NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE115064 Query DataSets for GSE115064
Status Public on May 30, 2018
Title Epigenetic maintenance of topological domains in the rearranged gibbon genome [ChIP-seq]
Organism Nomascus leucogenys
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400-600kb) TADs in human and other mammalian species. The co-localization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Lastly, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.
 
Overall design We performed ChIP-seq using H3K4me3 in two gibbon individuals (biological replicates).
 
Contributor(s) Carbone L, Lazar N
Citation(s) 29914971
Submission date May 29, 2018
Last update date Aug 29, 2018
Contact name Lucia Carbone
E-mail(s) carbone@ohsu.edu
Organization name Oregon Health & Science University
Street address 3303 SW Bond Ave.
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platforms (1)
GPL25055 Illumina NextSeq 500 (Nomascus leucogenys)
Samples (3)
GSM3164321 Gibbon_H3K4me3_rep1
GSM3164322 Gibbon_H3K4me3_rep2
GSM3164323 Gibbon_input
This SubSeries is part of SuperSeries:
GSE115065 Epigenetic maintenance of topological domains in the rearranged gibbon genome
Relations
BioProject PRJNA473602
SRA SRP149296

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115064_NLE-ChIP-H3K4me3-final-peaks.bw 4.1 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap