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https://www.readbyqxmd.com/read/29321672/phenotypic-interpretation-of-complex-chromosomal-rearrangements-informed-by-nucleotide-level-resolution-and-structural-organization-of-chromatin
#1
Cinthya J Zepeda-Mendoza, Alexandra Bardon, Tammy Kammin, David J Harris, Helen Cox, Claire Redin, Zehra Ordulu, Michael E Talkowski, Cynthia C Morton
Molecular characterization of balanced chromosomal abnormalities constitutes a powerful tool in understanding the pathogenic mechanisms of complex genetic disorders. Here we report a male with severe global developmental delay in the presence of a complex karyotype and normal microarray and exome studies. The subject, referred to as DGAP294, has two de novo apparently balanced translocations involving chromosomes 1 and 14, and chromosomes 4 and 10, disrupting several different transcripts of adhesion G protein-coupled receptor L2 (ADGRL2) and protocadherin 15 (PCDH15)...
January 10, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29305858/identification-of-a-candidate-enhancer-for-dmrt3-involved-in-spastic-cerebral-palsy-pathogenesis
#2
Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama
Cerebral palsy (CP) is a major neuronal disease and the most common movement disorder in children. Although environmental factors leading to CP have been greatly investigated, the genetic mechanism underlying CP is not well understood. Here we focused on two clinical reports that characterized a deletion involving the KANK1 gene locus in the 9p24.3 region. One report shows spastic CP and the other shows no spastic CP phenotype. Based on the epigenetic status and evolutionary conservation, we first found a functional genomic element at the noncoding region that was deleted only in patients with spastic CP...
January 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29301233/analyses-of-tissue-culture-adaptation-of-human-herpesvirus-6a-by-whole-genome-deep-sequencing-redefines-the-reference-sequence-and-identifies-virus-entry-complex-changes
#3
Joshua G Tweedy, Eric Escriva, Maya Topf, Ursula A Gompels
Tissue-culture adaptation of viruses can modulate infection. Laboratory passage and bacterial artificial chromosome (BAC)mid cloning of human cytomegalovirus, HCMV, resulted in genomic deletions and rearrangements altering genes encoding the virus entry complex, which affected cellular tropism, virulence, and vaccine development. Here, we analyse these effects on the reference genome for related betaherpesviruses, Roseolovirus, human herpesvirus 6A (HHV-6A) strain U1102. This virus is also naturally "cloned" by germline subtelomeric chromosomal-integration in approximately 1% of human populations, and accurate references are key to understanding pathological relationships between exogenous and endogenous virus...
December 31, 2017: Viruses
https://www.readbyqxmd.com/read/29290434/genome-wide-association-study-of-conformation-and-milk-yield-in-mixed-breed-dairy-goats
#4
Sebastian Mucha, Raphael Mrode, Mike Coffey, Mehmet Kizilaslan, Suzanne Desire, Joanne Conington
Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs...
December 28, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29285121/persistent-m%C3%A3-llerian-duct-syndrome-a-case-report-and-review
#5
Xiaoya Ren, Di Wu, Chunxiu Gong
Persistent Müllerian duct syndrome (PMDS) is a rare type of male pseudohermaphroditism caused by a deficiency in anti-Müllerian hormone (AMH) or a defect in its type II receptor. The current study reports the clinical data and results of the genetic analysis of a 17-month-old male diagnosed with PMDS. The clinical manifestations of the patient included a left transverse testicular ectopia and bilateral cryptorchidism. Pelvic ultrasonography indicated two testes on the same left inguinal ring and left inguinal hernia and uterine tissue located at the left rear of the bladder...
December 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29273625/the-nuclear-matrix-protein-hnrnpu-maintains-3d-genome-architecture-globally-in-mouse-hepatocytes
#6
Hui Fan, Pin Lv, Xiangru Huo, Jicheng Wu, Qianfeng Wang, Lu Cheng, Yun Liu, Qiqun Tang, Ling Zhang, Feng Zhang, Xiaoqi Zheng, Hao Wu, Bo Wen
The eukaryotic chromosomes are folded into higher-order conformation to coordinate genome functions. Besides long-range chromatin loops, recent chromosome conformation capture (3C)-based studies indicated the higher level of chromatin structures including compartments and topologically associating domains (TADs), which may serve as units of genome organization and functions. However, the molecular machinery underlying these hierarchically three-dimensional (3D) chromatin architectures remains poorly understood...
