Alternative pre-mRNA splicing in Drosophila spliceosomal assembly factor RNP-4F during development

• Published in: Gene Vol. 371; no. 2; pp. 234 - 245
• Main Authors: Fetherson, Rebecca A., Strock, Stephen B., White, Kristen N., Vaughn, Jack C.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 26.04.2006
• Subjects: 5' Untranslated Regions; 5′-UTR; Alternative Splicing; Animals; Base Sequence; Blotting, Northern; cis-regulatory elements; DNA; Drosophila; Drosophila melanogaster - genetics; Intron evolution; Introns; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleoproteins - genetics; RNA Precursors - genetics; RNA, Messenger - genetics; rnp-4f gene; Sequence Homology, Nucleic Acid; Spliceosomes - genetics; Alternative splicing; U-snRNP; cis-regulatory elements; nt; EST; mRNA; RRM; TI no; bp; PRP proteins; NLS; 5′-UTR; RNP-4F; RT-PCR; TPR; poly(A +); cDNA; rnp-4f gene; BLAST; CTM; PCR; PTC; Intron evolution
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2005.12.025

The 5′- and 3′-UTR regions in pre-mRNAs play a variety of roles in controlling eukaryotic gene expression, including translational modulation. Here we report the results of a systematic study of alternative splicing in rnp-4f, which encodes a Drosophila spliceosomal assembly factor. We show that most of the nine introns are constitutively spliced, but several patterns of alternative splicing are observed in two pre-mRNA regions including the 5′-UTR. Intron V is shown to be of recent evolutionary origin and is infrequently spliced, resulting in generation of an in-frame stop codon and a predicted truncated protein lacking a nuclear localization signal, so that alternative splicing regulates its subcellular localization. Intron 0, located in the 5′-UTR, is subject to three different splicing decisions in D. melanogaster. Northern analysis of poly(A +) mRNAs reveals two differently sized rnp-4f mRNA isoforms in this species. A switch in relative isoform abundance occurs during mid-embryo stages, when the larger isoform becomes more abundant. This isoform is shown to represent intron 0 unspliced mRNA, whereas the smaller transcript represents the product of alternative splicing. Comparative genomic analysis predicts that intron 0 is present in diverse Drosophila species. Intron 0 splicing results in loss of an evolutionarily conserved stem-loop constituting a potential cis-regulatory element at the 3′-splice site. A model is proposed for the role of this element both in 5′-UTR alternative splicing decisions and in RNP-4F translational modulation. Preliminary evidences in support of our model are discussed.