Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing

Hitoshi Suzuki, Yuhong Zuo, Jinhua Wang, Michael Q. Zhang, Arun Malhotra, Akila Mayeda

Research output: Contribution to journalArticle

211 Citations (Scopus)

Abstract

Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence of excised introns in total cellular RNA, we used three Escherichia coli 3′ to 5′ exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades the abundant linear RNAs and the Y-structure RNA, while preserving the loop portion of a lariat RNA. Ribonuclease II (RNase II) and polynucleotide phosphorylase (PNPase) also preserve the lariat loop, but are less efficient in degrading linear RNAs. RNase R digestion of the total RNA from human skeletal muscle generates an RNA pool consisting of lariat and circular RNAs. RT-PCR across the branch sites confirmed lariat RNAs and circular RNAs in the pool generated by constitutive and alternative splicing of the dystrophin pre-mRNA. Our results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented. The highly specific activity of RNase R implies its ability to screen for rare intragenic trans-splicing in any target gene with a large background of cis-splicing. Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing.

Original languageEnglish
Article numbere63
JournalNucleic Acids Research
Volume34
Issue number8
DOIs
StatePublished - Jul 10 2006

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RNA Precursors
RNA
Introns
Trans-Splicing
Alternative Splicing
Exons
ribonuclease R
circular RNA
Polyribonucleotide Nucleotidyltransferase
Dystrophin
Gene Library
Digestion
Skeletal Muscle
Escherichia coli
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Genetics

Cite this

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. / Suzuki, Hitoshi; Zuo, Yuhong; Wang, Jinhua; Zhang, Michael Q.; Malhotra, Arun; Mayeda, Akila.

In: Nucleic Acids Research, Vol. 34, No. 8, e63, 10.07.2006.

Research output: Contribution to journalArticle

Suzuki, Hitoshi ; Zuo, Yuhong ; Wang, Jinhua ; Zhang, Michael Q. ; Malhotra, Arun ; Mayeda, Akila. / Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. In: Nucleic Acids Research. 2006 ; Vol. 34, No. 8.
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