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https://www.readbyqxmd.com/read/28186589/-clinical-and-molecular-cytogenetic-analysis-of-a-family-with-mental-retardation-caused-by-an-unbalanced-translocation-involving-chromosomes-3-and-22
#1
Kaihui Zhang, Rui Dong, Yan Huang, Yali Yang, Ying Wang, Haiyan Zhang, Yufeng Zhang, Yi Liu, Zhongtao Gai
OBJECTIVE: To explore the genetic cause of a Chinese boy with unexplained mental retardation, and analyze the pattern of inheritance for his family. METHODS: Routine karyotyping, chromosomal microarray analysis (CMA), and fluorescence in situ hybridization (FISH) were used to detect chromosome abnormalities in the patient and his families. RESULTS: Chromosome analysis suggested that the proband and 7 affected individuals had an identical karyotype 46,XN,der(22)t(3;22)(q28;q13)pat, while his father and 5 other relatives carried a same karyotype of 46,XN,t(3;22)(q28;q13)...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28181049/condensin-master-organizer-of-the-genome
#2
REVIEW
Paul Kalitsis, Tao Zhang, Kathryn M Marshall, Christian F Nielsen, Damien F Hudson
A fundamental requirement in nature is for a cell to correctly package and divide its replicated genome. Condensin is a mechanical multisubunit complex critical to this process. Condensin uses ATP to power conformational changes in DNA to enable to correct DNA compaction, organization, and segregation of DNA from the simplest bacteria to humans. The highly conserved nature of the condensin complex and the structural similarities it shares with the related cohesin complex have provided important clues as to how it functions in cells...
February 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28174238/functional-characterisation-of-cis-regulatory-elements-governing-dynamic-eomes-expression-in-the-early-mouse-embryo
#3
Claire S Simon, Damien J Downes, Matthew E Gosden, Jelena Telenius, Douglas R Higgs, Jim R Hughes, Ita Costello, Elizabeth K Bikoff, Elizabeth J Robertson
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable and only the VPE is required for optimal Eomes expression in vivo Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28161540/genome-organization-in-the-nucleus-from-dynamic-measurements-to-a-functional-model
#4
REVIEW
Anat Vivante, Eugene Brozgol, Irena Bronshtein, Yuval Garini
A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed...
February 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28159771/improving-and-correcting-the-contiguity-of-long-read-genome-assemblies-of-three-plant-species-using-optical-mapping-and-chromosome-conformation-capture-data
#5
Wen-Biao Jiao, Gonzalo Garcia Accinelli, Benjamin Hartwig, Christiane Kiefer, David Baker, Edouard Severing, Eva-Maria Willing, Mathieu Piednoel, Stefan Woetzel, Eva Madrid-Herrero, Bruno Huettel, Ulrike Hümann, Richard Reinhard, Marcus A Koch, Daniel Swan, Bernardo Clavijo, George Coupland, Korbinian Schneeberger
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes, however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated PacBio long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding...
February 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28146474/molecular-mechanism-for-the-regulation-of-yeast-separase-by-securin
#6
Shukun Luo, Liang Tong
Separase is a cysteine protease with a crucial role in the dissolution of cohesion among sister chromatids during chromosome segregation. In human tumours separase is overexpressed, making it a potential target for drug discovery. The protease activity of separase is strictly regulated by the inhibitor securin, which forms a tight complex with separase and may also stabilize this enzyme. Separases are large, 140-250-kilodalton enzymes, with an amino-terminal α-helical region and a carboxy-terminal caspase-like catalytic domain...
February 9, 2017: Nature
https://www.readbyqxmd.com/read/28140585/discovery-of-2-3-acrylamido-4-methylphenyl-amino-n-2-methyl-5-3-4-5-trimethoxybenzamido-phenyl-4-methylamino-pyrimidine-5-carboxamide-chmfl-bmx-078-as-a-highly-potent-and-selective-type-ii-irreversible-bone-marrow-kinase-in-the-x-chromosome-bmx-kinase-inhibitor
#7
Xiaofei Liang, Fengchao Lv, Beilei Wang, Kailin Yu, Hong Wu, Ziping Qi, Zongru Jiang, Cheng Chen, Aoli Wang, Weili Miao, Wenchao Wang, Zhenquan Hu, Juan Liu, Xiaochuan Liu, Zheng Zhao, Li Wang, Shanchun Zhang, Zi Ye, Chu Wang, Tao Ren, Yinsheng Wang, Qingsong Liu, Jing Liu
BMX is a member of TEC family non-receptor tyrosine kinase and is involved in a variety of critical physiological and pathological processes. Through combination of irreversible inhibitor design and type II inhibitor design approaches, we have discovered a highly selective and potent type II irreversible BMX kinase inhibitor compound 41 (CHMFL-BMX-078), which exhibited an IC50 of 11 nM by formation of a covalent bond with cysteine 496 residue in the DFG-out inactive conformation of BMX. It displayed a high selectivity profile (S score(1)=0...
