The Mouse Meiotic Mutation Mei1 Disrupts Chromosome Synapsis with Sexually Dimorphic Consequences for Meiotic Progression
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ATR Pathway Inhibition Is Synthetically Lethal in Cancer Cells with ERCC1 Deficiency
Published OnlineFirst March 24, 2014; DOI: 10.1158/0008-5472.CAN-13-3229 Cancer Therapeutics, Targets, and Chemical Biology Research ATR Pathway Inhibition Is Synthetically Lethal in Cancer Cells with ERCC1 Deficiency Kareem N. Mohni, Gina M. Kavanaugh, and David Cortez Abstract The DNA damage response kinase ATR and its effector kinase CHEK1 are required for cancer cells to survive oncogene-induced replication stress. ATR inhibitors exhibit synthetic lethal interactions, with deficiencies in the DNA damage response enzymes ATM and XRCC1 and with overexpression of the cell cycle kinase cyclin E. Here, we report a systematic screen to identify synthetic lethal interactions with ATR pathway–targeted drugs, rationalized by their predicted therapeutic utility in the oncology clinic. We found that reduced function in the ATR pathway itself provided the strongest synthetic lethal interaction. In addition, we found that loss of the structure-specific endonuclease ERCC1-XPF (ERCC4) is synthetic lethal with ATR pathway inhibitors. ERCC1- deficient cells exhibited elevated levels of DNA damage, which was increased further by ATR inhibition. When treated with ATR or CHEK1 inhibitors, ERCC1-deficient cells were arrested in S-phase and failed to complete cell-cycle transit even after drug removal. Notably, triple-negative breast cancer cells and non–small cell lung cancer cells depleted of ERCC1 exhibited increased sensitivity to ATR pathway–targeted drugs. Overall, we concluded that ATR pathway–targeted drugs may offer particular utility in cancers with reduced ATR pathway function or reduced levels of ERCC4 activity. Cancer Res; 74(10); 1–11. Ó2014 AACR. Introduction repair pathway such as homologous recombination or post- – Replicating DNA is sensitive to a wide array of endogenous replicative repair to remove the PARP DNA complexes (7). -
Differential Gene Expression Analysis and Cytological Evidence Reveal a Sexual Stage of an Amoeba with Multiparental Cellular and Nuclear Fusion
PLOS ONE RESEARCH ARTICLE Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion ☯ ☯ Yonas I. TekleID *, Fang Wang , Alireza Heidari, Alanna Johnson Stewart Department of Biology, Spelman College, Atlanta, Georgia, United States of America a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary OPEN ACCESS for sexual reproduction. However, the mechanism of sexual development in a majority of Citation: Tekle YI, Wang F, Heidari A, Stewart AJ microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in (2020) Differential gene expression analysis and studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cytological evidence reveal a sexual stage of an cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investi- amoeba with multiparental cellular and nuclear fusion. PLoS ONE 15(11): e0235725. https://doi. gate sexual development using stage-specific Differential Gene Expression (DGE) and org/10.1371/journal.pone.0235725 cytological analyses. Both DGE and cytological results showed that most of the meiosis and Editor: Arthur J. Lustig, Tulane University Health sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Sciences Center, UNITED STATES Relative gene ontology (GO) category representations in unfused and fused cells revealed Received: June 19, 2020 a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. -
Genome-Wide Parent-Of-Origin DNA Methylation Analysis Reveals The
