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chromatin conformation capture

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https://www.readbyqxmd.com/read/29149895/novel-insights-into-chromosomal-conformations-in-cancer
#1
REVIEW
Ruobing Jia, Peiwei Chai, He Zhang, Xianqun Fan
Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between two distant fragments can regulate transactivation activity via mediator proteins. Thus, a series of chromosome conformation capture techniques have been developed, including chromosome conformation capture (3C), circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C), and high-resolution chromosome conformation capture (Hi-C)...
November 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#2
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29113562/utilizing-networks-for-differential-analysis-of-chromatin-interactions
#3
Lu Liu, Jianhua Ruan
Chromatin conformation capture with high-throughput sequencing (Hi-C) is a powerful technique to detect genome-wide chromatin interactions. In this paper, we introduce two novel approaches to detect differentially interacting genomic regions between two Hi-C experiments using a network model. To make input data from multiple experiments comparable, we propose a normalization strategy guided by network topological properties. We then devise two measurements, using local and global connectivity information from the chromatin interaction networks, respectively, to assess the interaction differences between two experiments...
October 19, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29106613/3div-a-3d-genome-interaction-viewer-and-database
#4
Dongchan Yang, Insu Jang, Jinhyuk Choi, Min-Seo Kim, Andrew J Lee, Hyunwoong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, Byungwook Lee
Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29094699/two-independent-modes-of-chromatin-organization-revealed-by-cohesin-removal
#5
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny, Francois Spitz
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes...
November 2, 2017: Nature
https://www.readbyqxmd.com/read/29093029/chromatin-conformation-links-distal-target-genes-to-ckd-loci
#6
Maarten M Brandt, Claartje A Meddens, Laura Louzao-Martinez, Noortje A M van den Dungen, Nico R Lansu, Edward E S Nieuwenhuis, Dirk J Duncker, Marianne C Verhaar, Jaap A Joles, Michal Mokry, Caroline Cheng
Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes...
November 1, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29091999/evaluation-and-comparison-of-methods-for-recapitulation-of-3d-spatial-chromatin-structures
#7
Jincheol Park, Shili Lin
How chromosomes fold and how distal genomic elements interact with one another at a genomic scale have been actively pursued in the past decade following the seminal work describing the Chromosome Conformation Capture (3C) assay. Essentially, 3C-based technologies produce two-dimensional (2D) contact maps that capture interactions between genomic fragments. Accordingly, a plethora of analytical methods have been proposed to take a 2D contact map as input to recapitulate the underlying whole genome three-dimensional (3D) structure of the chromatin...
October 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29080874/-computer-methods-of-analysis-of-chromosome-contacts-in-the-cell-nucleus-based-on-sequencing-technology-data
#8
Y L Orlov, O Thierry, A G Bogomolov, A V Tsukanov, E V Kulakova, E R Galieva, A O Bragin, G Li
The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29053968/multiscale-3d-genome-rewiring-during-mouse-neural-development
#9
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay, Giacomo Cavalli
Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo...
October 19, 2017: Cell
https://www.readbyqxmd.com/read/29052195/technical-review-a-hitchhiker-s-guide-to-chromosome-conformation-capture
#10
Stefan Grob, Giacomo Cavalli
The introduction of chromosome conformation capture (3C) technologies boosted the field of 3D-genome research and significantly enhanced the available toolset to study chromosomal architecture. 3C technologies not only offer increased resolution compared to the previously dominant cytological approaches but also allow the simultaneous study of genome-wide 3D chromatin contacts, thereby enabling a candidate-free perspective on 3D-genome architecture. Since its introduction in 2002, 3C technologies evolved rapidly and now constitute a collection of tools, each with their strengths and pitfalls with respect to specific research questions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29048467/identification-of-copy-number-variations-and-translocations-in-cancer-cells-from-hi-c-data
#11
Abhijit Chakraborty, Ferhat Ay
Motivation: Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29044247/regulation-of-genome-organization-and-gene-expression-by-nuclear-mechanotransduction
#12
REVIEW
Caroline Uhler, G V Shivashankar
It is well established that cells sense chemical signals from their local microenvironment and transduce them to the nucleus to regulate gene expression programmes. Although a number of experiments have shown that mechanical cues can also modulate gene expression, the underlying mechanisms are far from clear. Nevertheless, we are now beginning to understand how mechanical cues are transduced to the nucleus and how they influence nuclear mechanics, genome organization and transcription. In particular, recent progress in super-resolution imaging, in genome-wide application of RNA sequencing, chromatin immunoprecipitation and chromosome conformation capture and in theoretical modelling of 3D genome organization enables the exploration of the relationship between cell mechanics, 3D chromatin configurations and transcription, thereby shedding new light on how mechanical forces regulate gene expression...
