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Methods. 2014 May 1;67(1):13-9. doi: 10.1016/j.ymeth.2013.11.001. Epub 2013 Nov 17.

Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq.

Author information

1
SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA.
2
SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA. Electronic address: stenenbaum@albany.edu.

Abstract

Post-transcriptional regulation of messenger RNA contributes to numerous aspects of gene expression. The key component to this level of regulation is the interaction of RNA-binding proteins (RBPs) and their associated target mRNA. Splicing, stability, localization, translational efficiency, and alternate codon use are just some of the post-transcriptional processes regulated by RBPs. Central to our understanding of these processes is the need to characterize the network of RBP-mRNA associations and create a map of this functional post-transcriptional regulatory system. Here we provide a detailed methodology for mRNA isolation using RBP immunoprecipitation (RIP) as a primary partitioning approach followed by microarray (Chip) or next generation sequencing (NGS) analysis. We do this by using specific antibodies to target RBPs for the capture of associated RNA cargo. RIP-Chip/Seq has proven to be is a versatile, genomic technique that has been widely used to study endogenous RBP-RNA associations.

KEYWORDS:

Microarray expression profiling; Post-Transcription; RIP-Chip; RIP-Seq; RNA-binding proteins (RBPs); Ribonomics; mRNA localization

PMID:
24257445
PMCID:
PMC4004666
DOI:
10.1016/j.ymeth.2013.11.001
[Indexed for MEDLINE]
Free PMC Article

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