Alternative splicing of an rnp-4f mRNA isoform retaining an evolutionarily-conserved 5′-UTR intronic element is developmentally regulated and shown via RNAi to be essential for normal central nervous system development in Drosophila melanogaster

• Published in: Gene Vol. 399; no. 2; pp. 91 - 104
• Main Authors: Chen, Jing, Concel, Vincent J., Bhatla, Sunetra, Rajeshwaran, Rajkumar, Smith, Darcey L.H., Varadarajan, Malini, Backscheider, Kimberly L., Bockrath, Robyn A., Petschek, Jane P., Vaughn, Jack C.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.09.2007
• Subjects: 5' Untranslated Regions; 5′-UTR intron retention; Alternative Splicing; Animals; Central Nervous System - embryology; Central Nervous System - metabolism; Drosophila melanogaster; Drosophila melanogaster - embryology; Drosophila melanogaster - genetics; Drosophila melanogaster - metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Embryo, Nonmammalian - metabolism; Gene Expression Regulation, Developmental; Introns; mRNA isoform; Ribonucleoproteins - genetics; Ribonucleoproteins - metabolism; RNA Interference; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNAi knockdown; Translation modulation; Alternative splicing; nt; HRP; CNS; kDa; mRNA; RRM; bp; BSA; NLS; 5′-UTR; RT-PCR; TPR; cDNA; BLAST; MBT; DIC; dsRNA; RNAi; U-snRNP; DIG; mRNA isoform; DAB; RNAi knockdown; rRNA; 3′-UTR; PRP proteins; PMSF; RNP-4F; GAR; poly(A +); CTM; PCR; Translation modulation; 5′-UTR intron retention
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2007.04.038

Two major mRNA isoforms arise via alternative splicing in the 5′-UTR of Drosophila splicing assembly factor rnp-4f pre-mRNA, designated “long” (unspliced) and “short” (alternatively spliced). The coding potential for the two isoforms is identical, raising interesting questions as to the control mechanism and functional significance of this 5′-UTR intronic splicing decision. Developmental Northerns show that two temporally distinct rnp-4f mRNA degradation episodes occur during embryogenesis. The first occurs at the midblastula transition (MBT) stage and involves degradation of both maternally-derived transcripts, while the second involves only the long mRNA isoform and occurs during late embryo stages. Immunostaining of ovaries and staged embryos combined with results from developmental Westerns shows that maternal RNP-4F protein persists into fertilized eggs at high levels, associated with a burst of long isoform-specific transcription which begins just after the MBT and peaks in mid-embryo stages. These observations are discussed in support of a putative negative feedback control model for modulation of RNP-4F translation. In situ hybridization shows that the long isoform is relatively abundant throughout the developing embryonic germ band and central nervous system (CNS), especially along the dorsal roof of the ventral nerve cord. Long rnp-4f mRNA knockdown via RNAi reveals a variety of CNS abnormalities, which leads us to postulate that this isoform acts upstream of other genes which have been shown to be important for normal CNS development.