Microarray analysis of RNA processing and modification.
Most RNAs are processed from precursors by mechanisms that include covalent modifications, as well as the removal of flanking and intervening sequences. Traditional methods to detect RNA processing, such as Northern blotting, reverse-transcribed polymerase chain reaction and primer extension assays, are difficult to apply on a large scale. This chapter outlines several methods for analysis of the processing and modification of RNA using microarrays. These encompass protocols for the application of homemade microarrays and custom-designed commercial inkjet microarrays and are tailored for the large-scale analysis of processing of mRNA, including alternative splicing, as well as for the analysis of processing and modification of noncoding RNA. This chapter also describes practical aspects of microarray design, sample preparation, hybridization, and data analysis.
Hughes
Timothy R
TR
Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
Hiley
Shawna L
SL
Saltzman
Arneet L
AL
Babak
Tomas
T
Blencowe
Benjamin J
BJ
D000818:Animals; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000032:analysis* / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D017423:Sequence Analysis, RNA / Q000379:methods*
D012313:RNA