Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans.
Adjacent alternative 3' splice sites, those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron's 3' end depends upon sequence elements that define the branchpoint, polypyrimidine tract, and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched Caenorhabditis elegans samples, we identify hundreds of introns with adjacent alternative 3' splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is monodirectional, with somatic cells preferring to splice at the distal 3' splice site (furthest from the 5' end of the intron) and germline cells showing a distinct shift toward usage of the adjacent proximal 3' splice site (closer to the 5' end of the intron). Splicing patterns in somatic cells follow C. elegans consensus rules of 3' splice site definition; a short stretch of pyrimidines preceding an AG dinucleotide. Splicing in germline cells occurs at proximal 3' splice sites that lack a preceding polypyrimidine tract, and in three instances the germline-specific site lacks the AG dinucleotide. We provide evidence that use of germline-specific proximal 3' splice sites is conserved across Caenorhabditis species. We propose that there are differences between germline and somatic cells in the way that the basal splicing machinery functions to determine the intron terminus.
Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA;
James Matthew
JM
Ragle
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA;
Sol
S
Katzman
Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA;
Taylor F
TF
Akers
Gene Regulation, Stem Cells, and Cancer Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.
Sergio
S
Barberan-Soler
Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA;
Alan M
AM
Zahler
D017398:Alternative Splicing; D000818:Animals; D001482:Base Composition; D017173:Caenorhabditis elegans / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D005091:Exons; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D005854:Germ Cells / Q000378:metabolism; D007438:Introns; D009928:Organ Specificity / Q000235:genetics; D022821:RNA Splice Sites; D020871:RNA Stability; D016364:Reading Frames
D029742:Caenorhabditis elegans Proteins; D022821:RNA Splice Sites