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https://www.readbyqxmd.com/read/28912419/identifying-topologically-associating-domains-and-subdomains-by-gaussian-mixture-model-and-proportion-test
#1
Wenbao Yu, Bing He, Kai Tan
The spatial organization of the genome plays a critical role in regulating gene expression. Recent chromatin interaction mapping studies have revealed that topologically associating domains and subdomains are fundamental building blocks of the three-dimensional genome. Identifying such hierarchical structures is a critical step toward understanding the three-dimensional structure-function relationship of the genome. Existing computational algorithms lack statistical assessment of domain predictions and are computationally inefficient for high-resolution Hi-C data...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28903899/the-application-of-next-generation-sequencing-techniques-in-studying-transcriptional-regulation-in-embryonic-stem-cells
#2
Ya-Jun Liu, Feng Zhang, Hong-de Liu, Xiao Sun
The mechanism of transcriptional regulation has been the focus of many studies in the post-genomic era. The development of sequencing-based technologies for chromatin profiling enables current researchers to experimentally measure chromatin properties. Moreover, many studies aim at annotating the state of the chromatin into broad categories based on observed chromatin features and/or DNA sequences, then associating the resultant distal regulatory regions with the correct target genes based on DNA sequences, and predicting the dependence of epigenetic features on genetic variation...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28902867/analysis-of-the-relationship-between-coexpression-domains-and-chromatin-3d-organization
#3
María E Soler-Oliva, Jose A Guerrero-Martínez, Valentina Bachetti, Jose C Reyes
Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs...
September 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28892574/identification-of-a-novel-interspecific-hybrid-yeast-from-a-metagenomic-spontaneously-inoculated-beer-sample-using-hi-c
#4
Caiti Smukowski Heil, Joshua N Burton, Ivan Liachko, Anne Friedrich, Noah A Hanson, Cody L Morris, Joseph Schacherer, Jay Shendure, James H Thomas, Maitreya J Dunham
Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method's application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample...
September 11, 2017: Yeast
https://www.readbyqxmd.com/read/28890333/static-and-dynamic-dna-loops-form-ap-1-bound-activation-hubs-during-macrophage-development
#5
Douglas H Phanstiel, Kevin Van Bortle, Damek Spacek, Gaelen T Hess, Muhammad Saad Shamim, Ido Machol, Michael I Love, Erez Lieberman Aiden, Michael C Bassik, Michael P Snyder
The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops in human monocytes and differentiated macrophages. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops...
September 1, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28885554/advances-in-genomic-profiling-and-analysis-of-3d-chromatin-structure-and-interaction
#6
REVIEW
Binhua Tang, Xiaolong Cheng, Yunlong Xi, Zixin Chen, Yufan Zhou, Victor X Jin
Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensional (3D) chromatin architecture. It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation. To better interpret the 3D data dramatically accumulating in past five years and to gain deep biological insights, huge efforts have been made in developing novel quantitative analysis methods...
September 8, 2017: Genes
https://www.readbyqxmd.com/read/28882003/minimds-3d-structural-inference-from-high-resolution-hi-c-data
#7
Lila Rieber, Shaun Mahony
Motivation: Recent experiments have provided Hi-C data at resolution as high as 1 kbp. However, 3D structural inference from high-resolution Hi-C datasets is often computationally unfeasible using existing methods. Results: We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and then reassembles the partitions using low-resolution MDS. miniMDS is faster, more accurate, and uses less memory than existing methods for inferring the human genome at high resolution (10 kbp)...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28870212/chromosome-contacts-in-activated-t-cells-identify-autoimmune-disease-candidate-genes
#8
Oliver S Burren, Arcadio Rubio García, Biola-Maria Javierre, Daniel B Rainbow, Jonathan Cairns, Nicholas J Cooper, John J Lambourne, Ellen Schofield, Xaquin Castro Dopico, Ricardo C Ferreira, Richard Coulson, Frances Burden, Sophia P Rowlston, Kate Downes, Steven W Wingett, Mattia Frontini, Willem H Ouwehand, Peter Fraser, Mikhail Spivakov, John A Todd, Linda S Wicker, Antony J Cutler, Chris Wallace
BACKGROUND: Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4(+) T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes. RESULTS: Within 4 h, activation of CD4(+) T cells invokes changes in histone modifications and enhancer RNA transcription that correspond to altered expression of the interacting genes identified by promoter capture Hi-C...
