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Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis

¹ Institute of Biochemistry, Justus-Liebig-University of Giessen, D-35392 Giessen, Germany
² Genomics Core Facility, EMBL, D-69117 Heidelberg, Germany

Alternative mRNA splicing patterns are determined by the combinatorial control of regulator proteins and their target RNA sequences. We have recently characterized human hnRNP L as a global regulator of alternative splicing, binding to diverse C/A-rich elements. To systematically identify hnRNP L target genes on a genome-wide level, we have combined splice-sensitive microarray analysis and an RNAi-knockdown approach. As a result, we describe 11 target genes of hnRNP L that were validated by RT-PCR and that represent several new modes of hnRNP L-dependent splicing regulation, involving both activator and repressor functions: first, intron retention; second, inclusion or skipping of cassette-type exons; third, suppression of multiple exons; and fourth, alternative poly(A) site selection. In sum, this approach revealed a surprising diversity of splicing-regulatory processes as well as poly(A) site selection in which hnRNP L is involved.

Keywords: splicing; alternative splicing, hnRNP; polyadenylation; microarray

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