NDLI: The effects of common structural variants on 3D chromatin structure

Content Provider	Springer Nature : BioMed Central
Author	Shanta, Omar Noor, Amina Sebat, Jonathan
Abstract	Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs). Genetic factors that explain dynamic variation in TAD structure are not understood. We hypothesize that common structural variation (SV) in the human population can disrupt regulatory sequences and thereby influence TAD formation. To determine the effects of SVs on 3D chromatin organization, we performed chromosome conformation capture sequencing (Hi-C) of lymphoblastoid cell lines from 19 subjects for which SVs had been previously characterized in the 1000 genomes project. We tested the effects of common deletion polymorphisms on TAD structure by linear regression analysis of nearby quantitative chromatin interactions (contacts) within 240 kb of the deletion, and we specifically tested the hypothesis that deletions at TAD boundaries (TBs) could result in large-scale alterations in chromatin conformation. Results Large (> 10 kb) deletions had significant effects on long-range chromatin interactions. Deletions were associated with increased contacts that span the deleted region and this effect was driven by large deletions that were not located within a TAD boundary (nonTB). Some deletions at TBs, including a 80 kb deletion of the genes CFHR1 and CFHR3, had detectable effects on chromatin contacts. However for TB deletions overall, we did not detect a pattern of effects that was consistent in magnitude or direction. Large inversions in the population had a distinguishable signature characterized by a rearrangement of contacts that span its breakpoints. Conclusions Our study demonstrates that common SVs in the population impact long-range chromatin structure, and deletions and inversions have distinct signatures. However, the effects that we observe are subtle and variable between loci. Genome-wide analysis of chromatin conformation in large cohorts will be needed to quantify the influence of common SVs on chromatin structure.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-020-6516-1.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-020-6516-1
Journal	BMC Genomics
Issue Number	1
Volume Number	21
Language	English
Publisher	BioMed Central
Publisher Date	2020-01-30
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Hi-C Structural variation Deletion Inversion TAD TAD fusion Chromatin
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

TAD cliques predict key features of chromatin organization

Large-scale 3D chromatin reconstruction from chromosomal contacts

Chromatin loop anchors contain core structural components of the gene expression machinery in maize

EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

ProbC: joint modeling of epigenome and transcriptome effects in 3D genome

Fine mapping chromatin contacts in capture Hi-C data

Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide

Multiplex genomic structure variation mediated by TALEN and ssODN

HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences

The effects of common structural variants on 3D chromatin structure

Similar Documents

TAD cliques predict key features of chromatin organization

Large-scale 3D chromatin reconstruction from chromosomal contacts

Chromatin loop anchors contain core structural components of the gene expression machinery in maize

EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm

ProbC: joint modeling of epigenome and transcriptome effects in 3D genome

Fine mapping chromatin contacts in capture Hi-C data

Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide

Multiplex genomic structure variation mediated by TALEN and ssODN

HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences

The effects of common structural variants on 3D chromatin structure