September 4, 2017: Genome Biology
https://www.readbyqxmd.com/read/28866080/the-tartary-buckwheat-genome-provides-insights%C3%A2-into-rutin-biosynthesis-and-abiotic-stress%C3%A2-tolerance
#9
Lijun Zhang, Xiuxiu Li, Bin Ma, Qiang Gao, Huilong Du, Yuanhuai Han, Yan Li, Yinghao Cao, Ming Qi, Yaxin Zhu, Hongwei Lu, Mingchuan Ma, Longlong Liu, Jianping Zhou, Chenghu Nan, Yongjun Qin, Jun Wang, Lin Cui, Huimin Liu, Chengzhi Liang, Zhijun Qiao
Tartary buckwheat (Fagopyrum tataricum) is an important pseudocereal crop that is strongly adapted to growth in adverse environments. Its gluten-free grain contains complete proteins with a well-balanced composition of essential amino acids and is a rich source of beneficial phytochemicals that provide significant health benefits. Here, we report a high-quality, chromosome-scale Tartary buckwheat genome sequence of 489.3 Mb that is assembled by combining whole-genome shotgun sequencing of both Illumina short reads and single-molecule real-time long reads, sequence tags of a large DNA insert fosmid library, Hi-C sequencing data, and BioNano genome maps...
September 12, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28855260/hicrep-assessing-the-reproducibility-of-hi-c-data-using-a-stratum-adjusted-correlation-coefficient
#10
Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices...
August 30, 2017: Genome Research
https://www.readbyqxmd.com/read/28854926/single-molecule-sequencing-and-hi-c-based-proximity-guided-assembly-of-amaranth-amaranthus-hypochondriacus-chromosomes-provide-insights-into-genome-evolution
#11
D J Lightfoot, D E Jarvis, T Ramaraj, R Lee, E N Jellen, P J Maughan
BACKGROUND: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of the developing world. Here, we present a reference-quality assembly of the amaranth genome which will assist the agronomic development of the species...
August 31, 2017: BMC Biology
https://www.readbyqxmd.com/read/28826674/evolutionarily-conserved-principles-predict-3d-chromatin-organization
#12
M Jordan Rowley, Michael H Nichols, Xiaowen Lyu, Masami Ando-Kuri, I Sarahi M Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G Corces
Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28825727/condensin-mediated-remodeling-of-the-mitotic-chromatin-landscape-in-fission-yeast
#13
Yasutaka Kakui, Adam Rabinowitz, David J Barry, Frank Uhlmann
The eukaryotic genome consists of DNA molecules far longer than the cells that contain them. They reach their greatest compaction during chromosome condensation in mitosis. This process is aided by condensin, a structural maintenance of chromosomes (SMC) family member. The spatial organization of mitotic chromosomes and how condensin shapes chromatin architecture are not yet fully understood. Here we use chromosome conformation capture (Hi-C) to study mitotic chromosome condensation in the fission yeast Schizosaccharomyces pombe...
August 21, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28825700/smc-complexes-differentially-compact-mitotic-chromosomes-according-to-genomic-context
#14
Stephanie Andrea Schalbetter, Anton Goloborodko, Geoffrey Fudenberg, Jon-Matthew Belton, Catrina Miles, Miao Yu, Job Dekker, Leonid Mirny, Jonathan Baxter
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion...
September 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#15
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28805829/lineage-specific-dynamic-and-pre-established-enhancer-promoter-contacts-cooperate-in-terminal-differentiation
#16
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
#17
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
#18
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
#19
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/28765367/polycomb-mediated-chromatin-loops-revealed-by-a-subkilobase-resolution-chromatin-interaction-map
#20
Kyle P Eagen, Erez Lieberman Aiden, Roger D Kornberg
The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or "anchors" are associated with CTCF protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of polycomb repressive complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
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