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Research Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court,1,15 Chiharu Tayama,2,15 Valeria Romanelli,1,15 Alex Martin-Trujillo,1,15 Isabel Iglesias-Platas,3 Kohji Okamura,4 Naoko Sugahara,2 Carlos Simo´n,5 Harry Moore,6 Julie V. Harness,7 Hans Keirstead,7 Jose Vicente Sanchez-Mut,8 Eisuke Kaneki,9 Pablo Lapunzina,10 Hidenobu Soejima,11 Norio Wake,9 Manel Esteller,8,12,13 Tsutomu Ogata,14 Kenichiro Hata,2 Kazuhiko Nakabayashi,2,16,17 and David Monk1,16,17 1–14[Author affiliations appear at the end of the paper.] Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole- genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta. -
The Control of Spo11's Interaction with Meiotic Recombination Hotspots
Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press The control of Spo11’s interaction with meiotic recombination hotspots Silvia Prieler,1 Alexandra Penkner,1 Valérie Borde,2 and Franz Klein1,3 1Institute of Botany, Max F. Perutz Laboratories, Department of Chromosome Biology, A-1030 Vienna, Austria; 2CNRS UMR 144-Institut Curie, 75248 Paris Cedex 05, France Programmed double-strand breaks (DSBs), which initiate meiotic recombination, arise through the activity of the evolutionary conserved topoisomerase homolog Spo11. Spo11 is believed to catalyze the DNA cleavage reaction in the initial step of DSB formation, while at least a further 11 factors assist in Saccharomyces cerevisiae. Using chromatin-immunoprecipitation (ChIP), we detected the transient, noncovalent association of Spo11 with meiotic hotspots in wild-type cells. The establishment of this association requires Rec102, Rec104, and Rec114, while the timely removal of Spo11 from chromatin depends on several factors, including Mei4 and Ndt80. In addition, at least one further component, namely, Red1, is responsible for locally restricting Spo11’s interaction to the core region of the hotspot. In chromosome spreads, we observed meiosis-specific Spo11-Myc foci, independent of DSB formation, from leptotene until pachytene. In both rad50S and com1⌬/sae2⌬ mutants, we observed a novel reaction intermediate between Spo11 and hotspots, which leads to the detection of full-length hotspot DNA by ChIP in the absence of artificial cross-linking. Although this DNA does not contain a break, its recovery requires Spo11’s catalytic residue Y135. We propose that detection of uncross-linked full-length hotspot DNA is only possible during the reversible stage of the Spo11 cleavage reaction, in which rad50S and com1⌬/sae2⌬ mutants transiently arrest. -
A Mutation in the Putative MLH3 Endonuclease Domain Confers a Defect in Both Mismatch Repair and Meiosis in Saccharomyces Cerevisiae
Copyright Ó 2008 by the Genetics Society of America DOI: 10.1534/genetics.108.086645 A Mutation in the Putative MLH3 Endonuclease Domain Confers a Defect in Both Mismatch Repair and Meiosis in Saccharomyces cerevisiae K. T. Nishant, Aaron J. Plys and Eric Alani1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703 Manuscript received January 2, 2008 Accepted for publication March 20, 2008 ABSTRACT Interference-dependent crossing over in yeast and mammalian meioses involves the mismatch repair protein homologs MSH4-MSH5 and MLH1-MLH3. The MLH3 protein contains a highly conserved metal- binding motif DQHA(X)2E(X)4E that is found in a subset of MLH proteins predicted to have endonuclease activities (Kadyrov et al. 2006). Mutations within this motif in human PMS2 and Saccharomyces cerevisiae PMS1 disrupted the endonuclease and mismatch repair activities of MLH1-PMS2 and MLH1-PMS1, re- spectively (Kadyrov et al. 2006, 2007; Erdeniz et al. 2007). As a first step in determining whether such an activity is required during meiosis, we made mutations in the MLH3 putative endonuclease domain motif (-D523N, -E529K) and found that single and double mutations conferred mlh3-null-like defects with respect to meiotic spore viability and crossing over. Yeast two-hybrid and chromatography analyses showed that the interaction between MLH1 and mlh3-D523N was maintained, suggesting that the mlh3-D523N mutation did not disrupt the stability of MLH3. The mlh3-D523N mutant also displayed a mutator phenotype in vegetative growth that was similar to mlh3D. Overexpression of this allele conferred a dominant-negative phenotype with respect to mismatch repair. -
BTG2: a Rising Star of Tumor Suppressors (Review)
INTERNATIONAL JOURNAL OF ONCOLOGY 46: 459-464, 2015 BTG2: A rising star of tumor suppressors (Review) BIjING MAO1, ZHIMIN ZHANG1,2 and GE WANG1 1Cancer Center, Institute of Surgical Research, Daping Hospital, Third Military Medical University, Chongqing 400042; 2Department of Oncology, Wuhan General Hospital of Guangzhou Command, People's Liberation Army, Wuhan, Hubei 430070, P.R. China Received September 22, 2014; Accepted November 3, 2014 DOI: 10.3892/ijo.2014.2765 Abstract. B-cell translocation gene 2 (BTG2), the first 1. Discovery of BTG2 in TOB/BTG gene family gene identified in the BTG/TOB gene family, is involved in many biological activities in cancer cells acting as a tumor The TOB/BTG genes belong to the anti-proliferative gene suppressor. The BTG2 expression is downregulated in many family that includes six different genes in vertebrates: TOB1, human cancers. It is an instantaneous early response gene and TOB2, BTG1 BTG2/TIS21/PC3, BTG3 and BTG4 (Fig. 1). plays important roles in cell differentiation, proliferation, DNA The conserved domain of BTG N-terminal contains two damage repair, and apoptosis in cancer cells. Moreover, BTG2 regions, named box A and box B, which show a high level of is regulated by many factors involving different signal path- homology to the other domains (1-5). Box A has a major effect ways. However, the regulatory mechanism of BTG2 is largely on cell proliferation, while box B plays a role in combination unknown. Recently, the relationship between microRNAs and with many target molecules. Compared with other family BTG2 has attracted much attention. MicroRNA-21 (miR-21) members, BTG1 and BTG2 have an additional region named has been found to regulate BTG2 gene during carcinogenesis. -
Research in Biology Using Computation Doi
Journal of Bioinformatics and Genomics 2 (7) 2018 RESEARCH IN BIOLOGY USING COMPUTATION DOI: https://doi.org/10.18454/jbg.2018.2.7.1 Grishaeva T.M.* Department of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation * Correspodning author (grishaeva[at]vigg.ru) Received: 18.03.2018; Accepted: 05.04.2018; Published: 22.05.2018 COMPARATIVE CONSERVATION OF MEIOTIC PROTEINS IN DIFFERENT PHYLOGENETIC LINES OF EUKARYOTES Research article Abstract Motivation: Meiosis — a two-stage process of sex cell division — is served by several hundreds of proteins. A part of them went to eukaryotes from prokaryotes, others appeared in first eukaryotes, and some proteins appeared de novo in multicellular eukaryotes. We compared the conservation of proteins involved in various processes occurring in meiosis. Results: The conservations of five meiotic enzymes (MLH1, MRE11, MSH4, BRCA1, BRCA2) and three silencing markers (histone H2AX, SUMO1, ATR) were compared using a set of bioinformatics methods. Orthologs of these proteins from the proteomes of model species were compared, representing different lines of development of eukaryotes. Among the enzymes, the most conserved is MLH1, which provide correction of mismatch bases, and the least conserved are BRCA1 and BRCA2 repair enzymes which are present only in vertebrates. Among silencing proteins, histone H2AX is the most conserved one, playing the central part in the regulation of the transcription, in the repair and replication of DNA. The small protein SUMO1, which is involved in many cellular processes, is less conserved. ATR kinase in different species is similar only in the C-terminal part of the molecule. -
The Genetic Bases of Uterine Fibroids; a Review
