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Chromosome pairing

Gunjan Mehta, Guhan Kaliyaperumal Anbalagan, Akhilendra Pratap Bharati, Purna Gadre, Santanu Kumar Ghosh
Meiosis is a specialized cell division process by which haploid gametes are produced from a diploid mother cell. Reductional chromosome segregation during meiosis I (MI) is achieved by two unique and conserved events: centromeric cohesin protection (CCP) and sister kinetochore mono-orientation (SKM). In Saccharomyces cerevisiae, a meiosis-specific protein Spo13 plays a role in both these centromere-specific events. Despite genome-wide association of Spo13, we failed to detect its function in global processes such as cohesin loading, cohesion establishment and homologs pairing...
April 11, 2018: Current Genetics
Yuichi Ichiakwa, Paul D Kaufman
Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations...
March 20, 2018: Bio-protocol
Polliana Silva Rodrigues, Margarete Magalhães Souza, Cláusio Antônio Ferreira Melo, Telma Nair Santana Pereira, Ronan Xavier Corrêa
BACKGROUND: The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within this subfamily; together with these species' phenotypic plasticity and the similarities in their morphological descriptors, make this a complex group for taxonomic and phylogenetic studies. The objective of the present work was to evaluate the karyotypic diversity and the 2C DNA content variation in 10 species of the Caesalpinia group, representing six genera: Paubrasilia, Caesalpinia, Cenostigma, Poincianella, Erythrostemon and Libidibia...
April 11, 2018: BMC Genetics
Mihai Ciubotaru, Mihaela Georgiana Musat, Marius Surleac, Elena Ionita, Andrei Jose Petrescu, Edgars Abele, Ramona Abele
Currently used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes, changes these viral enzymes which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations...
April 5, 2018: Current Medicinal Chemistry
Karolina Pesz, Victor Murcia Pieńkowski, Agnieszka Pollak, Piotr Gasperowicz, Maciej Sykulski, Joanna Kosińska, Magdalena Kiszko, Bogusława Krzykwa, Magdalena Bartnik-Głaska, Beata Nowakowska, Małgorzata Rydzanicz, Maria Małgorzata Sasiadek, Rafał Płoski
Mapping of de novo balanced chromosomal translocations (BCTs) in patients with sporadic poorly characterized disease(s) is an unbiased method of finding candidate gene(s) responsible for the observed symptoms. We present a paediatric patient suffering from epilepsy, developmental delay (DD) and atrial septal defect IIº (ASD) requiring surgery. Karyotyping indicated an apparently balanced de novo reciprocal translocation 46,XX,t(3;4)(p25.3;q31.1), whereas aCGH did not reveal any copy number changes. Using shallow mate-pair whole genome sequencing and direct Sanger sequencing of breakpoint regions we found that translocation disrupted SLC6A1 and NAA15 genes...
April 2, 2018: European Journal of Medical Genetics
Yongwook Choi, Agnes P Chan, Ewen Kirkness, Amalio Telenti, Nicholas J Schork
Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not 'phase' the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available 'Genome-In-A-Bottle' (GIAB) phased version of the NA12878 genome as a gold standard...
April 5, 2018: PLoS Genetics
Valeriya Gaysinskaya, Brendan F Miller, Chiara De Luca, Godfried W van der Heijden, Kasper D Hansen, Alex Bortvin
BACKGROUND: Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair and recombine. Extensive changes in chromatin in MPI raise an important question concerning the contribution of epigenetic mechanisms such as DNA methylation to meiosis. Interestingly, previous studies concluded that in male mice, genome-wide DNA methylation patters are set in place prior to meiosis and remain constant subsequently...
April 4, 2018: Epigenetics & Chromatin
Vasileios Panagiotis E Lenis, Martin Swain, Denis M Larkin
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses...
April 3, 2018: GigaScience
Bin Zhu, Yang Xiang, Pan Zeng, Bowei Cai, Xiaolong Huang, Xianhong Ge, Qingbei Weng, Zaiyun Li
Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization...
2018: Frontiers in Plant Science
Toshihiro Mita, Francis Hombhanje, Nobuyuki Takahashi, Makoto Sekihara, Masato Yamauchi, Takahiro Tsukahara, Akira Kaneko, Hiroyoshi Endo, Jun Ohashi
The ability of the human malarial parasite Plasmodium falciparum to adapt to environmental changes depends considerably on its ability to maintain within-population genetic variation. Strong selection, consequent to widespread antimalarial drug usage, occasionally elicits a rapid expansion of drug-resistant isolates, which can act as founders. To investigate whether this phenomenon induces a loss of within-population genetic variation, we performed a population genetic analysis on 302 P. falciparum cases detected during two cross-sectional surveys in 2002/2003, just after the official introduction of sulphadoxine/pyrimethamine as a first-line treatment, and again in 2010/2011, in highly endemic areas in Papua New Guinea...
