossovers in mammalian meiosis

During meiosis, induction of DNA double strand breaks (DSB) leads to recombination between homologous chromosomes, resulting in crossovers (CO) and non-crossovers (NCO). Only 10% DSBs resolve as COs, mostly through a class I pathway dependent on MutS{gamma} (MSH4/ MSH5). Class II CO events represent a minor proportion of the total CO count and also arise from DSBs, but are not thought to involve MutS{gamma}. However, loading of MutS{gamma} occurs very early in prophase I at a frequency that far exceeds the final number of class I COs found in late prophase I. Moreover, loss of MutS{gamma} in mouse results in apoptosis before CO formation, preventing analysis of its CO function. We generated a mutation in the ATP binding domain of Msh5 (Msh5GA). While this mutation was not expected to affect MutS{gamma} complex formation, MutS{gamma} foci do not accumulate during prophase I. Nevertheless, while some spermatocytes from Msh5-/- animals progress into pachynema, most spermatocytes from Msh5GA/GA mice progress to late pachynema and beyond. Some spermatocytes from Msh5GA/GA mice complete prophase I entirely, allowing for the first time an assessment of MSH5 function in CO formation. At pachynema, Msh5GA/GA spermatocytes show persistent DSBs, incomplete homolog pairing, and fail to accumulate MutL{gamma} (MLH1/MLH3). Unexpectedly, Msh5GA/GA diakinesis-staged spermatocytes have no chiasmata at all from any CO pathway, indicating that a functional MutS{gamma} complex in early prophase I is a pre-requisite for all COs. ARTICLE SUMMARYMSH4/MSH5 are critical components of the class I crossover (CO) machinery, which is responsible for >90% of the COs that arise in mammalian meiosis. We generated a point mutation in the ATP binding motif of Msh5, and found that mutant spermatocytes lose all COs, not just those arising from the class I pathway.

genetics↗

bioRxiv2019

Mutation Of MLH3 Endonuclease Motif Reveals Integration Between Crossover Pathways In Mammalian Meiosis

During meiotic prophase I, double-strand breaks (DSBs) initiate homologous recombination leading to non-crossovers (NCOs) and crossovers (COs). In mouse, 10% of DSBs are designated to become COs, primarily through a pathway dependent on the MLH1-MLH3 heterodimer (MutL{gamma}). Mlh3 contains an endonuclease domain that is critical for resolving COs in yeast. We generated a mouse (Mlh3DN/DN) harboring a mutation within this conserved domain that is predicted to generate a protein that is catalytically inert. Mlh3DN/DN males, like fully null Mlh3-/- males, have no spermatozoa and are infertile, yet spermatocytes have normal DSBs and undergo normal synapsis events in early prophase I. Unlike Mlh3-/- males, mutation of the endonuclease domain within MLH3 permits normal loading and frequency of MutL{gamma} in pachynema. However, key DSB repair factors (RAD51) and mediators of CO pathway choice (BLM helicase) persist into pachynema in Mlh3DN/DN males, indicating a temporal delay in repair events and revealing a mechanism by which alternative DSB repair pathways may be selected. While Mlh3DN/DN spermatocytes retain only 22% of wildtype chiasmata counts, this frequency is greater than observed in Mlh3-/- males (10%), suggesting that the allele may permit partial endonuclease activity, or that other pathways can generate COs from these MutL{gamma}-defined repair intermediates in Mlh3DN/DN males. Double mutant mice homozygous for the Mlh3DN/DN and Mus81-/- mutations show losses in chiasmata that approach levels observed in Mlh3-/- males, indicating that the MUS81-EME1-regulated crossover pathway accounts for some of the increased residual chiasmata observed in Mlh3DN/DN spermatocytes. Our data demonstrate that mouse spermatocytes bearing the MLH1-MLH3DN/DN complex display the proper loading of factors essential for CO resolution (MutS{gamma}, CDK2, HEI10, MutL{gamma}). Despite these functions, mice bearing the Mlh3DN/DN allele show defects in the repair of meiotic recombination intermediates and a loss of most chiasmata. SUMMARYThe MLH1-MLH3 complex is essential for crossing over in mammalian meiosis. We generated a mutation in mouse MLH3 that alters its conserved endonuclease domain and show that it disrupts crossing over in a manner distinct from the full null Mlh3 mouse, but also results in male infertility.

genetics↗

bioRxiv2018

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

Spermatogenesis is the process by which male gametes are formed from a self-renewing population of spermatogonial stem cells (SSCs) residing in the testis. SSCs represent less than 1% of the total testicular cell population, but must achieve a stable balance between self-renewal and differentiation. Once differentiation has occurred, the newly formed and highly proliferative spermatogonia must then enter the meiotic program in which DNA content is doubled, then halved twice to create haploid gametes. While much is known about the critical cellular processes that take place during the specialized cell division that is meiosis, much less is known about how the spermatocytes in the \"first-wave\" compare to those that contribute to long-term, \"steady-state\" spermatogenesis. Given the strictly-defined developmental process of spermatogenesis, this study was aimed at exploring the transcriptional profiles of developmental cell stages over the age of the animal. Using a combination of comprehensive germ cell sampling with high-resolution, single-cell-mRNA-sequencing, we have generated a reference dataset of germ cell gene expression. We show that discrete developmental stages possess significant differences in the transcriptional profiles from neonates compared to juveniles and adults. Importantly, these gene expression dynamics are also reflected at the protein level in their respective cell types. We also show differential utilization of many biological pathways with age in both spermatogonia and spermatocytes, demonstrating significantly different underlying gene regulatory programs in these cell types over the course of testis development and spermatogenic waves. This dataset represents the first unbiased sampling of spermatogonia and spermatocytes in the developing testis over developmental age, at high-resolution, single-cell depth. Not only does this analysis reveal previously unknown transcriptional dynamics of a highly transitional cell population, it has also begun to reveal critical differences in biological pathway utilization in developing spermatogonia and spermatocytes, including response to DNA damage and double-strand breaks.\n\nAuthor SummarySpermatogenesis is the process by which male gametes - mature spermatozoa - are produced in the testis. This process requires exquisite control over many developmental transitions, including the self-renewal of the germline stem cell population, commitment to meiosis, and ultimately, spermiogenesis. While much is known about molecular mechanisms regulating single transitions at single time points in the mouse, much less is understood about how the spermatogenic progenitor cells, spermatogonia, or the meiotic cells, spermatocytes, of the testis change over developmental age.\n\nOur single-cell-mRNA-sequencing analysis is the first to profile both spermatogonia and spermatocytes from neonatal mice through adulthood, revealing novel gene expression dynamics and differential utilization of biological pathways. These discoveries help us to understand how the spermatogenic progenitors of this population modulate their activity to adapt to a changing testicular environment. Furthermore, they also begin to explain previously-observed differences - and deficiencies - in spermatocytes that are derived from the first \"wave\" of spermatogenesis. Overall, this dataset is the first of its kind to comprehensively profile gene expression dynamics in male germ cell populations over time, enriching our understanding of the complex and highly-orchestrated process of spermatogenesis.

genomics↗

bioRxiv2018

Characterization of Telomeric Repeat-Containing RNA (TERRA) localization and protein interactions in Primordial Germ Cells of the mouse

Telomeres are dynamic nucleoprotein structures capping the physical ends of linear eukaryotic chromosomes. They consist of telomeric DNA repeats (TTAGGG), the shelterin protein complex, and Telomeric Repeat-Containing RNA (TERRA). Proposed TERRA functions are wide-ranging and include telomere maintenance, telomerase inhibition, genomic stability, and alternative lengthening of telomere. However, the role of TERRA in primordial germ cells (PGCs), the embryonic precursors of germ cells, is unknown. Using RNA-fluorescence in situ hybridization (RNA-FISH) we identify TERRA in PGCs soon after these cells have migrated to, and become established in, the developing gonad. RNA-FISH showed the presence of TERRA transcripts in female PGCs at 11.5, 12.5 and 13.5 days post-coitum. In male PGCs, however, TERRA transcripts are observable from 12.5 dpc. Using qPCR we evaluated chromosome-specific TERRA expression, and demonstrated that TERRA levels vary with sex and gestational age, and that transcription of TERRA from specific chromosomes is sexually dimorphic. TERRA interacting proteins were evaluated using Identification of Direct RNA Interacting Proteins (iDRiP) which identified 48 in female and 26 in male protein interactors specifically within nuclear extracts from PGCs at 13.5 dpc. We validated two different proteins the splicing factor, proline- and glutamine-rich (SFPQ) in PGCs and Non-POU domain-containing octamer-binding protein (NONO) in somatic cells. Our results show that, TERRA interacting proteins are determined by sex in both PGCs and somatic cells. Taken together, our data indicate that TERRA expression and interactome during PGC development are regulated in a dynamic fashion that is dependent on gestational age and sex.\n\nResearch reported in this publication was supported in part by the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health under Award Number K99HD090289 to M.A.B-E. A seed grant from the Cornell Center for Reproductive Genomics to M.A.B-E, using funds obtained as part of the NICHD National Centers for Translational Research in Reproduction and Infertility (NCTRI), award number P50HD076210 to P.E.C. and Empire State Stem Cell Fund through New York State Department of Health Contract # C30293GG. Imaging data was acquired through the Cornell University Biotechnology Resource Center, with NSF funding #1428922 for the shared Zeiss Elyra Microscope. NIH SIG 1S10 OD017992-01 grant support the Orbitrap Fusion mass spectrometer. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

genetics↗

bioRxiv2017

NIMA-related kinase 1 (NEK1) regulates the localization and phosphorylation of α-Adducin (ADD1) and Myosin X (MYO10) during meiosis

Summary statementNEK1 kinase regulates the assembly and function of the meiosis I spindle by phosphorylating -adducin (ADD1) and thereby facilitating its interaction with Myosin X (MYO10)\n\nAbstractNIMA-related kinase 1 (NEK1) is a serine/threonine and tyrosine kinase that is highly expressed in mammalian germ cells. Mutations in Nek1 induce anemia, polycystic kidney and infertility. In this study we evaluated the role of NEK1 in meiotic spindle formation in both male and female gametes. Our results show that the lack of NEK1 provokes an abnormal organization of the meiosis I spindle characterized by elongated and/or multipolar spindles, and abnormal chromosome congression. The aberrant spindle structure is concomitant with the disruption in localization and protein levels of myosin X (MYO10) and -adducin (ADD1), both of which are implicated in the regulation of spindle formation during mitosis. Interaction of ADD1 with MYO10 is dependent on phosphorylation, whereby phosphorylation of ADD1 enables its binding to MYO10 on mitotic spindles. Reduction in ADD1 protein in NEK1 mutant mice is associated with hyperphosphorylation of ADD1, thereby preventing the interaction with MYO10 during meiotic spindle formation. Our results reveal a novel regulatory role for NEK1 in the regulation of spindle architecture and function during meiosis.

cell biology↗