January 31, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28139673/how-best-to-identify-chromosomal-interactions-a-comparison-of-approaches
#8
James O J Davies, A Marieke Oudelaar, Douglas R Higgs, Jim R Hughes
Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data...
January 31, 2017: Nature Methods
https://www.readbyqxmd.com/read/28137286/chrom3d-three-dimensional-genome-modeling-from-hi-c-and-nuclear-lamin-genome-contacts
#9
Jonas Paulsen, Monika Sekelja, Anja R Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells...
January 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/28135255/massively-multiplex-single-cell-hi-c
#10
Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
We present single-cell combinatorial indexed Hi-C (sciHi-C), a method that applies combinatorial cellular indexing to chromosome conformation capture. In this proof of concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells. We use sciHi-C data to separate cells by karyotypic and cell-cycle state differences and identify cell-to-cell heterogeneity in mammalian chromosomal conformation. Our results demonstrate that combinatorial indexing is a generalizable strategy for single-cell genomics...
January 30, 2017: Nature Methods
https://www.readbyqxmd.com/read/28131315/retrieving-chromatin-patterns-from-deep-sequencing-data-using-correlation-functions
#11
Jana Molitor, Jan-Philipp Mallm, Karsten Rippe, Fabian Erdel
Epigenetic modifications and other chromatin features partition the genome on multiple length scales. They define chromatin domains with distinct biological functions that come in sizes ranging from single modified DNA bases to several megabases in the case of heterochromatic histone modifications. Due to chromatin folding, domains that are well separated along the linear nucleosome chain can form long-range interactions in three-dimensional space. It has now become a routine task to map epigenetic marks and chromatin structure by deep sequencing methods...
February 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28129457/tumor-suppressor-gene-methylation-on-the-short-arm-of-chromosome-1-in-chronic-myelogenous-leukemia
#12
Naoki Mori, Mari Ohwashi-Miyazaki, Kentaro Yoshinaga, Michiko Okada, Masayuki Shiseki, Toshiko Motoji, Junji Tanaka
OBJECTIVES: We previously reported loss of heterozygosity on 1p in chronic myelogenous leukemia (CML). We analyzed promoter methylation and mutation of tumor suppressor genes on 1p36 in CML. METHODS: We performed methylation specific PCR (MS-PCR) analysis of the PRDM2, RUNX3, and TP73 genes in 61 patients with CML (43 chronic phase, CP; 2 accelerated phase; and 16 blast crisis, BC). Oxidative MS-PCR, PCR-single strand conformation polymorphism, and real time reverse transcriptase-PCR were also analyzed...
January 27, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/28129029/chromosome-conformation-and-gene-expression-patterns-differ-profoundly-in-human-fibroblasts-grown-in-spheroids-versus-monolayers
#13
Haiming Chen, Laura Seaman, Sijia Liu, Thomas Ried, Indika Rajapakse
Human cells derived for in vitro cultures are conventionally grown as adherent monolayers (2 D) which do not resemble natural three dimensional (3 D) tissue architecture. We examined genome structure with chromosome conformation capture (Hi-C) and gene expression with RNA-seq in fibroblasts derived from human foreskin grown in 2 D and 3 D conditions. Our combined analysis of Hi-C and RNA-seq data shows a large number of differentially expressed genes between 2 D and 3 D cells, and these changes are localized in genomic regions that displayed structural changes...
