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https://www.readbyqxmd.com/read/28808972/chromosome-conformation-capture-for-research-on-innate-antiviral-immunity
#1
Yoon Jung Kim, Tae Hoon Kim
Chromosome conformation capture (3C) technology has revolutionized our knowledge on chromatin folding and nuclear organization. This cis-loop detection approach can be used to identify candidate regulatory elements interacting with target gene of interest. This chapter introduces the application of 3C technique to investigate a dynamic alteration in the chromosome folding structure or genomic architecture resulting from interaction changes between the enhancer and its target gene. Innate antiviral immunity is one of the well-known gene induction systems, involving rapid first-line response to virus or pathogen to trigger gene expression changes in order to protect cells and to limit further infection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28805849/topology-of-polymer-chains-under-nanoscale-confinement
#2
Vahid Satarifard, Maziar Heidari, Samaneh Mashaghi, Sander J Tans, Mohammad Reza Ejtehadi, Alireza Mashaghi
Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc...
August 14, 2017: Nanoscale
https://www.readbyqxmd.com/read/28805829/lineage-specific-dynamic-and-pre-established-enhancer-promoter-contacts-cooperate-in-terminal-differentiation
#3
Adam J Rubin, Brook C Barajas, Mayra Furlan-Magaril, Vanessa Lopez-Pajares, Maxwell R Mumbach, Imani Howard, Daniel S Kim, Lisa D Boxer, Jonathan Cairns, Mikhail Spivakov, Steven W Wingett, Minyi Shi, Zhixin Zhao, William J Greenleaf, Anshul Kundaje, Michael Snyder, Howard Y Chang, Peter Fraser, Paul A Khavari
Chromosome conformation is an important feature of metazoan gene regulation; however, enhancer-promoter contact remodeling during cellular differentiation remains poorly understood. To address this, genome-wide promoter capture Hi-C (CHi-C) was performed during epidermal differentiation. Two classes of enhancer-promoter contacts associated with differentiation-induced genes were identified. The first class ('gained') increased in contact strength during differentiation in concert with enhancer acquisition of the H3K27ac activation mark...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#4
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28794204/chromosome-topology-guides-the-drosophila-dosage-compensation-complex-for-target-gene-activation
#5
Tamás Schauer, Yad Ghavi-Helm, Tom Sexton, Christian Albig, Catherine Regnard, Giacomo Cavalli, Eileen Em Furlong, Peter B Becker
X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific lethal dosage compensation complex (DCC) identifies and binds to X-chromosomal high-affinity sites (HAS) from which it boosts transcription. A sub-class of HAS, PionX sites, represent first contacts on the X. Here, we explored the chromosomal interactions of representative PionX sites by high-resolution 4C and determined the global chromosome conformation by Hi-C in sex-sorted embryos. Male and female X chromosomes display similar nuclear architecture, concordant with clustered, constitutively active genes...
August 9, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28792605/single-cell-hi-c-bridges-microscopy-and-genome-wide-sequencing-approaches-to-study-3d-chromatin-organization
#6
REVIEW
Sergey V Ulianov, Kikue Tachibana-Konwalski, Sergey V Razin
Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes...
August 9, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28776025/three-dimensional-positioning-and-structure-of-chromosomes-in-a-human-prophase-nucleus
#7
Bo Chen, Mohammed Yusuf, Teruo Hashimoto, Ana Katrina Estandarte, George Thompson, Ian Robinson
The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28771935/parallel-stranded-dna-and-rna-duplexes-structural-features-and-potential-applications
#8
REVIEW
Marta Szabat, Ryszard Kierzek
Nowadays, decades after the discovery of the right-handed B-DNA, it is well known that nucleic acids have a great conformational flexibility, exhibiting a large polymorphism of their structures. In nature, DNA and RNA exist in an antiparallel orientation, stabilized by Watson-Crick base pairs. However, in some cases, nucleic acid fragments with specific nucleotide sequences can adopt a parallel orientation involving noncanonical base pairing. Interestingly, parallel-stranded duplexes have been found in specific chromosome regions...
August 3, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28771695/challenges-for-visualizing-three-dimensional-data-in-genomic-browsers
#9
REVIEW
Mike Goodstadt, Marc A Marti-Renom
Genomic interactions reveal the spatial organization of genomes and genomic domains, which is known to play key roles in cell function. Physical proximity can be represented as two-dimensional heat maps or matrices. From these, three-dimensional (3D) conformations of chromatin can be computed revealing coherent structures that highlight the importance of non-sequential relationships across genomic features. Mainstream genomic browsers have been classically developed to display compact, stacked tracks based on a linear, sequential, per-chromosome coordinate system...
August 3, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28764714/testis-specific-histone-2b-is-associated-with-sperm-chromatin-dynamics-and-bull-fertility-a-pilot-study
#10
Naseer A Kutchy, Ana Velho, Erika S B Menezes, Marie Jacobsen, Giselle Thibaudeau, Robert W Wills, Arlindo Moura, Abdullah Kaya, Andy Perkins, Erdogan Memili
BACKGROUND: Bull fertility is the degree of sperm's ability to fertilize and activate the egg and support embryo development, and this is critical for herd reproductive performance. We used the bull as a unique model organism for the study of male fertility because cattle genetics and physiology is similar to those of other mammals including humans. Moreover, reliable fertility data along with well-established in vitro systems are available for bovine. The objective of this original study was to ascertain evolutionary diversification and expression dynamics of Testis Specific Histone 2B (TH2B) in sperm from Holstein bulls with different fertility scores...
