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Series GSE45530 Query DataSets for GSE45530
Status Public on Jul 09, 2013
Title DNA-RNA Immunoprecipitation sequencing (DRIP-seq) of human NT2 cells
Organism Homo sapiens
Experiment type Other
Summary Strand asymmetry in the distribution of guanines and cytosines, measured by GC skew, predisposes DNA sequences towards R-loop formation upon transcription. Previous work revealed that GC skew and R-loop formation associate with a core set of unmethylated CpG island (CGI) promoters in the human genome. Here, we show that GC skew can distinguish four classes of promoters, including three types of CGI promoters, each associated with unique epigenetic and gene ontology signatures. In particular, we identify a strong and a weak class of CGI promoters and show that these loci are enriched in distinct chromosomal territories reflecting the intrinsic strength of their protection against DNA methylation. Interestingly, we show that strong CGI promoters are depleted from the X chromosome while weak CGIs are enriched, a property consistent with the acquisition of DNA methylation during dosage compensation. Furthermore, we identify a third class of CGI promoters based on its unique GC skew profile and show that this gene set is enriched for Polycomb group targets. Lastly, we show that nearly 2,000 genes harbor GC skew at their 3’ ends and that these genes are preferentially located in gene-dense regions and tend to be closely arranged. Genomic profiling of R-loops accordingly showed that a large proportion of genes with terminal GC skew form R-loops at their 3’-ends, consistent with a role for these structures in permitting efficient transcription termination. Altogether, we show that GC skew and R-loop formation offer significant insights into the epigenetic regulation, genomic organization, and function of human genes.
 
Overall design DRIP-seq was performed on genomic DNA extracted from human pluripotent Ntera2 cells. The DNA was either fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI (DRIP-seq 1) or BamHI, NcoI, ApaLI, NheI and PvuII (DRIP-seq 2, two technical replicates). Input DNA was also fragmented with each restriction enzyme cocktail and sequenced alongside.
 
Contributor(s) Ginno PA, Lim YW
Citation(s) 23868195
Submission date Mar 27, 2013
Last update date Mar 20, 2019
Contact name Yoong Wearn Lim
E-mail ywlim@ucdavis.edu
Organization name University of California, Davis
Department Molecular and Cellular Biology
Lab Chedin
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (5)
GSM1108095 NT2 input 1
GSM1108096 NT2 DRIP-seq 1
GSM1108097 NT2 input 2
Relations
BioProject PRJNA194527
SRA SRP020088

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
GSE45530_RAW.tar 490.4 Mb (http)(custom) TAR (of WIG)
Raw data are available in SRA
Processed data provided as supplementary file

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