Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

Li, Zhihua, Ender, Christine, Meister, Gunter, Moore, Patrick S., Chang, Yuan and John, Bino (2012) Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Research, 40 14: 6787-6799. doi:10.1093/nar/gks307

Author Li, Zhihua
Ender, Christine
Meister, Gunter
Moore, Patrick S.
Chang, Yuan
John, Bino
Title Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2012-08-01
Sub-type Article (original research)
DOI 10.1093/nar/gks307
Open Access Status DOI
Volume 40
Issue 14
Start page 6787
End page 6799
Total pages 13
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Abstract Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations. More recently, ribosome-associated mRNA profiling has emerged as an alternative and a robust way of identifying translating mRNAs, which are a set of mRNAs associated with ribosomes and more likely to contribute to proteome abundance. In this article, we briefly review recent studies that examined the processes affecting the abundance of translating mRNAs, their regulation during plant development and tolerance to stress conditions and plant factors affecting the selection of translating mRNA pools. This review also highlights recent findings revealing differential roles of alternatively spliced mRNAs and their translational control during stress adaptation. Overall, better understanding of processes involved in the regulation of translating mRNAs has obvious implications for improvement of stress tolerance in plants.
Formatted abstract
Deep sequencing studies frequently identify small RNA fragments of abundant RNAs. These fragments are thought to represent degradation products of their precursors. Using sequencing, computational analysis, and sensitive northern blot assays, we show that constitutively expressed non-coding RNAs such as tRNAs, snoRNAs, rRNAs and snRNAs preferentially produce small 5′ and 3′ end fragments. Similar to that of microRNA processing, these terminal fragments are generated in an asymmetric manner that predominantly favors either the 5′ or 3′ end. Terminal-specific and asymmetric processing of these small RNAs occurs in both mouse and human cells. In addition to the known processing of some 3′ terminal tRNA-derived fragments (tRFs) by the RNase III endonuclease Dicer, we show that several RNase family members can produce tRFs, including Angiogenin that cleaves the TψC loop to generate 3′ tRFs. The 3′ terminal tRFs but not the 5′ tRFs are highly complementary to human endogenous retroviral sequences in the genome. Despite their independence from Dicer processing, these tRFs associate with Ago2 and are capable of down regulating target genes by transcript cleavage in vitro. We suggest that endogenous 3′ tRFs have a role in regulating the unwarranted expression of endogenous viruses through the RNA interference pathway.
Keyword development
ribosomal associations
translational regulation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 84 times in Thomson Reuters Web of Science Article | Citations
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Created: Mon, 05 Nov 2012, 18:54:01 EST by Susan Allen on behalf of Institute for Molecular Bioscience