Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data]

ABSTRACT: 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. 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.

ORGANISM(S): Mus musculus

SUBMITTER: Aly Khan

PROVIDER: E-GEOD-41285 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting.

Loeb Gabriel B GB Khan Aly A AA Canner David D Hiatt Joseph B JB Shendure Jay J Darnell Robert B RB Leslie Christina S CS Rudensky Alexander Y AY

Molecular cell 20121108 5

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 approximat ...[more]

PMID: 23142080

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Project description:Expression changes of competitive endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts that contain miRNA binding sites. Here, we find that although miRNA levels define the extent of repression, they do not affect the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ~20% of that observed for canonical 8-nt sites. Sites with extensive additional complementarity can be even more potent, but this occurs predominantly through miRNA degradation rather than competition. Cooperative binding of closely spaced sites for different miRNAs can also increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNA and target abundance, target-site spacing and affinity requirements for ceRNA-mediated gene regulation and specify the unusual circumstances in which ceRNA-mediated gene regulation might be observed. Sixty-four mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing sites matching miR-122, let-7, miR-192, miR-194 or a mutated site (no site) or 2) embryonic stem (ES) cells that were transfected with a Tet-inducible dual-color reporter construct expressing enhanced yellow fluorescent protein (eYFP) and mCherry that contains zero (0s) or three (3s) 8 nt miRNA seed matches for miR-293 or miR-92 in the 3â?² UTR. ES cells were sorted with a FACSAria IIIu flow cytometer into three bins based on their eYFP fluorescence intensity. All samples were sequenced in duplicates by an Illumina HiSeq 2500. Library preparation and sequencing were performed by Fasteris SA (Switzerland) or by the Functional Genomics Centre ZÃ¼rich (FGCZ). Three small RNA profiles or either primary hepatocytes or embryonic stem cells were also generated by Solexa sequencing.

Dataset Information

Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq data]

Publications

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting.

Similar Datasets

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