title: Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA.
abstract: Accurate pre-mRNA splicing is crucial for gene expression. The 5' splice site (5' ss)--the highly diverse element at the 5' end of introns--is initially recognized via base-pairing to the 5' end of the U1 small nuclear RNA (snRNA). However, many natural 5' ss have a poor match to the consensus sequence, and are predicted to be weak. Using genetic suppression experiments in human cells, we demonstrate that some atypical 5' ss are actually efficiently recognized by U1, in an alternative base-pairing register that is shifted by one nucleotide. These atypical 5' ss are phylogenetically widespread, and many of them are conserved. Moreover, shifted base-pairing provides an explanation for the effect of a 5' ss mutation associated with pontocerebellar hypoplasia. The unexpected flexibility in 5' ss-U1 base-pairing challenges an established paradigm and has broad implications for splice-site prediction algorithms and gene-annotation efforts in genome projects.
authors.affiliation: Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Xavier
authors.initials: X
authors.lastname: Roca
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D006367:HeLa Cells; D006801:Humans; D009690:Nucleic Acid Conformation; D022821:RNA Splice Sites; D012326:RNA Splicing; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000378:metabolism*
chemical_list: D022821:RNA Splice Sites; D012342:RNA, Small Nuclear; C405483:U1 small nuclear RNA