Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression

Shen, M. L., Eyras, E., Wu, J., Khanna, A., Josiah, S., Rederstorff, M., Zhang, M. Q., Stamm, S. (December 2011) Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Research, 39 (22). pp. 9720-9730. ISSN 0305-1048

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Abstract

We describe a new method that allows cloning of double-stranded RNAs (dsRNAs) that are generated in RNase protection experiments. We demonstrate that the mouse C/D box snoRNA MBII-85 (SNORD116) is processed into at least five shorter RNAs using processing sites near known functional elements of C/D box snoRNAs. Surprisingly, the majority of cloned RNAs from RNase protection experiments were derived from endogenous cellular RNA, indicating widespread antisense expression. The cloned dsRNAs could be mapped to genome areas that show RNA expression on both DNA strands and partially overlapped with experimentally determined argonaute-binding sites. The data suggest a conserved processing pattern for some C/D box snoRNAs and abundant expression of longer, non-coding RNAs in the cell that can potentially form dsRNAs.

Item Type: Paper
Uncontrolled Keywords: generation fragments cluster genome
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > dsRNA
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: December 2011
Date Deposited: 05 Feb 2013 14:39
Last Modified: 05 Feb 2013 14:39
PMCID: PMC3239178
Related URLs:
URI: https://repository.cshl.edu/id/eprint/27218

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