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

Manli Shen; Eduardo Eyras; Jie Wu; Amit Khanna; Serene Josiah; Mathieu Rederstorff; Michael Q. Zhang; Stefan Stamm

doi:10.1093/nar/gkr684

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

Manli Shen, Eduardo Eyras, Jie Wu, Amit Khanna, Serene Josiah, Mathieu Rederstorff, Michael Q. Zhang, Stefan Stamm

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

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.

Original language	English
Pages (from-to)	9720-9730
Number of pages	11
Journal	Nucleic Acids Research
Volume	39
Issue number	22
DOIs	https://doi.org/10.1093/nar/gkr684
State	Published - Dec 2011

Bibliographical note

Funding Information:
National Institutes of Health (RO1 GM083187 to S.S.; NIH GM074688 to M.Z.); the Prader-Willi Research Foundation USA and Shire Human Genetic Therapies; European Comission project EURASNET-LSHG-CT-2005-518238 (to S.S. and E.E.); Spanish Ministry of Science grant BIO2008-01091 (to E.E.). Funding for open access charge: National Institutes of Health (RO1 GM083187).

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkr684

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title = "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",

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.",

author = "Manli Shen and Eduardo Eyras and Jie Wu and Amit Khanna and Serene Josiah and Mathieu Rederstorff and Zhang, {Michael Q.} and Stefan Stamm",

note = "Funding Information: National Institutes of Health (RO1 GM083187 to S.S.; NIH GM074688 to M.Z.); the Prader-Willi Research Foundation USA and Shire Human Genetic Therapies; European Comission project EURASNET-LSHG-CT-2005-518238 (to S.S. and E.E.); Spanish Ministry of Science grant BIO2008-01091 (to E.E.). Funding for open access charge: National Institutes of Health (RO1 GM083187).",

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Shen, M, Eyras, E, Wu, J, Khanna, A, Josiah, S, Rederstorff, M, Zhang, MQ & Stamm, S 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, vol. 39, no. 22, pp. 9720-9730. https://doi.org/10.1093/nar/gkr684

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AU - Shen, Manli

AU - Eyras, Eduardo

AU - Wu, Jie

AU - Khanna, Amit

AU - Josiah, Serene

AU - Rederstorff, Mathieu

AU - Zhang, Michael Q.

AU - Stamm, Stefan

N1 - Funding Information: National Institutes of Health (RO1 GM083187 to S.S.; NIH GM074688 to M.Z.); the Prader-Willi Research Foundation USA and Shire Human Genetic Therapies; European Comission project EURASNET-LSHG-CT-2005-518238 (to S.S. and E.E.); Spanish Ministry of Science grant BIO2008-01091 (to E.E.). Funding for open access charge: National Institutes of Health (RO1 GM083187).

PY - 2011/12

Y1 - 2011/12

N2 - 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.

AB - 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.

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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

Abstract

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