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Homologous chromosome pairing

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https://www.readbyqxmd.com/read/28646875/genome-analysis-of-diploscapter-coronatus-insights-into-molecular-peculiarities-of-a-nematode-with-parthenogenetic-reproduction
#1
Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
BACKGROUND: Sexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis. RESULTS: We obtained a 170 Mbp draft genome in only 511 scaffolds with a N50 length of 1 Mbp...
June 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28642366/saccharomyces-cerevisiae-red1-protein-exhibits-nonhomologous-dna-end-joining-activity-and-potentiates-hop1-promoted-pairing-of-double-stranded-dna
#2
Rucha Kshirsagar, Indrajeet Ghodke, Kalappa Muniyappa
Elucidation of the function of synaptonemal complex (SC) in <Saccharomyces cerevisiae> has mainly focused on in vivo analysis of recombination-defective meiotic mutants. Consequently, significant gaps remain in the mechanistic understanding of the activities of different SC proteins and the functional relationships among them. S. cerevisiae Hop1 and Red1 are essential structural components of the SC axial/lateral elements. Previous studies have demonstrated that Hop1 is a structure-specific DNA-binding protein that exhibits high affinity for the Holliday junction, promotes DNA bridging, condensation and pairing between duplex DNA molecules...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28640973/production-of-red-flowered-oilseed-rape-via-the-ectopic-expression-of-orychophragmus-violaceus-ovpap2
#3
Wenqin Fu, Daozong Chen, Qi Pan, Fengfeng Li, Zhigang Zhao, Xianhong Ge, Zaiyun Li
Oilseed rape (Brassica napus L.), which has yellow flowers, is both an important oil crop and a traditional tourism resource in China, whereas the Orychophragmus violaceus, which has purple flowers, likely possesses a candidate gene or genes to alter the flower color of oilseed rape. A previously established B. napus line has a particular pair of O. violaceus chromosomes (M4) and exhibits slightly red petals. In this study, the transcriptomic analysis of M4, B. napus (H3), and O. violaceus with purple petals (OvP) and with white petals (OvW) revealed that most anthocyanin biosynthesis genes were up-regulated in both M4 and OvP...
June 22, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28630130/how-a-genetically-stable-extremophile-evolves-modes-of-genome-diversification-in-the-archaeon-sulfolobus-acidocaldarius
#4
Dominic Mao, Dennis W Grogan
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 x 10(-6), which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28627638/meiotic-defects-and-decreased-expression-of-genes-located-around-the-chromosomal-breakpoint-in-the-testis-of-a-patient-with-a-novel-46-x-t-y-1-p11-3-p31-translocation
#5
Guangyuan Li, Furhan Iqbal, Liu Wang, Zhipeng Xu, Xiaoyan Che, Wen Yu, Liang Shi, Tonghang Guo, Guixiang Zhou, Xiaohua Jiang, Huan Zhang, Yuanwei Zhang, Dexin Yu
Balanced translocations are known to be associated with infertility, spontaneous abortions and birth defects in mammals. Spermatocyte spreading and immunostaining were applied to detect meiotic prophase I progression, homologous chromosome pairing, synapsis and recombination in an azoospermic reciprocal translocation 46,X,t(Y;1)(p11.3;p31) carrier. Histological examination of testicular sections revealed a severely reduced number of germ cells with no spermatids or sperm in the carrier. A significant reduction in XY recombination was observed in the patient...
June 14, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28623274/reduction-in-chromosome-mobility-accompanies-nuclear-organization-during-early-embryogenesis-in-caenorhabditis-elegans
#6
Ritsuko Arai, Takeshi Sugawara, Yuko Sato, Yohei Minakuchi, Atsushi Toyoda, Kentaro Nabeshima, Hiroshi Kimura, Akatsuki Kimura
In differentiated cells, chromosomes are packed inside the cell nucleus in an organised fashion. In contrast, little is known about how chromosomes are packed in undifferentiated cells and how nuclear organization changes during development. To assess changes in nuclear organization during the earliest stages of development, we quantified the mobility of a pair of homologous chromosomal loci in the interphase nuclei of Caenorhabditis elegans embryos. The distribution of distances between homologous loci was consistent with a random distribution up to the 8-cell stage but not at later stages...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28602622/homoeologous-chromosome-pairing-across-the-eukaryote-phylogeny
#7
REVIEW
Amanda L Grusz, Erin M Sigel, Colby Witherup
During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28591177/identification-and-characterization-of-constans-like-col-gene-family-in-upland-cotton-gossypium-hirsutum-l
#8
Darun Cai, Hui Liu, Na Sang, Xianzhong Huang
The CONSTANS/FLOWERING LOCUS T (CO/FT) regulon plays a central role in the control of flowering time in photoperiod-sensitive plants. Flowering time in wild cotton (Gossypium spp.) has strict photoperiod sensitivity, but domesticated cotton is day-neutral. Information on the molecular characterization of the CO and CO-like (COL) genes in cotton is very limited. In this study, we identified 42 COL homologs (GhCOLs) in the G. hirsutum genome, and many of them were previously unreported. We studied their chromosome distribution, phylogenetic relationships, and structures of genes and proteins...
