Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing.
The conserved pre-mRNA splicing factor SF1 is implicated in 3' splice site recognition by binding directly to the intron branch site. However, because SF1 is not essential for constitutive splicing, its role in pre-mRNA processing has remained mysterious. Here, we used crosslinking and immunoprecipitation (CLIP) to analyze short RNAs directly bound by human SF1 in vivo. SF1 bound mainly pre-mRNAs, with 77% of target sites in introns. Binding to target RNAs in vitro was dependent on the newly defined SF1 binding motif ACUNAC, strongly resembling human branch sites. Surprisingly, the majority of SF1 binding sites did not map to the expected position near 3' splice sites. Instead, target sites were distributed throughout introns, and a smaller but significant fraction occurred in exons within coding and untranslated regions. These data suggest a more complex role for SF1 in splicing regulation. Indeed, SF1 silencing affected alternative splicing of endogenous transcripts, establishing a previously unexpected role for SF1 and branch site-like sequences in splice site selection.
Department of Cell Biology, Faculty of Sciences, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva.
Margherita
M
Corioni
Nicolas
N
Antih
Goranka
G
Tanackovic
Mihaela
M
Zavolan
Angela
A
Krämer
D017398:Alternative Splicing; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism / Q000502:physiology*; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000378:metabolism; D034622:RNA Interference; D012322:RNA Precursors / Q000302:isolation & purification / Q000378:metabolism*; D000072260:RNA Splicing Factors; D012333:RNA, Messenger / Q000302:isolation & purification / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism / Q000502:physiology*; D012261:Ribonucleoproteins / Q000378:metabolism; D000072668:Splicing Factor U2AF; D014157:Transcription Factors / Q000037:antagonists & inhibitors / Q000378:metabolism / Q000502:physiology*
D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D012322:RNA Precursors; D000072260:RNA Splicing Factors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; C107467:SF1 protein, human; D000072668:Splicing Factor U2AF; D014157:Transcription Factors; C000607494:U2AF2 protein, human