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RNA-binding protein immunopurification-microarray (RIP-Chip) analysis to profile localized RNAs
- Source :
- Methods in molecular biology (Clifton, N.J.). 714
- Publication Year :
- 2011
-
Abstract
- Post-transcriptional gene regulation is largely mediated by RNA-binding proteins (RBPs) that modulate mRNA expression at multiple levels, from RNA processing to translation, localization, and degradation. Thereby, the genome-wide identification of mRNAs regulated by RBPs is crucial to uncover post--transcriptional gene regulatory networks. In this chapter, we provide a detailed protocol for one of the techniques that has been developed to systematically examine RNA targets for RBPs. This technique involves the purification of endogenously formed RBP-mRNA complexes with specific antibodies from cellular extracts, followed by the identification of associated RNAs using DNA microarrays. Such RNA-binding protein immunopurification-microarray profiling, also called RIP-Chip, has also been applied to identify mRNAs that are transported to distinct subcellular compartments by RNP-motor complexes. The application and further development of this method could provide global insights into the subcellular architecture of the RBP-RNA network, and how it is restructured upon changing environmental conditions, during development, and possibly in disease.
- Subjects :
- Cell Extracts
Time Factors
Sepharose
Color
Nucleic Acid Hybridization
RNA-Binding Proteins
Nerve Tissue Proteins
Antibodies
Microspheres
RNA Transport
Ribonucleoproteins
Antibody Specificity
Animals
Humans
RNA
RNA, Antisense
Staphylococcal Protein A
Edetic Acid
Fluorescent Dyes
Oligonucleotide Array Sequence Analysis
Subjects
Details
- ISSN :
- 19406029
- Volume :
- 714
- Database :
- OpenAIRE
- Journal :
- Methods in molecular biology (Clifton, N.J.)
- Accession number :
- edsair.pmid..........faa1e921f9e24ba486221825198c621a