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https://www.readbyqxmd.com/read/28644379/physical-forces-may-cause-the-hoxd-gene-cluster-elongation
#1
Spyros Papageorgiou
Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains...
June 23, 2017: Biology
https://www.readbyqxmd.com/read/28642500/genome-wide-mapping-of-dnase-i-hypersensitive-sites-reveals-chromatin-accessibility-changes-in-arabidopsis-euchromatin-and-heterochromatin-regions-under-extended-darkness
#2
Yue Liu, Wenli Zhang, Kang Zhang, Qi You, Hengyu Yan, Yuannian Jiao, Jiming Jiang, Wenying Xu, Zhen Su
Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642229/evolutionary-dynamics-of-the-kinetochore-network-in-eukaryotes-as-revealed-by-comparative-genomics
#3
Jolien Je van Hooff, Eelco Tromer, Leny M van Wijk, Berend Snel, Geert Jpl Kops
During eukaryotic cell division, the sister chromatids of duplicated chromosomes are pulled apart by microtubules, which connect via kinetochores. The kinetochore is a multiprotein structure that links centromeres to microtubules, and that emits molecular signals in order to safeguard the equal distribution of duplicated chromosomes over daughter cells. Although microtubule-mediated chromosome segregation is evolutionary conserved, kinetochore compositions seem to have diverged. To systematically inventory kinetochore diversity and to reconstruct its evolution, we determined orthologs of 70 kinetochore proteins in 90 phylogenetically diverse eukaryotes...
June 22, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28637491/stable-centromere-positioning-in-diverse-sequence-contexts-of-complex-and-satellite-centromeres-of-maize-and-wild-relatives
#4
Jonathan I Gent, Na Wang, R Kelly Dawe
BACKGROUND: Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3)...
June 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28637346/an-ion-beam-induced-arabidopsis-mutant-with-marked-chromosomal-rearrangement
#5
Ayako N Sakamoto, Vo Thi Thuong Lan, Satoru Fujimoto, Sachihiro Matsunaga, Atsushi Tanaka
Ion beams have been used as an effective tool in mutation breeding for the creation of crops with novel characteristics. Recent analyses have revealed that ion beams induce large chromosomal alterations, in addition to small mutations comprising base changes or frameshifts. In an effort to understand the potential capability of ion beams, we analyzed an Arabidopsis mutant possessing an abnormal genetic trait. The Arabidopsis mutant uvh3-2 is hypersensitive to UVB radiation when photoreactivation is unavailable...
June 15, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/28634123/clinical-utility-of-chromosomal-aneusomy-in-individuals-at-high-risk-of-lung-cancer
#6
Anna E Barón, Severine Kako, William J Feser, Heather Malinowski, Daniel Merrick, Kavita Garg, Stephen Malkoski, Shannon Pretzel, Jill M Siegfried, Wilbur A Franklin, York Miller, Holly J Wolf, Marileila Varella-Garcia
INTRODUCTION: Low dose CT screening for lung cancer has a high false positive rate with frequent discovery of indeterminate pulmonary nodules. Noninvasive biomarkers are needed to reduce false positives and improve risk stratification. A retrospective longitudinal evaluation was performed to assess chromosomal aneusomy in sputum via fluorescence in situ hybridization (CA-FISH) in four nested case-control studies. METHODS: ROC analysis resulted in two grouped cohorts: High Risk (CO High Risk and CO Nodule; 68 Cases, 69 controls) and Screening (ACRIN/NLST and PLuSS; 97 Cases, 185 controls)...
