scholarly journals Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

10.3791/57001 ◽  
2018 ◽  
Author(s):  
Clemens B. Hug ◽  
Juan M. Vaquerizas
Keyword(s):  
Chromatin Conformation ◽  
Chromatin Conformation Capture ◽  
Genome Wide

scholarly journals Hi-Cpipe: a pipeline for high-throughput chromosome capture

2015 ◽  
Author(s):  
Giancarlo Castellano ◽  
François Le Dily ◽  
Antonio Hermoso Pulido ◽  
Miguel Beato ◽  
Guglielmo Roma
Keyword(s):  
High Throughput ◽  
Visual Inspection ◽  
Automated Analysis ◽  
Chromatin Conformation ◽  
Interaction Data ◽  
Alignment Quality ◽  
Bioinformatics Pipeline ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Analysis Workflow

Hi-Cpipe is a bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome alignment, quality control and filtering, identification of genome-wide chromatin interactions, visualization and statistics. An interactive browser enables visual inspection of interaction data and results.

scholarly journals A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

2017 ◽  
Author(s):  
Michael R. Stadler ◽  
Michael B. Eisen
Keyword(s):  
High Resolution ◽  
Physical Space ◽  
Structural Features ◽  
Chromatin Conformation ◽  
Chromatin Conformation Capture ◽  
Insulator Function ◽  
Extension Model ◽  
Insulator Proteins ◽  
Topologically Associated Domains ◽  
Insulator Elements

AbstractInsulator proteins bind to specific genomic loci and have been shown to play a role in partitioning genomes into independent domains of gene expression and chromatin structure. Despite decades of study, the mechanism by which insulators establish these domains remains elusive. Here, we use genome-wide chromatin conformation capture (Hi-C) to generate a high-resolution map of spatial interactions of chromatin from Drosophila melanogaster embryos. We show that from the earliest stages of development the genome is divided into distinct topologically associated domains (TADs), that we can map the boundaries between TADs to sub-kilobase resolution, and that these boundaries correspond to 500-2000 bp insulator elements. Comparing this map with a detailed assessment of the banding pattern of a region of a polytene chromosome, we show that these insulator elements correspond to low density polytene interbands that divide compacted bands, which correspond to TADs. It has been previously shown that polytene interbands have low packing ratios allowing the conversion of small genomic distances (in base pairs) into a large physical distances. We therefore suggest a simple mechanism for insulator function whereby insulators increase the physical space between adjacent domains via the unpacking and extension of intervening chromatin. This model provides an intuitive explanation for known features of insulators, including the ability to block enhancer-promoter interactions, limit the spread of heterochromatin, and organize the structural features of interphase chromosomes.

scholarly journals Associating disease-related genetic variants in intergenic regions to the genes they impact

2014 ◽  
Author(s):  
Geoff Macintyre ◽  
Antonio Jimeno Yepes ◽  
Cheng Soon Ong ◽  
Karin Verspoor
Keyword(s):  
Genetic Variants ◽  
Target Genes ◽  
Three Dimensional ◽  
Biomedical Literature ◽  
Dimensional Structure ◽  
Chromatin Conformation ◽  
Functional Interpretation ◽  
Chromatin Conformation Capture ◽  
Intergenic Regions ◽  
Small Test

We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.

Straightforward protocol for allele-specific chromatin conformation capture

Gene ◽  
2021 ◽  
Vol 767 ◽  
pp. 145185
Author(s):  
R.D. Acemel ◽  
J.J. Tena ◽  
J.L. Gomez-Skarmeta ◽  
J. Fibla ◽  
J.L. Royo
Keyword(s):  
Chromatin Conformation ◽  
Chromatin Conformation Capture ◽  
Allele Specific

scholarly journals HUGIn: Hi-C Unifying Genomic Interrogator

2017 ◽  
Author(s):  
Joshua S. Martin ◽  
Zheng Xu ◽  
Alex P. Reiner ◽  
Karen L. Mohlke ◽  
Patrick Sullivan ◽  
...  
Keyword(s):  
High Throughput ◽  
Regulatory Elements ◽  
Supplementary Information ◽  
Chromatin Conformation ◽  
Organization Studies ◽  
Web Browser ◽  
Functional Roles ◽  
Gwas Snps ◽  
Genome Wide ◽  
Coding Variants

AbstractMotivationHigh throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChlA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell lines, limiting their generalizability.ResultsWe developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell liens. HUGIn enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data.AvailabilityHUGIn is available at http://yunliweb.its.unc.edu/[email protected] and [email protected] information:

scholarly journals 3C (Chromatin Conformation Capture): A Technique to Study Chromatin Organization

2012 ◽  
Vol 22 (11) ◽  
pp. 1587-1594
Author(s):  
Yea Woon Kim ◽  
AeRi Kim
Keyword(s):  
Chromatin Organization ◽  
Chromatin Conformation ◽  
Chromatin Conformation Capture

scholarly journals Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

2020 ◽  
Author(s):  
Mikhail G. Dozmorov ◽  
Katarzyna M. Tyc ◽  
Nathan C. Sheffield ◽  
David C. Boyd ◽  
Amy L. Olex ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Material ◽  
Human Tumor ◽  
Chromatin Conformation ◽  
Library Preparation ◽  
Rna Seq ◽  
Chromatin Conformation Capture ◽  
Alignment Strategy ◽  
Preparation Strategy

AbstractSequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined.We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated two experimental PDX Hi-C datasets using different library preparation strategies. We evaluated three alignment strategies (Direct, Xenome, Combined) and three processing pipelines (Juicer, HiC-Pro, HiCExplorer) on the quality of Hi-C data.Removal of mouse reads had little-to-no effect on data quality than the results obtained with Direct alignment strategy. Juicer pipeline extracted the most useful information from PDX Hi-C data. However, library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.

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