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https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#1
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28513628/an-integrated-model-for-detecting-significant-chromatin-interactions-from-high-resolution-hi-c-data
#2
Mark Carty, Lee Zamparo, Merve Sahin, Alvaro González, Raphael Pelossof, Olivier Elemento, Christina S Leslie
Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts-for example, distance-dependent random polymer ligation and GC content and mappability bias-and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks...
May 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28510289/genome-organization-during-the-cell-cycle-unity-in-division
#3
REVIEW
Rosela Golloshi, Jacob T Sanders, Rachel Patton McCord
During the cell cycle, the genome must undergo dramatic changes in structure, from a decondensed, yet highly organized interphase structure to a condensed, generic mitotic chromosome and then back again. For faithful cell division, the genome must be replicated and chromosomes and sister chromatids physically segregated from one another. Throughout these processes, there is feedback and tension between the information-storing role and the physical properties of chromosomes. With a combination of recent techniques in fluorescence microscopy, chromosome conformation capture (Hi-C), biophysical experiments, and computational modeling, we can now attribute mechanisms to many long-observed features of chromosome structure changes during cell division...
May 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28496157/rna-seq-based-genome-wide-analysis-reveals-loss-of-inter-chromosomal-regulation-in-breast-cancer
#4
Jesús Espinal-Enríquez, Cristóbal Fresno, Guillermo Anda-Jáuregui, Enrique Hernández-Lemus
Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28490498/shelterin-components-mediate-genome-reorganization-in-response-to-replication-stress
#5
Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter FitzGerald, Job Dekker, Shiv I S Grewal
The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization...
May 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28475875/dynamic-rewiring-of-promoter-anchored-chromatin-loops-during-adipocyte-differentiation
#6
Rasmus Siersbæk, Jesper Grud Skat Madsen, Biola Maria Javierre, Ronni Nielsen, Emilie Kristine Bagge, Jonathan Cairns, Steven William Wingett, Sofie Traynor, Mikhail Spivakov, Peter Fraser, Susanne Mandrup
Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter-anchored chromatin loops within 4 hr after inducing differentiation of 3T3-L1 preadipocytes. The establishment of new promoter-enhancer loops is tightly coupled to activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1, and P300 proteins to these regions, as well as to activation of target genes...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28475589/long-range-control-of-gene-expression-via-rna-directed-dna-methylation
#7
M Jordan Rowley, M Hafiz Rothi, Gudrun Böhmdorfer, Jan Kuciński, Andrzej T Wierzbicki
RNA-mediated transcriptional silencing, in plants known as RNA-directed DNA methylation (RdDM), is a conserved process where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) help establish repressive chromatin modifications. This process represses transposons and affects the expression of protein-coding genes. We found that in Arabidopsis thaliana AGO4 binding sites are often located distant from genes differentially expressed in ago4. Using Hi-C to compare interactions between genotypes, we show that RdDM-targeted loci have the potential to engage in chromosomal interactions, but these interactions are inhibited in wild-type conditions...
May 5, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28472433/exploring-spatially-adjacent-tfbs-clustered-regions-with-hi-c-data
#8
Hebing Chen, Shuai Jiang, Zhuo Zhang, Hao Li, Yiming Lu, Xiaochen Bo
Motivation: Transcription factor binding sites (TFBSs) are clustered in the human genome, forming the TFBS-clustered regions that regulate gene transcription, which requires dynamic chromatin configurations between promoters and distal regulatory elements. Here, we propose a regulatory model called spatially adjacent TFBS-clustered regions (SAT), in which TFBS-clustered regions are connected by spatial proximity as identified by high-resolution Hi-C data. Results: TFBS-clustered regions forming SATs appeared less frequently in gene promoters than did isolated TFBS-clustered regions, whereas SATs as a whole appeared more frequently...
May 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28468906/whole-genome-restriction-mapping-by-subhaploid-based-rad-sequencing-an-efficient-and-flexible-approach-for-physical-mapping-and-genome-scaffolding
#9
Jinzhuang Dou, Huaiqian Dou, Chuang Mu, Lingling Zhang, Yangping Li, Jia Wang, Tianqi Li, Yuli Li, Xiaoli Hu, Shi Wang, Zhenmin Bao
Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultra-dense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/BAC clone pools, and by restriction site-associated DNA (RAD) sequencing of these clone pools to produce an ultra-dense whole-genome restriction map to facilitate genome scaffolding...
