GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE85764 Query DataSets for GSE85764
Status Public on Aug 01, 2021
Title RNA-Chromatin Interactome Reveals ncRNA Functions for Transcription Regulation in 3D Genome Organization
Organisms Drosophila melanogaster; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Noncoding RNAs (ncRNAs) are an emerging class of regulatory molecules with a broad range of regulatory functions believed to be mediated by ncRNA-chromatin interactions. Genome-wide understanding of ncRNA functions requires precise mapping of all ncRNAs and their target loci. Current methods for studying chromatin-associated ncRNA lack specificity or are limited to singly assessing RNAs. We devised an unbiased strategy to identify all RNA Interactions with Chromatin by Paired-End-Taging (RICh-PET) and applied this approach to characterize the Drosophila RNA-chromatin interactome. We discovered that ncRNAs primarily target promoters and enhancers in open chromatin regions in colocalization with RNAPII and other TFs, suggesting combinatorial regulatory instructions for each locus. Enzymatic nuclear digestion followed by examination of specific chromatin loci indicated that ncRNAs collectively promote chromatin accessability, RNAPII-mediated interactions and overall 3D-genome organization. Our study demonstrates that RICh-PET and related methods represent a powerful suite of tools to interrogate the genome biology of ncRNAs.
Overall design Investigation of RNA-chromatin Interactome by RICh-PET
Contributor(s) Zheng M, Luo O, Tian S, Ruan Y
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 17, 2016
Last update date Aug 02, 2021
Contact name Zhongyuan Tian
Phone 860-837-2358
Organization name The Jackson Laboratory for Genomic Medicine
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
Platforms (2)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
GPL22339 Illumina NextSeq 500 (Drosophila melanogaster; Homo sapiens)
Samples (19)
GSM2283709 RICh-PET_Rep1
GSM2283710 RICh-PET_Rep2
BioProject PRJNA339288
SRA SRP082316

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
GSE85764_RAW.tar 2.0 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
GSE85764_RICh-PET_Combined_DNA-RNA_PET.txt.gz 13.0 Mb (ftp)(http) TXT
GSE85764_RNAPII-RICh-PET_Combined_DNA-RNA_PET.txt.gz 76.6 Mb (ftp)(http) TXT
GSE85764_S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt.gz 3.7 Mb (ftp)(http) TXT
GSE85764_S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph.gz 179.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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