Trends in Molecular Medicine
ReviewSmall RNA Modifications: Integral to Function and Disease
Section snippets
A Glimpse into RNA Modifications
RNAs are post-transcriptionally altered with a variety of chemical modifications in all domains of life. More than 100 types of RNA modification have been identified to date, in many cases showing context-dependent functions that are only beginning to become clear [1]. Post-transcriptional modifications are known to be especially prevalent in stable, structured RNAs such as tRNA and rRNA where they play important roles in biogenesis, correct structural folding, and function [2]. Emerging
2′-O-Methylation in Small RNAs: Stability and Beyond
miRNAs are key players in RNA silencing pathways inducing mRNA degradation, translational repression, and transcriptional silencing [17]. 2′-O-Methylation, mediated by HUA enhancer 1 (HEN1), was first recognized in plants [18], where it protects miRNAs from small RNA decay pathways that are triggered by 3′-uridylation 19, 20, a well-characterized RNA decay pathway [21] (Figure 2A). Although mature miRNAs in animals lack 2′-O-methylation, other mammalian small RNAs such as siRNAs and
m5C: A Stress Sensor and Transgenerational Mark in tRNA and tsRNAs
m5Cs are frequently detected in various non-coding RNAs such as tRNA, rRNA, and, more recently, mRNAs. While the full range of potential functions for m5C in RNA is not completely understood, bisulfite RNA sequencing, which pinpoints m5C residues [31], has helped reveal the importance of these residues in tRNAs 32, 33, 34, 35, 36. One group has shown that m5C modifications of tRNAs by the methyltransferases DNA methyltransferase 2 (Dnmt2) and NOP2/Sun RNA methyltransferase family member 2
RNA Editing Events in Small RNAs: Biology and Disease Associations
RNA editing is a process that alters the primary nucleotide sequence of RNA by specific enzymes. The chief distinction between RNA editing and RNA modification is that editing is usually irreversible and generally understood to produce altered base-pairing behavior. RNA editing events are widely observed in mRNA, tRNA, rRNA, and miRNA in all kingdoms of life. The most frequent editing events are deaminations that convert adenosine to inosine (A to I) and cytidine to uridine (C to U) [52].
Profiling Small RNA Modifications As Biomarkers of Disease
Several different approaches have been used for high-throughput analysis of RNA modifications; each has different strengths in terms of its ability to monitor specific RNA modifications, characterize global modification profiles in biological samples, or reveal the identity of modified RNAs with sequence-level specificity. Antibody-based detection of modified small RNAs has shown promise as a sensitive diagnostic for identifying early markers of disease. For example, m1A antibodies can detect
Emerging Methods for Profiling and Mapping RNA Modifications in Small RNAs
While LC-MS/MS is a powerful approach for quantifying the compositional changes of RNA modifications, this method requires digestion of RNAs into short segments or single nucleosides before detection, therefore making it difficult to unambiguously assign modifications to specific transcripts (Figure 4A) 51, 66, 67. Thus, complementary approaches to map RNA modifications to specific RNAs are required to gain a more comprehensive view of modified small RNAs.
Sequencing-based protocols have been
Concluding Remarks: How Many New Bits of Information?
Compared with the accelerating rate of discovery of many types of small RNAs [75], the study of small RNA modifications in biology and disease remains in its infancy. Emerging evidence indicates that RNA modifications are important molecular markers that can alter the biogenesis, function, and informational capacity of small RNAs. New techniques including high-throughput LC-MS/MS and sequencing-based approaches that specifically target modified RNAs using antibodies, enzymatic treatments, or
Acknowledgments
This research was partially supported by the NIH/NHGRI (HG006753-02 to T.M.L, P30GM110767-03 to Q.C.) and start-up support from the University of Nevada, Reno School of Medicine (to Q.C.).
Glossary
- Bisulfite RNA sequencing
- method to detect m5C methylation patterns in RNAs by bisulfite treatment of RNAs.
- cDNA library preparation
- synthesis of single-strand complementary DNAs from RNA samples by reverse transcription.
- Eraser
- a demethylase or associated enzymatic complex that removes RNA modifications.
- P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs)
- the largest class of small non-coding RNAs expressed in animal cells; form RNA–protein complexes with PIWI proteins.
- Reader
- proteins that
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These authors contributed equally to this work.