Dataset Information

HUGIn: Hi-C Unifying Genomic Interrogator.

ABSTRACT:

Motivation

High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-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.

Results

We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. 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 eQTL results and functional genomics data.

Availability and implementation

HUGIn is available at http://yunliweb.its.unc.edu/HUGIn.

Contact

yunli@med.unc.edu or hum@ccf.org.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Martin JS

PROVIDER: S-EPMC5860315 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

HUGIn: Hi-C Unifying Genomic Interrogator.

Martin Joshua S JS Xu Zheng Z Reiner Alex P AP Mohlke Karen L KL Sullivan Patrick P Ren Bing B Hu Ming M Li Yun Y

Bioinformatics (Oxford, England) 20171201 23

<h4>Motivation</h4>High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-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.<h4>Results</h4>We developed a web browser, HUGIn, to visualize Hi-C data generated from 21 human primary tissues and cell lines. HUGIn enables assessment of chromatin c ...[more]

PMID: 28582503

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Project description:BackgroundComplex genomic rearrangements (CGRs) drive the restructuring of chromatin architecture, resulting in significant interactions among rearranged fragments, visible as anomalous interaction blocks in chromatin contact maps generated by chromosome conformation capture technologies such as Hi-C. These blocks not only offer the orientation and genome coordinates of rearranged fragments but also filter out false positive CGRs, thereby facilitating CGR assembly. Despite this, there is a lack of interactive graphical software tailored for this purpose.ResultsWe present DeCGR, a user-friendly Python toolbox specifically designed for deciphering CGRs in Hi-C data. DeCGR consists of four independent execution components. The Breakpoint Filtering module identifies and filters simple rearrangements, providing the coordinates of rearrangement breakpoints. The Fragment Assembly module automatically assembles CGRs and visualizes the assembly process, facilitating the direct association between anomalous interaction blocks and CGR events. The Validation CGRs module verifies the completeness and accuracy of CGRs by generating the Hi-C map with CGRs through a simulation process and examines the difference from the original Hi-C maps. This module displays both the original and the simulated Hi-C map with highlighted rearranged fragment boundaries for rapid review to assess the CGRs. Finally, the Reconstruct Hi-C Map module provides the reconstructed Hi-C map based on the determined CGRs, allowing users to directly observe the impact of rearrangements on chromatin structure.ConclusionsDeCGR is designed specifically for biologists who aim to explore CGRs from Hi-C data. It provides a validation module to ensure the completeness and correctness of CGRs. Additionally, it allows users to generate CGR assembly results and reconstruct the Hi-C map with just one click. DeCGR provides intuitive visualization results for each module, allowing users to easily associate CGRs with Hi-C maps. DeCGR is operable through a user-friendly graphical interface. Source codes are freely available at https://github.com/GaoLabXDU/DeCGR .

Project description:BackgroundKaryotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line.ResultsWe obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH.ConclusionsIn the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.

Dataset Information

HUGIn: Hi-C Unifying Genomic Interrogator.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

HUGIn: Hi-C Unifying Genomic Interrogator.

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