2017: PloS One
https://www.readbyqxmd.com/read/28590593/the-proteasome-enters-the-meiotic-prophase-fray
#9
REVIEW
Aleksandar Vujin, Monique Zetka
The segregation of homologous chromosomes in meiosis depends on their ability to locate one another in the nucleus and establish a physical association through crossing over. A tightly regulated number of crossovers (COs) emerges following repair of induced DNA double-strand breaks by homologous recombination (HR), but the process of how HR intermediates transition into COs is still poorly understood. Two recent studies by Ahuja et al. and Rao et al. have revealed a role for chromosomally localized proteasomes in choreographing both homologous chromosome pairing and the evolution of HR intermediates into segregation-competent COs...
June 7, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28588601/in-favor-of-establishment-regulation-of-chromatid-cohesion-in-plants
#10
REVIEW
Pablo Bolaños-Villegas, Kuntal De, Mónica Pradillo, Desheng Liu, Christopher A Makaroff
In eukaryotic organisms, the correct regulation of sister chromatid cohesion, whereby sister chromatids are paired and held together, is essential for accurate segregation of the sister chromatids and homologous chromosomes into daughter cells during mitosis and meiosis, respectively. Sister chromatid cohesion requires a cohesin complex comprised of structural maintenance of chromosome adenosine triphosphatases and accessory proteins that regulate the association of the complex with chromosomes or that are involved in the establishment or release of cohesion...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28559338/superresolution-microscopy-reveals-the-three-dimensional-organization-of-meiotic-chromosome-axes-in-intact-caenorhabditis-elegans-tissue
#11
Simone Köhler, Michal Wojcik, Ke Xu, Abby F Dernburg
When cells enter meiosis, their chromosomes reorganize as linear arrays of chromatin loops anchored to a central axis. Meiotic chromosome axes form a platform for the assembly of the synaptonemal complex (SC) and play central roles in other meiotic processes, including homologous pairing, recombination, and chromosome segregation. However, little is known about the 3D organization of components within the axes, which include cohesin complexes and additional meiosis-specific proteins. Here, we investigate the molecular organization of meiotic chromosome axes in Caenorhabditis elegans through STORM (stochastic optical reconstruction microscopy) and PALM (photo-activated localization microscopy) superresolution imaging of intact germ-line tissue...
May 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28548965/inhibition-of-colorectal-cancer-genomic-copy-number-alterations-and-chromosomal-fragile-site-tumor-suppressor-fhit-and-wwox-deletions-by-dna-mismatch-repair
#12
Sohail Jahid, Jian Sun, Ozkan Gelincik, Pedro Blecua, Winfried Edelmann, Raju Kucherlapati, Kathy Zhou, Maria Jasin, Zeynep H Gümüş, Steven M Lipkin
Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537556/the-dynamic-three-dimensional-organization-of-the-diploid-yeast-genome
#13
Seungsoo Kim, Ivan Liachko, Donna G Brickner, Kate Cook, William S Noble, Jason H Brickner, Jay Shendure, Maitreya J Dunham
The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. However, even in this well-studied model, it is unclear how homolog pairing in diploids or environmental conditions influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation using a polymer model, we observe significant homolog proximity that increases in saturated culture conditions...
May 24, 2017: ELife
https://www.readbyqxmd.com/read/28501862/chromosome-painting-in-trogon-s-surrucura-aves-trogoniformes-reveals-a-karyotype-derived-by-chromosomal-fissions-fusions-and-inversions
#14
Tiago M Degrandi, Analía Del Valle Garnero, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Rafael Kretschmer, Edivaldo H C de Oliveira, Ricardo J Gunski
Trogons are forest birds with a wide distribution, being found in Africa, Asia, and America, and are included in the order Trogoniformes, family Trogonidae. Phylogenetic studies using molecular data have not been able to determine the phylogenetic relationship among the different genera of trogons. So far, no cytogenetic data for these birds exist. Hence, the aim of this study was to characterize the karyotype of Trogon surrucura surrucura by means of classical and molecular cytogenetics. We found a diploid chromosome number of 2n = 82, similar to most birds, with several derived features compared to chicken and the putative ancestral avian karyotype...
