||March 7, 2011
||Assoc. Prof. Mikita Suyama, Graduate School of Medicine, Kyoto University
||Searching for regulatory sequences of alternative splicing by using genome sequence alignment and RNA-seq data
Cis-acting short sequence motifs play important roles in alternative
splicing. It is now possible to identify such sequence motifs as
conserved sequence patterns in genome sequence alignments. We
systematically analyzed the motifs in the neighboring introns of skipped
exons (cassette exons) by using comparative analysis of mammalian genome
alignments. We identified 11 conserved sequence motifs that might be
involved in the regulation of alternative splicing. These motifs are not
only significantly overrepresented near alternatively spliced exons, but
they also co-occur with each other, thus, forming a network of
cis-elements, likely to be the basis for context-dependent regulation.
Now I expand the analysis to mutually exclusive splicing, one of the
most strictly regulated patterns of alternative splicing, by using
RNA-seq data from next-generation sequencing platforms.