June 17, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28630649/a-complete-duplication-of-x-chromosome-resulting-in-a-tricentric-isochromosome-originated-by-centromere-repositioning
#7
N Villa, D Conconi, D Gambel Benussi, G Tornese, F Crosti, E Sala, L Dalprà, V Pecile
BACKGROUND: Neocentromeres are rare and considered chromosomal aberrations, because a non-centromeric region evolves in an active centromere by mutation. The literature reported several structural anomalies of X chromosome and they influence the female reproductive capacity or are associated to Turner syndrome in the presence of monosomy X cell line. CASE PRESENTATION: We report a case of chromosome X complex rearrangement found in a prenatal diagnosis. The fetal karyotype showed a mosaicism with a 45,X cell line and a 46 chromosomes second line with a big marker, instead of a sex chromosome...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28630129/the-polar-organizing-protein-popz-is-required-for-chromosome-segregation-in-agrobacterium-tumefaciens
#8
Haley M Ehrle, Jacob T Guidry, Rebecca Iacovetto, Anne K Salisbury, D J Sandidge, Grant Bowman
Despite being perceived as relatively simple organisms, many bacteria exhibit an impressive degree of sub-cellular organization. In Caulobacter crescentus, the evolutionarily conserved polar organizing protein PopZ facilitates cytoplasmic organization by recruiting chromosome centromeres and regulatory proteins to the cell poles. Here, we characterize the localization and function of PopZ in Agrobacterium tumefaciens, a genetically related species with distinct anatomy. In this species, we find that PopZ molecules are relocated from the old pole to the new pole in the minutes following cell division...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28616571/a-time-out-for-cenp-a
#9
S Hoffmann, D Fachinetti
Proper chromosome segregation relies on a functional centromere-kinetochore interface. We showed that chromatin containing CENtromere Protein A (CENP-A) is essential for centromere assembly, but dispensable for chromosome segregation in the presence of CENP-B-bound DNA sequences. This demonstrates the existence of two contact points between the DNA and the kinetochore to mediate successful chromosome segregation.
2017: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/28616075/proximity-ligation-scaffolding-and-comparison-of-two-trichoderma-reesei-strains-genomes
#10
Etienne Jourdier, Lyam Baudry, Dante Poggi-Parodi, Yoan Vicq, Romain Koszul, Antoine Margeot, Martial Marbouty, Frédérique Bidard
BACKGROUND: The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, regarding for instance the evolution of entire clades, the analysis of chromosome rearrangements, and is pivotal to sexual crossing studies. In non-conventional but industrially relevant model organisms, such as the ascomycete Trichoderma reesei, a complete genome assembly is seldom available...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28607452/transmission-of-induced-chromosomal-aberrations-through-successive-mitotic-divisions-in-human-lymphocytes-after-in-vitro-and-%C3%AF-in%C3%AF-vivo-radiation
#11
Akram Kaddour, Bruno Colicchio, Diane Buron, Elie El Maalouf, Eric Laplagne, Claire Borie, Michelle Ricoul, Aude Lenain, William M Hempel, Luc Morat, Mustafa Al Jawhari, Corina Cuceu, Leonhard Heidingsfelder, Eric Jeandidier, Georges Deschênes, Alain Dieterlen, Michèle El May, Theodore Girinsky, Annelise Bennaceur-Griscelli, Patrice Carde, Laure Sabatier, Radhia M'kacher
The mechanisms behind the transmission of chromosomal aberrations (CA) remain unclear, despite a large body of work and major technological advances in chromosome identification. We reevaluated the transmission of CA to second- and third-division cells by telomere and centromere (TC) staining followed by M-FISH. We scored CA in lymphocytes of healthy donors after in vitro irradiation and those of cancer patients treated by radiation therapy more than 12 years before. Our data demonstrate, for the first time, that dicentric chromosomes (DCs) decreased by approximately 50% per division...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606917/quantitative-temporal-viromics-of-an-inducible-hiv-1-model-yields-insight-to-global-host-targets-and-phospho-dynamics-associated-with-vpr
#12
John D Lapek, Mary K Lewinski, Jacob M Wozniak, John Guatelli, David J Gonzalez
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist...
June 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28605751/improved-maize-reference-genome-with-single-molecule-technologies
#13
Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael S Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael R May, Nathan M Springer, Eric Antoniou, W Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping...
June 12, 2017: Nature
https://www.readbyqxmd.com/read/28605141/anti-ena-antibody-profiles-in-patients-with-hepatitis-c-virus-infection
#14
Christine M Litwin, Angela R Rourk
BACKGROUND: The presence of antinuclear antibodies (ANA) has been described following hepatitis C virus (HCV). Very few studies have investigated the presence of anti-extractable nuclear antigens (ENA) in HCV infection. METHODS: The aim of this study was to assess the prevalence of ENA antibodies in 100 patients with HCV infection compared to the prevalence of ENA antibodies in 100 healthy control patients. Sera from patients were tested for ENA using a multiplex microbead immunoassay...
