RNA Processing Events Affecting C. elegans Operons: A Computational and Mutational Analysis

In C. elegans, the combined actions of trans-splicing, 3’ end formation and inhibition of transcription termination by RNA polymerase II (Pol II) are necessary to generate monocistronic transcripts from primary polycistronic transcripts. However, how these processes are regulated to create functional monocistronic units out of polycistronic transcripts is poorly understood. From a global perspective, certain transcripts are trans-spliced to either SL1, SL2 or both. The genes encoding SL1 trans-spliced transcripts have longer distances between the trans-splice site and the nearest upstream gene, and also have evidence of promoters adjacent to the trans-splice sites. The converse is true for genes encoding SL2 trans-spliced transcripts. These properties demonstrate that the genes of SL2 trans-spliced transcripts are located within operons. The transcripts that are trans-spliced to a mixture of SL1/SL2, share features of both the SL1 and SL2 groups. These transcripts can be produced from two promoters: an operon promoter and an adjacent promoter. Using a unique mutation within a C. elegans operon that alters transcription termination, I demonstrate that, cids-1 and cids-2, proteins that bind to Pol II and, SRp20, known as an alternative splicing factor have effects on operon transcription. In this context, Both CIDS-1 and CIDS-2 are able to enhance 3’ end formation. In the same context, SRp20 enhances either transcription termination and/or RNA degradation downstream of the 3’ cleavage site. These proteins may have similar roles in 3’ end formation and transcription termination in other genes and organisms as they are conserved across species