April 3, 2018: Scientific Reports
Hiroyuki Yoshikawa, Dongdong Xu, Yasuko Ino, Tasuku Yoshino, Takao Hayashida, Junije Wang, Ryosuke Yazawa, Goro Yoshizaki, Yutaka Takeuchi
Sterility in hybrid animals is widely known to be due to a cytological mechanism of aberrant homologous chromosome pairing during meiosis in hybrid germ cells. In this study, the gametes of four marine fish species belonging to Sciaenid were artificially fertilized, and germ cell development was examined at the cellular and molecular levels. One of the intergeneric hybrids had gonads that were testis-like in structure, small in size, and lacked germ cells. Specification of primordial germ cells (PGCs) and their migration towards genital ridges were normally occurred in hybrid embryos, but these PGCs did not proliferate in the hybrid gonads...
April 2, 2018: Genetics
Benjamin L S Furman, Ben J Evans
There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy...
March 1, 2018: Genome Biology and Evolution
Erlyana K Clarke, Katherine A Rivera Gomez, Zaki Mustachi, Mikaela C Murph, Mara Schvarzstein
Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C...
March 15, 2018: Journal of Visualized Experiments: JoVE
Bomyi Lim, Tyler Heist, Michael Levine, Takashi Fukaya
How remote enhancers interact with appropriate target genes persists as a central mystery in gene regulation. Here, we exploit the properties of transvection to explore enhancer-promoter communication between homologous chromosomes in living Drosophila embryos. We successfully visualized the activation of an MS2-tagged reporter gene by a defined developmental enhancer located in trans on the other homolog. This trans-homolog activation depends on insulator DNAs, which increase the stability-but not the frequency-of homolog pairing...
March 23, 2018: Molecular Cell
Dong-Mei Fu, Yu-Lin Zhou, Jing Zhao, Ping Hu, Zheng-Feng Xu, Shi-Ming Lv, Jun-Jie Hu, Zhong-Min Xia, Qi-Wei Guo
Klinefelter syndrome (KS) is the set of symptoms that result from the presence of an extra X chromosome in males. Postnatal population-based KS screening will enable timely diagnosis of this common chromosomal disease, providing the opportunity for early intervention and therapy at the time point when they are most effective and may prevent later symptoms or complications. Therefore, through this study, we introduced a simple high-resolution melting (HRM) assay for KS screening and evaluated its clinical sensitivity and specificity in three medical centers using 1373 clinical blood samples...
March 30, 2018: Asian Journal of Andrology
Hongtao Song, Kui Lin, Jinglu Hu, Erli Pang
Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes...
2018: Frontiers in Plant Science
L Leggio, F Guarino, A Magrì, R Accardi-Gheit, S Reina, V Specchia, F Damiano, M F Tomasello, M Tommasino, A Messina
The eukaryotic porin, also called the Voltage Dependent Anion-selective Channel (VDAC), is the main pore-forming protein of the outer mitochondrial membrane. In Drosophila melanogaster, a cluster of genes evolutionarily linked to VDAC is present on chromosome 2L. The main VDAC isoform, called VDAC1 (Porin1), is expressed from the first gene of the cluster. The porin1 gene produces two splice variants, 1A-VDAC and 1B-VDAC, with the same coding sequence but different 5' untranslated regions (UTRs). Here, we studied the influence of the two 5' UTRs, 1A-5' UTR and 1B-5' UTR, on transcription and translation of VDAC1 mRNAs...
March 28, 2018: Scientific Reports
Abolfazl Hashemi, Banghua Zhu, Haris Vikalo
BACKGROUND: Haplotype assembly is the task of reconstructing haplotypes of an individual from a mixture of sequenced chromosome fragments. Haplotype information enables studies of the effects of genetic variations on an organism's phenotype. Most of the mathematical formulations of haplotype assembly are known to be NP-hard and haplotype assembly becomes even more challenging as the sequencing technology advances and the length of the paired-end reads and inserts increases. Assembly of haplotypes polyploid organisms is considerably more difficult than in the case of diploids...
March 21, 2018: BMC Genomics
Luke M Evans, Rasool Tahmasbi, Matt Jones, Scott I Vrieze, Gonçalo R Abecasis, Sayantan Das, Douglas W Bjelland, Teresa R de Candia, Jian Yang, Michael E Goddard, Peter M Visscher, Matthew C Keller
Heritability is a fundamental parameter in genetics. Traditional estimates based on family or twin studies can be biased due to shared environmental or non-additive genetic variance. Alternatively, those based on genotyped or imputed variants typically underestimate narrow-sense heritability contributed by rare or otherwise poorly tagged causal variants. Identical-by-descent (IBD) segments of the genome share all variants between pairs of chromosomes except new mutations that have arisen since the last common ancestor...
March 28, 2018: Heredity
Patrick K Gonzales, Christine M Roberts, Virginia Fonte, Connor Jacobsen, Gretchen H Stein, Christopher D Link
Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones...
2018: PloS One
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