June 12, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28603453/centromeric-non-coding-transcription-opening-the-black-box-of-chromosomal-instability
#15
REVIEW
Rodrigo Cáceres-Gutiérrez, Luis A Herrera
In eukaryotes, mitosis is tightly regulated to avoid the generation of numerical chromosome aberrations, or aneuploidies. The aneuploid phenotype is a consequence of chromosomal instability (CIN), i.e., an enhanced rate of chromosome segregation errors, which is frequently found in cancer cells and is associated with tumor aggressiveness and increased tumor cell survival potential. To avoid the generation of aneuploidies, cells rely on the spindle assembly checkpoint (SAC), a widely conserved mechanism that protects the genome against this type of error...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28600324/reconstitution-of-the-oocyte-nucleolus-in-mice-by-a-single-nucleolar-protein-npm2
#16
Sugako Ogushi, Kazuo Yamagata, Chikashi Obuse, Keiko Furuta, Teruhiko Wakayama, Martin M Matzuk, Mitinori Saitou
The mammalian oocyte nucleolus, the most prominent subcellular organelle in the oocyte, is vital in early development, yet its key functions and constituents remain unclear. We show here that the parthenotes/zygotes derived from enucleolated oocytes exhibited abnormal heterochromatin formation around parental peri-centromeric DNAs, which led to a significant mitotic delay and frequent chromosome mis-segregation upon the first mitotic division. A proteomic analysis identified NPM2 as a dominant component of the oocyte nucleolus...
June 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28600058/prenatal-diagnosis-and-molecular-cytogenetic-characterization-of-mosaicism-for-a-small-supernumerary-marker-chromosome-derived-from-chromosome-11
#17
Chih-Ping Chen, Ming Chen, Pu-Tsui Wang, Schu-Rern Chern, Shin-Wen Chen, Shih-Ting Lai, Peih-Shan Wu, Shun-Ping Chang, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome (sSMC) derived from chromosome 11. CASE REPORT: A 37-year-old, gravida 3, para 2, woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XX,+mar[18]/46,XX[4]. The parental karyotypes were normal. Level II ultrasound findings were unremarkable. Array comparative genomic hybridization (aCGH) on the DNA extracted from cultured amniocytes revealed no genomic imbalance...
June 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28598821/overexpression-of-centromere-protein-k-cenp-k-gene-in-hepatocellular-carcinoma-promote-cell-proliferation-by-activating-akt-tp53-signal-pathway
#18
Haiyan Wang, Weilong Liu, Lei Liu, Chi Wu, Weigang Wu, Juan Zheng, Mingxia Zhang, Xinchun Chen, Boping Zhou, Zhiliang Gao, Jian Huang
Hepatocellular carcinoma (HCC) is one of the high-incidence malignant tumors with very poor prognosis. Identification of potential oncogenes is critical to discovering novel therapeutic targets for many cancers, including HCC. In our previous studies, using microarray technology, we conformed that CENP-K was overexpressed in HCCs. However, whether the overexpression of CENP-K contributes to hepatocarcinogenesis remains unclear. In this study, we found that CENP-K was significantly up-regulated in 60% (63 of 105) of HCC specimens at the mRNA level compared to adjacent non-cancerous liver specimens, as determined by RT-qPCR...
May 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28598437/centromeres-are-maintained-by-fastening-cenp-a-to-dna-and-directing-an-arginine-anchor-dependent-nucleosome-transition
#19
Lucie Y Guo, Praveen Kumar Allu, Levani Zandarashvili, Kara L McKinley, Nikolina Sekulic, Jennine M Dawicki-McKenna, Daniele Fachinetti, Glennis A Logsdon, Ryan M Jamiolkowski, Don W Cleveland, Iain M Cheeseman, Ben E Black
Maintaining centromere identity relies upon the persistence of the epigenetic mark provided by the histone H3 variant, centromere protein A (CENP-A), but the molecular mechanisms that underlie its remarkable stability remain unclear. Here, we define the contributions of each of the three candidate CENP-A nucleosome-binding domains (two on CENP-C and one on CENP-N) to CENP-A stability using gene replacement and rapid protein degradation. Surprisingly, the most conserved domain, the CENP-C motif, is dispensable...
June 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28598241/critical-histone-post-translational-modifications-for-centromere-function-and-propagation
#20
Tatsuo Fukagawa
The centromere is a critical genomic region that enables faithful chromosome segregation during mitosis, and must be distinguishable from other genomic regions to facilitate establishment of the kinetochore. The centromere-specific histone H3-variant CENP-A forms a special nucleosome that functions as a marker for centromere specification. In addition to the CENP-A nucleosomes, there are additional H3 nucleosomes that have been identified in centromeres, both of which are predicted to exhibit specific features...
June 9, 2017: Cell Cycle
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