May 13, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28493118/position-matters-multiple-functions-of-linc-dependent-chromosome-positioning-during-meiosis
#15
Kazuhiro Katsumata, Eriko Nishi, Sadia Afrin, Kaoru Narusawa, Ayumu Yamamoto
Chromosome positioning is crucial for multiple chromosomal events, including DNA replication, repair, and recombination. The linker of nucleoskeleton and cytoskeleton (LINC) complexes, which consist of conserved nuclear membrane proteins, were shown to control chromosome positioning and facilitate various biological processes by interacting with the cytoskeleton. However, the precise functions and regulation of LINC-dependent chromosome positioning are not fully understood. During meiosis, the LINC complexes induce clustering of telomeres, forming the bouquet chromosome arrangement, which promotes homologous chromosome pairing...
May 10, 2017: Current Genetics
https://www.readbyqxmd.com/read/28455351/the-nucleoporin-nup2-contains-a-meiotic-autonomous-region-that-promotes-the-dynamic-chromosome-events-of-meiosis
#16
Daniel B Chu, Tatiana Gromova, Trent A C Newman, Sean M Burgess
Meiosis is a specialized cellular program required to create haploid gametes from diploid parent cells. Homologous chromosomes pair, synapse, and recombine in a dynamic environment that accommodates gross chromosome reorganization and significant chromosome motion, which are critical for normal chromosome segregation. In Saccharomyces cerevisiae, Ndj1 is a meiotic telomere-associated protein required for physically attaching telomeres to proteins embedded in the nuclear envelope. In this study, we identified additional proteins that act at the nuclear periphery from meiotic cell extracts, including Nup2, a nonessential nucleoporin with a known role in tethering interstitial chromosomal loci to the nuclear pore complex...
April 28, 2017: Genetics
https://www.readbyqxmd.com/read/28420610/the-diversity-of-dna-fragment-editing-by-crispr-cas9-in-highly-homologous-or-repetitive-sequences
#17
Wang Leyang, Huang Haiyan, Wu Qiang
In complex genomes, there are a large number of duplicated genes in the coding regions and many more repetitive sequences in the non-coding regions. Repetitive sequences can exert great impacts on the heredity and evolution of the organisms, as well as their genome 3D architecture and transcriptional regulation. The high homology nature of repetitive sequences renders their editing by CRISPR/Cas9 very complex. At diploid or polyploid situations, such repetitive sequences could be edited differently on each chromosome or chromatid...
April 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28413152/loss-of-pten-expression-is-associated-with-high-microrna-24-level-and-poor-prognosis-in-patients-with-tongue-squamous-cell-carcinoma
#18
Jingzhu Zhao, Jiadong Chi, Ming Gao, Jingtai Zhi, Yigong Li, Xiangqian Zheng
PURPOSE: The aim of this study was to detect the relationship between phosphatase and tensin homolog deletion on chromosome 10 (PTEN) and microRNA 24 (miR-24) and correlate PTEN expression with important clinical parameters of patients with tongue squamous cell carcinoma (TSCC). MATERIALS AND METHODS: In this retrospective case series, all TSCC patients treated at Tianjin Medical University Cancer Institute and Hospital between March 2005 and October 2011 were retrospectively reviewed...
March 23, 2017: Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/28396582/a-pair-of-maternal-chromosomes-derived-from-meiotic-nondisjunction-in-trisomy-21-affects-nuclear-architecture-and-transcriptional-regulation
#19
Sayaka Omori, Hideyuki Tanabe, Kimihiko Banno, Ayumi Tsuji, Nobutoshi Nawa, Katsuya Hirata, Keiji Kawatani, Chikara Kokubu, Junji Takeda, Hidetoshi Taniguchi, Hitomi Arahori, Kazuko Wada, Yasuji Kitabatake, Keiichi Ozono
Eukaryotic genomes are organised into complex higher-order structures within the nucleus, and the three-dimensional arrangement of chromosomes is functionally important for global gene regulation. The existence of supernumerary chromosome 21 in Down syndrome may perturb the nuclear architecture at different levels, which is normally optimised to maintain the physiological balance of gene expression. However, it has not been clearly elucidated whether and how aberrant configuration of chromosomes affects gene activities...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28380054/meioc-maintains-an-extended-meiotic-prophase-i-in-mice
#20
Y Q Shirleen Soh, Maria M Mikedis, Mina Kojima, Alexander K Godfrey, Dirk G de Rooij, David C Page
The meiosis-specific chromosomal events of homolog pairing, synapsis, and recombination occur over an extended meiotic prophase I that is many times longer than prophase of mitosis. Here we show that, in mice, maintenance of an extended meiotic prophase I requires the gene Meioc, a germ-cell specific factor conserved in most metazoans. In mice, Meioc is expressed in male and female germ cells upon initiation of and throughout meiotic prophase I. Mouse germ cells lacking Meioc initiate meiosis: they undergo pre-meiotic DNA replication, they express proteins involved in synapsis and recombination, and a subset of cells progress as far as the zygotene stage of prophase I...
April 2017: PLoS Genetics
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