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.
Document Type
Article
Publication Date
2011
Digital Object Identifier (DOI)
http://dx.doi.org/10.1093/nar/gkr684
Repository Citation
Shen, Manli; Eyras, Eduardo; Wu, Jie; Khanna, Amit; Josiah, Serene; Rederstorff, Mathieu; Zhang, Michael Q.; and Stamm, Stefan, "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" (2011). Molecular and Cellular Biochemistry Faculty Publications. 55.
https://uknowledge.uky.edu/biochem_facpub/55
Supplementary Data
Notes/Citation Information
Published in Nucleic Acids Research, v. 39, no. 22, p. 9720-9730.
© The Author(s) 2011. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.