Review Article The Genetic Bases of Uterine Fibroids; A Review Veronica Medikare 1, Lakshmi Rao Kandukuri 2, Venkateshwari Ananthapur 3, Mamata Deenadayal 4, Pratibha Nallari 1* 1- Department of Genetics, Osmania University, Hyderabad, India 2- Center for Cellular and Molecular Biology, Habsiguda, Hyderabad, India 3- Institute of Genetics and Hospital for Genetic Diseases, Begumpet, Hyderabad, India 4- Infertility Institute and research Center, Secunderabad, India Abstract Uterine leiomyomas/fibroids are the most common pelvic tumors of the female genital tract. The initiators remaining unknown, estrogens and progesterone are considered as promoters of fibroid growth. Fibroids are monoclonal tumors showing 40-50% karyo- typically detectable chromosomal abnormalities. Cytogenetic aberrations involving chromosomes 6, 7, 12 and 14 constitute the major chromosome abnormalities seen in leiomyomata. This has led to the discovery that disruptions or dysregulations of HMGIC and HMGIY genes contribute to the development of these tumors. Genes such as RAD51L1 act as translocation partners to HMGIC and lead to disruption of gene structure leading to the pathogenesis of uterine fibroids. The mechanism underlying * Corresponding Author: this disease is yet to be identified. The occurrence of PCOLCE amid a cluster of at Downloaded from http://www.jri.ir Pratibha Nallari, Department of Genetics, least eight Alu sequences is potentially relevant to the possible involvement of Osmania University, PCOLCE in the 7q22 rearrangements that occur in many leiomyomata. PCOLCE is Hyderabad, 500 007, implicated in cell growth processes. Involvement of Alu sequences in rearrangements India can lead to the disruption of this gene and, hence, loss of control for gene expression E-mail: leading to uncontrolled cell growth. -
Insights Into Regulation of Human RAD51 Nucleoprotein Filament Activity During
Insights into Regulation of Human RAD51 Nucleoprotein Filament Activity During Homologous Recombination Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ravindra Bandara Amunugama, B.S. Biophysics Graduate Program The Ohio State University 2011 Dissertation Committee: Richard Fishel PhD, Advisor Jeffrey Parvin MD PhD Charles Bell PhD Michael Poirier PhD Copyright by Ravindra Bandara Amunugama 2011 ABSTRACT Homologous recombination (HR) is a mechanistically conserved pathway that occurs during meiosis and following the formation of DNA double strand breaks (DSBs) induced by exogenous stresses such as ionization radiation. HR is also involved in restoring replication when replication forks have stalled or collapsed. Defective recombination machinery leads to chromosomal instability and predisposition to tumorigenesis. However, unregulated HR repair system also leads to similar outcomes. Fortunately, eukaryotes have evolved elegant HR repair machinery with multiple mediators and regulatory inputs that largely ensures an appropriate outcome. A fundamental step in HR is the homology search and strand exchange catalyzed by the RAD51 recombinase. This process requires the formation of a nucleoprotein filament (NPF) on single-strand DNA (ssDNA). In Chapter 2 of this dissertation I describe work on identification of two residues of human RAD51 (HsRAD51) subunit interface, F129 in the Walker A box and H294 of the L2 ssDNA binding region that are essential residues for salt-induced recombinase activity. Mutation of F129 or H294 leads to loss or reduced DNA induced ATPase activity and formation of a non-functional NPF that eliminates recombinase activity. DNA binding studies indicate that these residues may be essential for sensing the ATP nucleotide for a functional NPF formation. -
Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database