August 1, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28760140/the-three-dimensional-genome-organization-of-drosophila-melanogaster-through-data-integration
#11
Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo, Frank Alber
BACKGROUND: Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments...
July 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28752814/a-matter-of-scale-and-dimensions-chromatin-of-chromosome-landmarks-in-the-fungi
#12
Allyson A Erlendson, Steven Friedman, Michael Freitag
Chromatin and chromosomes of fungi are highly diverse and dynamic, even within species. Much of what we know about histone modification enzymes, RNA interference, DNA methylation, and cell cycle control was first addressed in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Neurospora crassa. Here, we examine the three landmark regions that are required for maintenance of stable chromosomes and their faithful inheritance, namely, origins of DNA replication, telomeres and centromeres...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28751856/synucleins-and-gene-expression-ramblers-in-a-crowd-or-cops-regulating-traffic
#13
REVIEW
Alexei A Surguchev, Andrei Surguchov
Synuclein family consists of three members, α, β, and γ-synuclein. Due to their involvement in human diseases, they have been thoroughly investigated for the last 30 years. Since the first synuclein identification and description, members of this family are found in all vertebrates. Sequencing of their genes indicates high evolutionary conservation suggesting important function(s) of these proteins. They are small naturally unfolded proteins prone to aggregate, easily change their conformation, and bind to the membranes...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28741795/a-novel-molecular-mechanism-of-cellular-transformation-via-a-mutant-molecular-chaperone-in-myeloproliferative-neoplasms
#14
REVIEW
Marito Araki, Norio Komatsu
Deregulation of the cytokine-receptor signaling pathway plays a significant role in tumorigenesis. Such deregulation is frequently caused by alterations in the genes involved in the signaling pathway. At the end of 2013, recurrent somatic mutations in the calreticulin (CALR) gene that encodes a molecular chaperone were identified in a subset of patients with Philadelphia-chromosome negative myeloproliferative neoplasms (MPNs). This review focuses on the role of CALR mutations in the oncogenic transformations observed in MPNs...
July 25, 2017: Cancer Science
https://www.readbyqxmd.com/read/28736439/genome-organization-tracking-chromosomal-conformation-through-the-cell-cycle
#15
Carolina Perdigoto
No abstract text is available yet for this article.
September 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28735859/computational-prediction-of-position-effects-of-apparently-balanced-human-chromosomal-rearrangements
#16
Cinthya J Zepeda-Mendoza, Jonas Ibn-Salem, Tammy Kammin, David J Harris, Debra Rita, Karen W Gripp, Jennifer J MacKenzie, Andrea Gropman, Brett Graham, Ranad Shaheen, Fowzan S Alkuraya, Campbell K Brasington, Edward J Spence, Diane Masser-Frye, Lynne M Bird, Erica Spiegel, Rebecca L Sparkes, Zehra Ordulu, Michael E Talkowski, Miguel A Andrade-Navarro, Peter N Robinson, Cynthia C Morton
Interpretation of variants of uncertain significance, especially chromosomal rearrangements in non-coding regions of the human genome, remains one of the biggest challenges in modern molecular diagnosis. To improve our understanding and interpretation of such variants, we used high-resolution three-dimensional chromosomal structural data and transcriptional regulatory information to predict position effects and their association with pathogenic phenotypes in 17 subjects with apparently balanced chromosomal abnormalities...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28735107/integrative-modelling-of-cellular-assemblies
#17
REVIEW
Agnel Praveen Joseph, Guido Polles, Frank Alber, Maya Topf
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively...
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28728680/at-the-base-of-colinear-hox-gene-expression-cis-features-and-trans-factors-orchestrating-the-initial-phase-of-hox-cluster-activation
#18
REVIEW
Roel Neijts, Jacqueline Deschamps
Hox genes are crucial players in the generation and pattering of the vertebrate trunk and posterior body during embryogenesis. Their initial expression takes place shortly after the establishment of the primitive streak, in the posterior-most part of the mouse embryo and is a determinant step for setting up the definitive Hox expression boundaries along the antero-posterior body axis. The developmental signals and epigenetic mechanisms underlying this early activation remained unsolved until recently. The development of novel embryo-derived model systems, combined with methods that examine chromatin status and chromosome conformation, led to deeper understanding of the process of Hox activation in the early embryo...
August 15, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28726804/diagnostic-cytogenetic-testing-following-positive-noninvasive-prenatal-screening-results-a-clinical-laboratory-practice-resource-of-the-american-college-of-medical-genetics-and-genomics-acmg
#19
Athena M Cherry, Yassmine M Akkari, Kimberly M Barr, Hutton M Kearney, Nancy C Rose, Sarah T South, James H Tepperberg, Jeanne M Meck
Disclaimer: ACMG Clinical Laboratory Practice Resources are developed primarily as an educational tool for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these practice resources is voluntary and does not necessarily assure a successful medical outcome. This Clinical Laboratory Practice Resource should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results...
August 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#20
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 2017: PLoS Computational Biology
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