October 18, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29036650/characteristic-arrangement-of-nucleosomes-is-predictive-of-chromatin-interactions-at-kilobase-resolution
#13
Hui Zhang, Feifei Li, Yan Jia, Bingxiang Xu, Yiqun Zhang, Xiaoli Li, Zhihua Zhang
High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interactions (CCIs) from low-resolution Hi-C data...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28986784/capturing-three-dimensional-genome-organization-in-individual-cells-by-single-cell-hi-c
#14
Takashi Nagano, Steven W Wingett, Peter Fraser
Hi-C is a powerful method to investigate genome-wide, higher-order chromatin and chromosome conformations averaged from a population of cells. To expand the potential of Hi-C for single-cell analysis, we developed single-cell Hi-C. Similar to the existing "ensemble" Hi-C method, single-cell Hi-C detects proximity-dependent ligation events between cross-linked and restriction-digested chromatin fragments in cells. A major difference between the single-cell Hi-C and ensemble Hi-C protocol is that the proximity-dependent ligation is carried out in the nucleus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28981716/computational-construction-of-3d-chromatin-ensembles-and-prediction-of-functional-interactions-of-alpha-globin-locus-from-5c-data
#15
Gamze Gürsoy, Yun Xu, Amy L Kenter, Jie Liang
Conformation capture technologies measure frequencies of interactions between chromatin regions. However, understanding gene-regulation require knowledge of detailed spatial structures of heterogeneous chromatin in cells. Here we describe the nC-SAC (n-Constrained-Self Avoiding Chromatin) method that transforms experimental interaction frequencies into 3D ensembles of chromatin chains. nC-SAC first distinguishes specific from non-specific interaction frequencies, then generates 3D chromatin ensembles using identified specific interactions as spatial constraints...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28978434/dna-methylation-landscape-reflects-the-spatial-organization-of-chromatin-in-different-cells
#16
Ling Zhang, Wen Jun Xie, Sirui Liu, Luming Meng, Chan Gu, Yi Qin Gao
The relationship between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of published sequencing data, we observed a long-range power law correlation of DNA methylation with cell class-specific scaling exponents in the range of tens of kilobases. We showed that such cell class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using high-resolution chromosome conformation capture data and mapping the methylation level onto the modeled structure, we demonstrated that the patchiness of DNA methylation is related to chromatin structure...
October 3, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28978027/functional-dissection-of-breast-cancer-risk-associated-tert-promoter-variants
#17
Sonja Helbig, Leesa Wockner, Annick Bouendeu, Ursula Hille-Betz, Karen McCue, Juliet D French, Stacey L Edwards, Hilda A Pickett, Roger R Reddel, Georgia Chenevix-Trench, Thilo Dörk, Jonathan Beesley
The multi-cancer susceptibility locus at 5p15.33 includes TERT, encoding the telomerase catalytic subunit. Genome-wide association studies (GWAS) have identified six single nucleotide polymorphisms (SNPs) in the TERT promoter associated with decreased breast cancer risk, although the precise causal variants and their mechanisms of action have remained elusive. Luciferase reporter assays indicated that the protective haplotype reduced TERT promoter activity in human mammary epithelial and cancer cells in an estrogen-independent manner...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28970326/heat-shock-protein-genes-undergo-dynamic-alteration-in-their-3d-structure-and-genomic-organization-in-response-to-thermal-stress
#18
Surabhi Chowdhary, Amoldeep S Kainth, David S Gross
Three-dimensional chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here we use a highly sensitive version of chromosome conformation capture (3C) in combination with fluorescence microscopy to investigate Heat Shock Protein (HSP) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5' -3' gene looping previously described for Pol II genes...
October 2, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28964259/three-dimensional-genome-architecture-and-emerging-technologies-looping-in-disease
#19
REVIEW
Arpit Mishra, R David Hawkins
Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. Compaction is maintained by a multitude of architectural proteins, long non-coding RNAs (lncRNAs), and regulatory DNA. Each component comprises interlinked regulatory circuits that organize the genome in three-dimensional (3D) space to manage gene expression. In this review, we update the current state of 3D genome catalogues and focus on how recent technological advances in 3D genomics are leading to an enhanced understanding of disease mechanisms...
September 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28936982/optimization-and-quality-control-of-genome-wide-hi-c-library-preparation
#20
Xiang-Yuan Zhang, Chao He, Bing-Yu Ye, De-Jian Xie, Ming-Lei Shi, Yan Zhang, Wen-Long Shen, Ping Li, Zhi-Hu Zhao
Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells...
September 20, 2017: Yi Chuan, Hereditas
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