Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling.
In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs to facilitate gene expression patterns. On this basis, post-transcriptional and transcriptional gene expression networks appear to be very analogous. Our previous research focused on targeting RBPs to develop a better understanding of post-transcriptional gene-expression processing and the regulation of mRNA networks. We developed technologies for purifying endogenously formed RBP-mRNA complexes from cellular extracts and identifying the associated messages using genome-scale, microarray technology, a method called ribonomics or RNA-binding protein immunoprecipitation-microarray (Chip) profiling or RIP-Chip. The use of the RIP-Chip methods has provided great insight into the infrastructure of coordinated eukaryotic post-transcriptional gene expression, insights which could not have been obtained using traditional RNA expression profiling approaches (1). This chapter describes the most current RIP-Chip techniques as we presently practice them. We also discuss some of the informatic aspects that are unique to analyzing RIP-Chip data.
Baroni
Timothy E
TE
Department of Biomedical Sciences, University at Albany-SUNY, School of Public Health, Rensselaer, NY, USA.
Chittur
Sridar V
SV
George
Ajish D
AD
Tenenbaum
Scott A
SA
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers; D047468:Immunoprecipitation / Q000379:methods* / Q000706:statistics & numerical data / Q000639:trends; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D040081:Protein Array Analysis / Q000379:methods* / Q000706:statistics & numerical data / Q000639:trends; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000302:isolation & purification* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012261:Ribonucleoproteins / Q000302:isolation & purification / Q000378:metabolism
D017931:DNA Primers; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; C026452:messenger ribonucleoprotein