December 22, 2017: Genome Research
https://www.readbyqxmd.com/read/29246937/genome-wide-association-study-identifies-a-new-locus-at-7q21-13-associated-with-hepatitis-b-virus-related-hepatocellular-carcinoma
#7
Gang-Qiao Zhou, Hongxing Zhang, Fuchu He, Yuanfeng Li, Yun Zhai, Qingfeng Song, Haitao Zhang, Pengbo Cao, Jie Ping, Xinyi Liu, Bingqian Guo, Guanjun Liu, Jin Song, Ying Zhang, Aiqing Yang, Hongbo Yan, Liang Yang, Ying Cui, Yilong Ma, Jinliang Xing, Xizhong Shen, Hongxin Zhang, Jiaze An, Jin-Xin Bei, Weihua Jia, Longli Kang, Lijun Liu, Dongya Yuan, Zhibin Hu, Hongbing Shen, Lei Lu, Xuan Wang, Hua Li, Tao-Tao Liu
PURPOSE: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. In China, chronic hepatitis B virus (HBV) infection remains the major risk factor for HCC. In the present study, we performed a genome-wide association study (GWAS) among Chinese populations to identify novel genetic loci contributing to susceptibility to HBV-related HCC. EXPERIMENTAL DESIGN: GWAS scan is performed in a collection of 205 HBV-related HCC trios (each trio includes an affected proband and his/her both parents), and 355 chronic HBV carriers with HCC (cases) and 360 chronic HBV carriers without HCC (controls), followed by two rounds of replication studies totally consisting of 3,796 cases and 2,544 controls...
December 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29244056/cscoretool-fast-hi-c-compartment-analysis-at-high-resolution
#8
Xiaobin Zheng, Yixian Zheng
Summary: The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth...
December 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#9
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#10
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29226983/combing-chromosomal-dna-mediated-by-the-smc-complex-structure-and-mechanisms
#11
REVIEW
Katsuhiko Kamada, Daniela Barillà
Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC (Structural Maintenance of Chromosomes) protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery responsible for DNA loop extrusion, like eukaryotic condensin or cohesin complexes, which act as chromosome organizers...
December 11, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29222670/venetoclax-for-treating-chronic-lymphocytic-leukaemia-an-evidence-review-group-perspective-of-a-nice-single-technology-appraisal
#12
REVIEW
Hema Mistry, Chidozie Nduka, Martin Connock, Jill Colquitt, Theodoros Mantopoulos, Emma Loveman, Renata Walewska, James Mason
Venetoclax is licensed to treat relapsed or refractory (R/R) chronic lymphocytic leukaemia (CLL). As part of the Single Technology Appraisal (STA) ID944, the National Institute for Health and Care Excellence (NICE) invited AbbVie, the manufacturer, to submit evidence on the use of venetoclax, within its licensed indication. The Evidence Review Group (ERG), Warwick Evidence, was asked to provide an independent and critical review of the submitted evidence. Evidence came from three single-arm trials in CLL patients with or without 17p deletion [del(17p])/TP53 chromosomal abnormalities...
December 8, 2017: PharmacoEconomics
https://www.readbyqxmd.com/read/29217590/a-mechanism-of-cohesin-dependent-loop-extrusion-organizes-zygotic-genome-architecture
#13
Johanna Gassler, Hugo B Brandão, Maxim Imakaev, Ilya M Flyamer, Sabrina Ladstätter, Wendy A Bickmore, Jan-Michael Peters, Leonid A Mirny, Kikuë Tachibana
Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl...
December 7, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29196799/3c-pcr-a-novel-proximity-ligation-based-approach-to-phase-chromosomal-rearrangement-breakpoints-with-distal-allelic-variants
#14
Samantha L P Schilit, Cynthia C Morton
Recent advances in molecular cytogenetics highlight the importance of noncoding structural variation in human disease. Genomic rearrangements can disrupt chromatin architecture, leading to long-range alterations in gene expression. With increasing ability to assess distal gene dysregulation comes new challenges in clinical interpretation of rearrangements. While haplotyping methods to determine compound heterozygosity in a single gene with two pathogenic variants are established, such methods are insufficient for phasing larger distances between a pathogenic variant and a genomic rearrangement breakpoint...
