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Series GSE75770 Query DataSets for GSE75770
Status Public on Jul 14, 2016
Title TE-associated chromatin variation in mice livers
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility is a hallmark of active regulatory function in the genome and variation of chromatin accessibility across individuals has been shown to contribute to complex traits and disease susceptibility. However, the mechanisms responsible for chromatin variation among different individuals and how this variation contributes to phenotypic diversity remain poorly understood.
We examined chromatin accessibility variation in liver tissue from seven strains of adult mice that have phenotypic diversity in response to a high-fat/high-sucrose diet. Remarkably, nearly 40% of the loci with the greatest degree of chromatin variability across the strains are associated with transposable elements (TEs), with evolutionarily younger TEs being particularly enriched for regions of chromatin variation. We found that evolutionary younger and older TEs have differential chromatin accessibility profiles and are enriched for binding sites of different transcription factors, indicating the role of TEs in the evolution of regulatory networks in the liver. We also demonstrate that TE polymorphisms and epigenetic regulation of TEs contribute to regulatory variation across different strains through providing binding sites for liver transcription factors. Intriguingly, variable chromatin loci that are associated with liver metabolism are primarily TE-associated.
We demonstrate that TEs contribute to regulatory variation in liver and have downstream effects on metabolism. Our data reveal TEs as a novel and important contributor to regulatory and phenotypic variation in the liver and suggest that regulatory variation at TEs is a major contributor to phenotypic variation in populations.
 
Overall design Examination of chromatin accessibility with FAIRE-seq in livers of male mice (A/J, AKR/J, BALB/cJ, C57BL/6J, C3H/HeJ, CBA/J, DBA/2J, BXH2/TyJ, and BXH19/TyJ) fed a high-fat, high-sucrose diet.
 
Contributor(s) Du J, Leung A, Trac C, Lee M, Parks B, Lusis AJ, Natarajan R, Schones DE
Citation(s) 27398095
Submission date Dec 07, 2015
Last update date May 15, 2019
Contact name Juan Du
Organization name Beckman Research Institute, City of Hope
Street address 1500 E. Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (18)
GSM1967235 A/J FAIRE Replicate 1
GSM1967236 A/J FAIRE Replicate 2
GSM1967237 AKR/J FAIRE Replicate 1
Relations
BioProject PRJNA305303
SRA SRP067086

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
GSE75770_AJ-peaks.npf.txt.gz 532.2 Kb (ftp)(http) TXT
GSE75770_AJ.bw 531.7 Mb (ftp)(http) BW
GSE75770_AKR-peaks.npf.txt.gz 518.7 Kb (ftp)(http) TXT
GSE75770_AKR.bw 1014.4 Mb (ftp)(http) BW
GSE75770_BALB-peaks.npf.txt.gz 539.0 Kb (ftp)(http) TXT
GSE75770_BALB.bw 511.5 Mb (ftp)(http) BW
GSE75770_BL6-peaks.npf.txt.gz 528.8 Kb (ftp)(http) TXT
GSE75770_BL6.bw 794.8 Mb (ftp)(http) BW
GSE75770_BXH19-peaks.npf.txt.gz 534.8 Kb (ftp)(http) TXT
GSE75770_BXH19.bw 705.0 Mb (ftp)(http) BW
GSE75770_BXH2-peaks.npf.txt.gz 530.2 Kb (ftp)(http) TXT
GSE75770_BXH2.bw 819.8 Mb (ftp)(http) BW
GSE75770_C3HHeJ-peaks.npf.txt.gz 544.9 Kb (ftp)(http) TXT
GSE75770_C3HHeJ.bw 542.5 Mb (ftp)(http) BW
GSE75770_CBA-peaks.npf.txt.gz 538.6 Kb (ftp)(http) TXT
GSE75770_CBA.bw 879.8 Mb (ftp)(http) BW
GSE75770_DBA-peaks.npf.txt.gz 460.8 Kb (ftp)(http) TXT
GSE75770_DBA.bw 738.6 Mb (ftp)(http) BW
GSE75770_common-chromatin.bed.gz 24.0 Kb (ftp)(http) BED
GSE75770_variable-chromatin.bed.gz 23.7 Kb (ftp)(http) BED
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Processed data are available on Series record

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