Supplementary Table S1. Correlation between the mutant p53-interacting partners and PTTG3P, PTTG1 and PTTG2, based on data from StarBase v3.0 database. PTTG3P PTTG1 PTTG2 Gene ID Coefficient-R p-value Coefficient-R p-value Coefficient-R p-value NF-YA ENSG00000001167 −0.077 8.59e-2 −0.210 2.09e-6 −0.122 6.23e-3 NF-YB ENSG00000120837 0.176 7.12e-5 0.227 2.82e-7 0.094 3.59e-2 NF-YC ENSG00000066136 0.124 5.45e-3 0.124 5.40e-3 0.051 2.51e-1 Sp1 ENSG00000185591 −0.014 7.50e-1 −0.201 5.82e-6 −0.072 1.07e-1 Ets-1 ENSG00000134954 −0.096 3.14e-2 −0.257 4.83e-9 0.034 4.46e-1 VDR ENSG00000111424 −0.091 4.10e-2 −0.216 1.03e-6 0.014 7.48e-1 SREBP-2 ENSG00000198911 −0.064 1.53e-1 −0.147 9.27e-4 −0.073 1.01e-1 TopBP1 ENSG00000163781 0.067 1.36e-1 0.051 2.57e-1 −0.020 6.57e-1 Pin1 ENSG00000127445 0.250 1.40e-8 0.571 9.56e-45 0.187 2.52e-5 MRE11 ENSG00000020922 0.063 1.56e-1 −0.007 8.81e-1 −0.024 5.93e-1 PML ENSG00000140464 0.072 1.05e-1 0.217 9.36e-7 0.166 1.85e-4 p63 ENSG00000073282 −0.120 7.04e-3 −0.283 1.08e-10 −0.198 7.71e-6 p73 ENSG00000078900 0.104 2.03e-2 0.258 4.67e-9 0.097 3.02e-2 Supplementary Table S2. -
Homologous Recombination As a Potential Target for Ca€Eine
Oncogene (2000) 19, 5788 ± 5800 ã 2000 Macmillan Publishers Ltd All rights reserved 0950 ± 9232/00 $15.00 www.nature.com/onc Homologous recombination as a potential target for caeine radiosensitization in mammalian cells: reduced caeine radiosensitization in XRCC2 and XRCC3 mutants Nesrin A Asaad1, Zhao-Chong Zeng1, Jun Guan1, John Thacker2 and George Iliakis*,1 1Department of Radiation Oncology of Kimmel Cancer Center, Jeerson Medical College, Philadelphia, Pennsylvania, PA 19107, USA; 2Medical Research Council, Radiation and Genome Stability Unit, Harwell, Oxfordshire, OX11 ORD, UK The radiosensitizing eect of caeine has been associated Introduction with the disruption of multiple DNA damage-responsive cell cycle checkpoints, but several lines of evidence also Caeine (1,3,7-trimethylxanthine) at submillimolar implicate inhibition of DNA repair. The role of DNA concentrations exerts a wide variety of physiological repair inhibition in caeine radiosensitization remains eects on dierent organisms from bacteria to man uncharacterized, and it is unknown which repair process, (Garattini, 1993; Timson, 1977). At higher concentra- or lesion, is aected. We show that a radiosensitive cell tions (0.5 ± 10 mM), it strongly enhances the cytotoxic line, mutant for the RAD51 homolog XRCC2 and eect of ionizing radiation and other physical or defective in homologous recombination repair (HRR), chemical agents that act by inducing damage in DNA displays signi®cantly diminished caeine radiosensitiza- (Kihlman, 1977; Murnane, 1995; Timson, 1977; tion that can be restored by expression of XRCC2. Waldren and Rasko, 1978). Radiosensitization is Despite the reduced radiosensitization, caeine eec- manifest at non-cytotoxic concentrations and therefore tively abrogates checkpoints in S and G2 phases in caeine is considered a model radiosensitizer. -
Lineage-Specific Programming Target Genes Defines Potential for Th1 Temporal Induction Pattern of STAT4
Downloaded from http://www.jimmunol.org/ by guest on October 1, 2021 is online at: average * The Journal of Immunology published online 26 August 2009 from submission to initial decision 4 weeks from acceptance to publication J Immunol http://www.jimmunol.org/content/early/2009/08/26/jimmuno l.0901411 Temporal Induction Pattern of STAT4 Target Genes Defines Potential for Th1 Lineage-Specific Programming Seth R. Good, Vivian T. Thieu, Anubhav N. Mathur, Qing Yu, Gretta L. Stritesky, Norman Yeh, John T. O'Malley, Narayanan B. Perumal and Mark H. Kaplan Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/suppl/2009/08/26/jimmunol.090141 1.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 1, 2021. Published August 26, 2009, doi:10.4049/jimmunol.0901411 The Journal of Immunology Temporal Induction Pattern of STAT4 Target Genes Defines Potential for Th1 Lineage-Specific Programming1 Seth R. Good,2* Vivian T. Thieu,2† Anubhav N. Mathur,† Qing Yu,† Gretta L.