December 1, 2017: Human Genetics
https://www.readbyqxmd.com/read/29196559/remarkable-evolutionary-plasticity-of-centromeric-chromatin
#15
Steven Henikoff, Jitendra Thakur, Sivakanthan Kasinathan, Paul B Talbert
Centromeres were familiar to cell biologists in the late 19th century, but for most eukaryotes the basis for centromere specification has remained enigmatic. Much attention has been focused on the cenH3 (CENP-A) histone variant, which forms the foundation of the centromere. To investigate the DNA sequence requirements for centromere specification, we applied a variety of epigenomic approaches, which have revealed surprising diversity in centromeric chromatin properties. Whereas each point centromere of budding yeast is occupied by a single precisely positioned tetrameric nucleosome with one cenH3 molecule, the "regional" centromeres of fission yeast contain unphased presumably octameric nucleosomes with two cenH3s...
December 1, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29193442/visualization-of-the-native-shape-of-bodipy-labeled-dna-in-escherichia-coli-by-correlative-microscopy
#16
Alexandre Loukanov, Polina Mladenova, Svetlin Toshev, Hibiki Udono, Seiichiro Nakabayashi
The native shape and intracellular distribution of newly synthesized DNA was visualized by correlative (light and electron) microscopy in ice embedded whole cells of Escherichia coli. For that purpose, the commercially available modified nucleoside triphosphate named BODIPY® FL-14-dUTP was enzymatically incorporated in vivo into the genome of E. coli mutant K12 strain, which cannot synthesize thymine. The successful incorporation of this thymidine analogue was confirmed first by fluorescence microscope, where the cells were stained in the typical for bodipy green color...
November 27, 2017: Microscopy Research and Technique
https://www.readbyqxmd.com/read/29190286/nucleolar-sub-compartments-in-motion-during-rrna-synthesis-inhibition-contraction-of-nucleolar-condensed-chromatin-and-gathering-of-fibrillar-centers-are-concomitant
#17
Pavel Tchelidze, Aassif Benassarou, Hervé Kaplan, Marie-Françoise O'Donohue, Laurent Lucas, Christine Terryn, Levan Rusishvili, Giorgi Mosidze, Nathalie Lalun, Dominique Ploton
The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules...
2017: PloS One
https://www.readbyqxmd.com/read/29187575/a-role-for-the-smc3-hinge-domain-in-the-maintenance-of-sister-chromatid-cohesion
#18
Brett Robison, Vincent Guacci, Douglas Koshland
Cohesin is a conserved protein complex required for sister chromatid cohesion, chromosome condensation, DNA damage repair, and regulation of transcription. Although cohesin functions to tether DNA duplexes, the contribution of its individual domains to this activity remains poorly understood. We interrogated the Smc3p subunit of cohesin by random insertion mutagenesis. Analysis of a mutant in the Smc3p hinge revealed an unexpected role for this domain in cohesion maintenance and condensation. Further investigation revealed that the Smc3p hinge functions at a step following cohesin's stable binding to chromosomes and independently of Smc3p's regulation by the Eco1p acetyltransferase...
November 29, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29187162/isolation-and-characterization-of-a-new-naturally-immortalized-human-breast-carcinoma-cell-line-kaimrc1
#19
Rizwan Ali, Nosaibah Samman, Hajar Al Zahrani, Atef Nehdi, Sabhi Rahman, Abdul Latif Khan, Mohamed Al Balwi, Lolwah Abdullah Alriyees, Manal Alzaid, Ahmed Al Askar, Mohamed Boudjelal
BACKGROUND: Breast cancer is one of the most common cancer and a leading cause of death in women. Up to date the most commonly used breast cancer cell lines are originating from Caucasians or Afro-Americans but rarely cells are being derived from other ethnic groups. Here we describe for the first time the establishment of a naturally transformed breast cancer cell line, KAIMRC1 from an Arab woman of age 62 suffering from stage IIB breast cancer (T2N1M0). Moreover, we have characterized these cells for the biological and molecular markers, induction of MAPK pathways as well as its response to different commercially available drugs and compounds...
November 29, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29186573/conformational-dynamics-of-the-hop1-horma-domain-reveal-a-common-mechanism-with-the-spindle-checkpoint-protein-mad2
#20
Alan M V West, Elizabeth A Komives, Kevin D Corbett
The HORMA domain is a highly conserved protein-protein interaction module found in eukaryotic signaling proteins including the spindle assembly checkpoint protein Mad2 and the meiotic HORMAD proteins. HORMA domain proteins interact with short 'closure motifs' in partner proteins by wrapping their C-terminal 'safety belt' region entirely around these motifs, forming topologically-closed complexes. Closure motif binding and release requires large-scale conformational changes in the HORMA domain, but such changes have only been observed in Mad2...
November 25, 2017: Nucleic Acids Research
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