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Series GSE50676 Query DataSets for GSE50676
Status Public on Dec 19, 2013
Title Landscape and variation of RNA secondary structure across the human transcriptome
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. The ability of RNA to base pair with itself and other nucleic acids endow RNA with the capacity to form extensive structures, which are known to influence practically every step in the gene expression program1. Yet the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSS) in a human family trio, providing a comprehensive RSS map of human coding and noncoding RNAs. We identify unique RSS signatures that demarcate open reading frames, splicing junctions, and define authentic microRNA binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over one thousand transcribed single nucleotide variants (~15% of all transcribed SNVs) alter local RNA structure; these “RiboSNitches”2 occur in disease-associated variants. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSS. Selective depletion of RiboSNitches versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3’UTRs, binding sites of miRNAs and RNA binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.
Overall design RNA structure probing is performed at 37˚C on poly(A)+ selected RNAs from GM12878, GM12891 and GM12892 cell lines, as well as on native proteinized RNAs from GM12878. The structure probed RNAs is then cloned into a sequencing library using modied Ambion RNA sequencing kit compatible with the Illumina platform. The samples were deep sequenced using Illumina's Hi-Seq platform.
AGO CLIP was performed as reported. Cells were crosslinked with UV and lysed using published protocols. AGO2 was enriched using immunopurification. The RNA-protein complex was digested with ribonuclease and purified by gel electrophoresis. Purified RNA was reverse transcribed and cDNA molecules were amplified and sequenced as described.
Contributor(s) Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E, Chang HY
Citation(s) 24476892
Submission date Sep 06, 2013
Last update date May 15, 2019
Contact name Kun Qu
Organization name Stanford University
Department Dermatology
Lab Howard Chang
Street address 269 Campus Dr. CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM1226157 GM12878 renatured S1
GSM1226158 GM12878 renatured V1
GSM1226159 GM12891 renatured S1
BioProject PRJNA218468
SRA SRP029656

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
GSE50676_GM12878_iCLIP.peaks.bed.gz 21.6 Kb (ftp)(http) BED
GSE50676_GM12891_iCLIP.peaks.bed.gz 31.9 Kb (ftp)(http) BED
GSE50676_GM12892_iCLIP.peaks.bed.gz 18.1 Kb (ftp)(http) BED
GSE50676_RAW.tar 93.7 Mb (http)(custom) TAR (of TAB)
GSE50676_per_level_gene_count.txt.gz 1008.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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