May 3, 2017: Genetics
https://www.readbyqxmd.com/read/28468672/inferring-the-physical-properties-of-yeast-chromatin-through-bayesian-analysis-of-whole-nucleus-simulations
#10
Jean-Michel Arbona, Sébastien Herbert, Emmanuelle Fabre, Christophe Zimmer
BACKGROUND: The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture. However, how assumed chromatin properties affect model predictions was not previously systematically investigated. RESULTS: We used hundreds of dynamic chromosome simulations and Bayesian inference to determine chromatin properties consistent with an extensive dataset that includes hundreds of measurements from imaging in fixed and live cells and two Hi-C studies...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28467502/correction-gothic-a-probabilistic-model-to-resolve-complex-biases-and-to-identify-real-interactions-in-hi-c-data
#11
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pone.0174744.].
2017: PloS One
https://www.readbyqxmd.com/read/28448065/construction-of-a-map-based-reference-genome-sequence-for-barley-hordeum-vulgare-l
#12
Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao-Qi Zhang, Roberto A Barrero, Qisen Zhang, Lin Li, Micha Bayer, Daniel Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A Poland, Matthew I Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J Muehlbauer, Paul Kersey, Matthew D Clark, Mario Caccamo, Alan H Schulman, Matthias Platzer, Timothy J Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. 'Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C)...
April 27, 2017: Scientific Data
https://www.readbyqxmd.com/read/28435001/hi-c-2-0-an-optimized-hi-c-procedure-for-high-resolution-genome-wide-mapping-of-chromosome-conformation
#13
Houda Belaghzal, Job Dekker, Johan H Gibcus
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28426659/three-distinct-mechanisms-of-long-distance-modulation-of-gene-expression-in-yeast
#14
Manyu Du, Qian Zhang, Lu Bai
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise)...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#15
Joanna Achinger-Kawecka, Phillippa C Taberlay, Susan J Clark
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28420341/genetic-sequence-based-prediction-of-long-range-chromatin-interactions-suggests-a-potential-role-of-short-tandem-repeat-sequences-in-genome-organization
#16
Sarvesh Nikumbh, Nico Pfeifer
BACKGROUND: Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions - the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28411415/chromosome-conformation-capture-based-studies-reveal-novel-features-of-plant-nuclear-architecture
#17
REVIEW
Stefan Grob, Ueli Grossniklaus
Nuclear genome organization has recently received increasing attention due to its manifold functions in basic nuclear processes, such as replication, transcription, and the maintenance of genome integrity. Using technologies based on chromosome conformation capture, such as Hi-C, we now have the possibility to study the three-dimensional organization of the genome at unprecedented resolution, shedding light onto a previously unexplored level of nuclear architecture. In plants, research in this field is still in its infancy but a number of publications provided first insights into basic principles of nuclear genome organization and the factors that influence it...
April 12, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28388874/pgltools-a-genomic-arithmetic-tool-suite-for-manipulation-of-hi-c-peak-and-other-chromatin-interaction-data
#18
William W Greenwald, He Li, Erin N Smith, Paola Benaglio, Naoki Nariai, Kelly A Frazer
BACKGROUND: Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies...
April 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28388850/auditory-and-visual-executive-functions-in-children-and-response-to-methylphenidate-a-randomized-controlled-trial
#19
Yaffa Hadar, Shraga Hocherman, Oren Lamm, Emanuel Tirosh
OBJECTIVES: The aim of the study was to assess auditory and visually based executive functions (EFs) and the effect of methylphenidate (MPH) in children with ADHD. METHODS: Thirty-six boys between the ages of 8.3 and 9.7 years with ADHD and 36 matched controls were included. The study group was randomized into MPH and placebo for 7 days each in a crossover design. A Cued Choice Reaction Time (CCRT) test that included incongruent cuing was administered at baseline and following 1 and 2 weeks...
April 1, 2017: Journal of Attention Disorders
https://www.readbyqxmd.com/read/28387224/multi-scale-chromatin-state-annotation-using-a-hierarchical-hidden-markov-model
#20
Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Chromatin-state analysis is widely applied in the studies of development and diseases. However, existing methods operate at a single length scale, and therefore cannot distinguish large domains from isolated elements of the same type. To overcome this limitation, we present a hierarchical hidden Markov model, diHMM, to systematically annotate chromatin states at multiple length scales. We apply diHMM to analyse a public ChIP-seq data set. diHMM not only accurately captures nucleosome-level information, but identifies domain-level states that vary in nucleosome-level state composition, spatial distribution and functionality...
April 7, 2017: Nature Communications
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