Suzuki, H., Zuo, Y., Wang, J., Zhang, M. Q., Malhotra, A., Mayeda, A. (2006) Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Research, 34 (8). ISSN 03051048
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. © 2006 Oxford University Press.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Escherichia coli protein exoribonuclease messenger RNA RNA RNA precursor RNA splicing Escherichia coli Proteins Exoribonucleases RNA RNA Precursors RNA Splicing RNA, Messenger |
| Subjects: | organism description > bacteria > escherichia coli bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > introns bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > lRNA bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > lRNA > linear_RNA |
| CSHL Authors: | |
| Communities: | CSHL labs > Zhang lab |
| Depositing User: | CSHL Librarian |
| Date: | 2006 |
| Date Deposited: | 08 Dec 2011 18:17 |
| Last Modified: | 27 Apr 2018 19:31 |
| PMCID: | PMC1458517 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/22912 |
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