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Series GSE41285 Query DataSets for GSE41285
Status Public on Nov 09, 2012
Title Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation.
Argonaute (AGO) HITS-CLIP Libraries generated from wild type and miR-155 knockout activated T cells.
Overall design AGO HITS-CLIP libraries were generated from activated wild type and miR-155 knockout T cells with two different 3' linkers. Libraries were generated and sequenced with an 11nt index read that contained both a 5nt multiplexing index and a 6nt degenerate barcode. Files have been demultiplexed and the 6nt degenerate barcode has been appended as the first 6 nucleotides of the read.
Contributor(s) Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY
Citation(s) 23142080
Submission date Oct 02, 2012
Last update date May 15, 2019
Contact name Aly Azeem Khan
Organization name University of Chicago
Street address 6045 S. Kenwood Ave.
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (24)
GSM1013575 CD4+ T cells, 155KO, biological rep1
GSM1013576 CD4+ T cells, 155KO, biological rep2
GSM1013577 CD4+ T cells, 155KO, biological rep3
This SubSeries is part of SuperSeries:
GSE41288 Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting
BioProject PRJNA176456
SRA SRP015971

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Supplementary file Size Download File type/resource
GSE41285_clip_peaks.txt.gz 651.8 Kb (ftp)(http) TXT
GSE41285_clip_supplemental.pdf.gz 113.2 Kb (ftp)(http) PDF
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