January 27, 2017: Nucleus
https://www.readbyqxmd.com/read/28126037/molecular-dissection-of-germline-chromothripsis-in-a-developmental-context-using-patient-derived-ips-cells
#14
Sjors Middelkamp, Sebastiaan van Heesch, A Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J van Roosmalen, Martijn J E Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E Verbeek, Elly F Ippel, Youri Adolfs, R Jeroen Pasterkamp, Wigard P Kloosterman, Ewart W Kuijk, Edwin Cuppen
BACKGROUND: Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phenotypes of patients with complex germline genomic rearrangements is generally unknown. METHODS: To dissect the impact of germline chromothripsis in a relevant developmental context, we performed trio-based RNA expression analysis on blood cells, induced pluripotent stem cells (iPSCs), and iPSC-derived neuronal cells from a patient with de novo germline chromothripsis and both healthy parents...
January 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28108933/modelling-genome-wide-topological-associating-domains-in-mouse-embryonic-stem-cells
#15
REVIEW
Y Zhan, L Giorgetti, G Tiana
Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre...
January 20, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28087737/a-homozygous-mutation-in-trim36-causes-autosomal-recessive-anencephaly-in-an-indian-family
#16
Nivedita Singh, Vishwanath Kumble Bhat, Ankana Tiwari, Srinivas G Kodaganur, Sagar J Tontanahal, Astha Sarda, K V Malini, Arun Kumar
Anencephaly is characterized by the absence of brain tissues and cranium. During primary neurulation stage of the embryo, the rostral part of the neural pore fails to close, leading to anencephaly. Anencephaly shows a heterogeneous etiology, ranging from environmental to genetic causes. The autosomal recessive inheritance of anencephaly has been reported in several populations. In this study, we employed whole-exome sequencing and identified a homozygous missense mutation c.1522C>A (p.Pro508Thr) in the TRIM36 gene as the cause of autosomal recessive anencephaly (APH) in an Indian family...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28078515/capturing-genomic-relationships-that-matter
#17
REVIEW
Cameron S Osborne, Borbála Mifsud
There is a strong interrelationship within the cell nucleus between form and function of the genome. This connection is exhibited across multiple hierarchies, ranging from grand-scale positioning of chromosomes and their intersection with specific nuclear functional activities, the segregation of chromosome structure into distinct domains and long-range regulatory contacts that drive spatial and temporal expression patterns of genes. Fifteen years ago, the development of the chromosome conformation capture method placed the nature of specific, long-range regulatory interactions under scrutiny...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28057745/reciprocal-insulation-analysis-of-hi-c-data-shows-that-tads-represent-a-functionally-but-not-structurally-privileged-scale-in-the-hierarchical-folding-of-chromosomes
#18
Yinxiu Zhan, Luca Mariani, Iros Barozzi, Edda G Schulz, Nils Bluthgen, Michael Stadler, Guido Tiana, Luca Giorgetti
Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions...
January 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28056052/the-glucocorticoid-receptor-regulates-the-angptl4-gene-in-a-ctcf-mediated-chromatin-context-in-human-hepatic-cells
#19
Masafumi Nakamoto, Ko Ishihara, Takehisa Watanabe, Akiyuki Hirosue, Shinjiro Hino, Masanori Shinohara, Hideki Nakayama, Mitsuyoshi Nakao
Glucocorticoid signaling through the glucocorticoid receptor (GR) plays essential roles in the response to stress and in energy metabolism. This hormonal action is integrated to the transcriptional control of GR-target genes in a cell type-specific and condition-dependent manner. In the present study, we found that the GR regulates the angiopoietin-like 4 gene (ANGPTL4) in a CCCTC-binding factor (CTCF)-mediated chromatin context in the human hepatic HepG2 cells. There are at least four CTCF-enriched sites and two GR-binding sites within the ANGPTL4 locus...
2017: PloS One
https://www.readbyqxmd.com/read/28043971/mechanosensing-by-the-nucleus-from-pathways-to-scaling-relationships
#20
REVIEW
Sangkyun Cho, Jerome Irianto, Dennis E Discher
The nucleus is linked mechanically to the extracellular matrix via multiple polymers that transmit forces to the nuclear envelope and into the nuclear interior. Here, we review some of the emerging mechanisms of nuclear mechanosensing, which range from changes in protein conformation and transcription factor localization to chromosome reorganization and membrane dilation up to rupture. Nuclear mechanosensing encompasses biophysically complex pathways that often converge on the main structural proteins of the nucleus, the lamins...
February 2017: Journal of Cell Biology
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