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Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing

Aggarwal, Neha
http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397

Abstract Details

2010, Master of Science in Biology, Cleveland State University, College of Science.
Nuclear pre-mRNA splicing is an important step in eukaryotic RNA processing and can yield a variety of transcripts. Further, it is known that nuclear pre-mRNA introns are of two types, U2-dependent and U12-dependent. Recently discovered, microRNAs (miRNA) are short, endogenous, 20-22 nucleotide long, non-coding RNA molecules that base pair with target mRNAs to modulate translation. Current evidence suggests that processing of intronic miRNA does not affect the splicing. Since, intronic miRNAs are involved in essential cellular processes, we surmised if splice sites of miRNA coding introns are flexible to support productive precursor and mature miRNA processing. We constructed a minigene reporter consisting exons 26-29 including introns from MYH6 gene and an intronic miRNA, miR-208 harbored in intron 27. Using in vivo and in vitro methods, we examined splicing of MYH6 intron 27 and processing of miR-208. The predicted stem-loop structure of miR-208 and the 5’ splice site of the intron 27 were mutated. Stem-loop mutations had no recordable splicing defect of intron 27. The 5’SS mutant activated a cryptic splicing event using a sub-optimal splice site located 50 nucleotides upstream of wild-type splice site. Interestingly, conversion of U2-type 5' splice site to consensus U12-type 5' splice site did not affect in vivo splicing of the intron, suggesting potential conversion of intron to U12-type, albeit without a consensus U12-type branch site sequence. However, miRNA processing was affected as established by in vitro splicing assay and qRT-PCR analysis of miR-208. We mutated nucleotides from position 3 to 7 in intron 27 to study if changes in splice site will allow miRNA processing to occur and if splicing will also be affected. Our data indicates significant changes in spliced phenotype as well as in miR-208 expression level. Since, all known intronic miRNAs are harbored in U2-dependent introns of mammalian genes, we wanted to study if miRNA processing will be compatible with U12-dependent intron. With this aim, we incorporated miR-208 in a U12-dependent intron. However, it appears that spliceosome and microprocessor cannot act together in a U12-dependent intron. This is first time that a miRNA has been incorporated in a U12-dependent intron to study its processing and also if splice sites are plastic for miRNA processing.
Girish Shukla, PhD (Advisor)
Crystal Weyman, PhD (Committee Member)
Barsanjit Mazumder, PhD (Committee Member)
88 p.
Biology; Molecular Biology
microRNA processing; nuclear pre-mRNA splicing; miRNA; intron

Recommended Citations

Citations

  • Aggarwal, N. (2010). Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing [Master's thesis, Cleveland State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397

    APA Style (7th edition)

  • Aggarwal, Neha. Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing. 2010. Cleveland State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397.

    MLA Style (8th edition)

  • Aggarwal, Neha. "Characterization of a microRNA Harboring Intron for pre-mRNA Splicing and microRNA Processing." Master's thesis, Cleveland State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=csu1275407397

    Chicago Manual of Style (17th edition)

csu1275407397
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© 2010, all rights reserved.
This open access ETD is published by Cleveland State University and OhioLINK.