Genome-wide analysis of pre-mRNA splicing

Sapra, Aparna K. ; Arava, Yoav ; Khandelia, Piyush ; Vijayraghavan, Usha (2004) Genome-wide analysis of pre-mRNA splicing Journal of Biological Chemistry, 279 (50). pp. 52437-52446. ISSN 0021-9258

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Official URL: http://www.jbc.org/content/279/50/52437.short

Related URL: http://dx.doi.org/10.1074/jbc.M408815200

Abstract

Removal of pre-mRNA introns is an essential step in eukaryotic genome interpretation. The spliceosome, a ribonucleoprotein performs this critical function; however, precise roles for many of its proteins remain unknown. Genome-wide consequences triggered by the loss of a specific factor can elucidate its function in splicing and its impact on other cellular processes. We have employed splicing-sensitive DNA microarrays, with yeast open reading frames and intron sequences, to detect changes in splicing efficiency and global expression. Comparison of expression profiles, for intron-containing transcripts, among mutants of two second-step factors, Prp17 and Prp22, reveals their unique and shared effects on global splicing. This analysis enabled the identification of substrates dependent on Prp17. We find a significant Prp17 role in splicing of introns which are longer than 200nts and note its dispensability when introns have a ≤13-nucleotide spacing between their branch point nucleotide and 3' splice site. In vitro splicing of substrates with varying branch nucleotide to 3' splice site distances supports the differential Prp17 dependencies inferred from the in vivo analysis. Furthermore, we tested the predicted dispensability of Prp17 for splicing short introns in the evolutionarily distant yeast, Schizosaccharomyces pombe, where the genome contains predominantly short introns. SpPrp17 was non-essential at all growth temperatures implying that functional evolution of splicing factors is integrated with genome evolution. Together our studies point to a role for budding yeast Prp17 in splicing of subsets of introns and have predictive value for deciphering the functions of splicing factors in gene expression and regulation in other eukaryotes.

Item Type:Article
Source:Copyright of this article belongs to The American Society for Biochemistry and Molecular Biology.
ID Code:58578
Deposited On:31 Aug 2011 12:09
Last Modified:31 Aug 2011 12:09

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