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Abstract

RNA is a versatile informational molecule. Besides carrying information in the form of its linear primary sequence, RNA can adopt various structures. Secondary and tertiary structured RNA offer a higher level of structural information that influences various steps of gene regulation. Pre-mRNA splicing is a defining feature of eukaryotic genomes. There is a wealth of information on regulatory signatures within introns that dictate splicing in terms of cis-elements such as primary sequence, and trans elements such as proteins. Yet it is not known whether the next level of information coded by RNA, i.e., its tertiary structure, can regulate splicing. I wanted to investigate if the tertiary structure of intronic polycistronic microRNA cluster, pri-miR-17-92a can influence the splicing of its host transcript. ,To address this hypothesis, I first chose a -globin reporter gene and engineered the tertiary structured pri-miR-17-92a in its intron2. Using overexpression studies, I have addressed the effect of this tertiary structure on removal of both the introns of a -globin reporter transcript. The presence of tertiary structured pri-miR in a constitutively spliced -globin showed that it impedes splicing of upstream intron suggesting that effective miRNA processing is required for splicing. In vitro splicing assay of the -globin and its related transcript with the pri-miR was developed to address the kinetics of splicing. The slow kinetics of intron removal were observed with the TS-pri-miR suggesting that it might play a role in facilitating proper exon tethering and determining splicing choices of the host transcript. This could be a general mechanism by which intronic pri-miR clusters could regulate splicing. In its endogenous context of C13orf25, this tertiary structured pri-miR is important in regulating the abundance of various spliced forms that is a reflection of altered splice site choices of the host transcript.

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