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Alternative intronic polyadenylation influences cancer metastasis and response to therapy [CLIP-seq]

ABSTRACT: CLIP-seq analysis of TIA1 protein in 4T1 invasive mammary tumor cells

ORGANISM(S): Mus musculus

PROVIDER: GSE94369 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA369516

REPOSITORIES: GEO

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Alternative intronic polyadenylation influences cancer metastasis and response to therapy

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Alternative intronic polyadenylation generates the interleukin-6 trans-signaling inhibitor sgp130-E10.

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Cold induced RNA-binding proteins influence alternative polyadenylation

Project description:We employed PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3M-bM-^@M-^YUTR lengthening whereas the loss of Cirbp or Rbm3 resulted in 3M-bM-^@M-^YUTR shortening. Combining with PAR-CLIP results, we found that these two RBPs repress the polyadenylation adjacent to their binding sites. Examination of the binding sites of Cirbp and Rbm3 by PAR-CLIP and their influence on the transcriptome by RNA-seq. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129M-bM-^@M-^S141, with MEFs cell lines stably expressing FLAG-tagged Cirbp and Rbm3. We used 4-thiouridine (4SU) to enhance the crosslink. For RNA-seq, polyadenylated RNA from the mock-transfected cells at 37M-BM-0C or 32M-BM-0C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37M-BM-0C were sequenced on Solexa GAII using 76bp single-end kits according to the manufacturerM-bM-^@M-^Ys instructions.

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