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Series GSE56862 Query DataSets for GSE56862
Status Public on Oct 09, 2014
Title Genome-wide quantification of microRNA processing efficiency from RNA-seq data
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Microprocessor is responsible for conversion of pri-miRNA transcripts into pre-miRNA hairpins in miRNA biogenesis. The in vivo properties of this process remain enigmatic. Here, we present the first study of in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile, from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. Based on differential processing efficiencies we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.
Overall design We performed polyA independent deep sequencing of the chromatin-isolated RNA fraction for 5 samples: 2 replicates in HeLa cells, 1 Drosha knock down in HeLa cells, 1 sample for A549 cells and 1 sample for HEK293 cells. We also performed deep sequencing of the small RNA fraction in the same cell lines.
Contributor(s) Conrad T, Marsico A, Gehre M, Orom UA
Citation(s) 25310978, 28250203
Submission date Apr 16, 2014
Last update date May 15, 2019
Contact name Annalisa Marsico
Organization name Max Planck Institute for Molecular Genetics
Department Computational Biology
Street address Ihnestra├če 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1370360 HeLa_rep1_RNASeq
GSM1370361 HeLa_rep2_RNASeq
GSM1370362 HeLa_Droshasi_RNASeq
BioProject PRJNA244784
SRA SRP041228

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56862_RAW.tar 110.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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