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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data

ABSTRACT: To assess whether the transcripts identified by PAR-CLIP are regulated by the RNA-binding protein (RBP) Quaking (QKI), we analyzed the mRNA levels of mock-transfected and QKI-specific siRNA-transfected cells with microarrays. Transcripts crosslinked to QKI were significantly upregulated upon siRNA transfection, indicating that QKI negatively regulates bound mRNAs (Figure 3H of PMID 20371350), consistent with previous reports of QKI being a repressor. The RBP QKI was depleted by siRNAs and the expression level was compared to mock-transfected HEK 293 cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Markus Hafner

PROVIDER: E-GEOD-21574 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Hafner Markus M Landthaler Markus M Burger Lukas L Khorshid Mohsen M Hausser Jean J Berninger Philipp P Rothballer Andrea A Ascano Manuel M Jungkamp Anna-Carina AC Munschauer Mathias M Ulrich Alexander A Wardle Greg S GS Dewell Scott S Zavolan Mihaela M Tuschl Thomas T

Cell 20100401 1

RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thio ...[more]

PMID: 20371350

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

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Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

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