An unexpected ending: Noncanonical 3′ end processing mechanisms

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
RNA (Impact Factor: 4.94). 12/2009; 16(2):259-66. DOI: 10.1261/rna.1907510
Source: PubMed


Proper 3' end processing of a nascent transcript is critical for the functionality of the mature RNA. Although it has long been thought that virtually all long RNA polymerase II transcripts terminate in a poly(A) tail that is generated by endonucleolytic cleavage followed by polyadenylation, noncanonical 3' end processing mechanisms have recently been identified at several gene loci. Unexpectedly, enzymes with well-characterized roles in other RNA processing events, such as tRNA biogenesis and pre-mRNA splicing, cleave these nascent transcripts to generate their mature 3' ends despite the presence of nearby polyadenylation signals. In fact, the presence of multiple potential 3' end cleavage sites is the norm at many human genes, and recent work suggests that the choice among sites is regulated during development and in response to cellular cues. It is, therefore, becoming increasing clear that the selection of a proper 3' end cleavage site represents an important step in the regulation of gene expression and that the mature 3' ends of RNA polymerase II transcripts can be generated via multiple mechanisms.

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Available from: Jeremy E Wilusz, Jun 09, 2015
    • "One major surprise that has come from studying the biogenesis of various long noncoding RNAs is that they can be processed in noncanonical ways (reviewed in [45] [46] [47]). Although most appear to be capped, spliced, and polyadenylated, some of the most abundant long noncoding RNAs transcribed by RNA polymerase II defy these dogmas. "
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    ABSTRACT: Most of the human genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs. Many of these transcripts have a 5' cap and a poly(A) tail, yet some of the most abundant long noncoding RNAs are processed in unexpected ways and lack these canonical structures. Here, I highlight the mechanisms by which several of these well-characterized noncoding RNAs are generated, stabilized, and function. The MALAT1 and MEN β (NEAT1_2) long noncoding RNAs each accumulate to high levels in the nucleus, where they play critical roles in cancer progression and the formation of nuclear paraspeckles, respectively. Nevertheless, MALAT1 and MEN β are not polyadenylated as the tRNA biogenesis machinery generates their mature 3' ends. In place of a poly(A) tail, these transcripts are stabilized by highly conserved triple helical structures. Sno-lncRNAs likewise lack poly(A) tails and instead have snoRNA structures at their 5' and 3' ends. Recent work has additionally identified a number of abundant circular RNAs generated by the pre-mRNA splicing machinery that are resistant to degradation by exonucleases. As these various transcripts use non-canonical strategies to ensure their stability, it is becoming increasingly clear that long noncoding RNAs may often be regulated by unique post-transcriptional control mechanisms. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy. Copyright © 2015. Published by Elsevier B.V.
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    • "Recent work has identified additional Pol II transcripts that are subjected to noncanonical 39 end processing mechanisms (for review, see Wilusz and Spector 2010). "
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    ABSTRACT: The MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) locus is misregulated in many human cancers and produces an abundant long nuclear-retained noncoding RNA. Despite being transcribed by RNA polymerase II, the 3' end of MALAT1 is produced not by canonical cleavage/polyadenylation but instead by recognition and cleavage of a tRNA-like structure by RNase P. Mature MALAT1 thus lacks a poly(A) tail yet is expressed at a level higher than many protein-coding genes in vivo. Here we show that the 3' ends of MALAT1 and the MEN β long noncoding RNAs are protected from 3'-5' exonucleases by highly conserved triple helical structures. Surprisingly, when these structures are placed downstream from an ORF, the transcript is efficiently translated in vivo despite the lack of a poly(A) tail. The triple helix therefore also functions as a translational enhancer, and mutations in this region separate this translation activity from simple effects on RNA stability or transport. We further found that a transcript ending in a triple helix is efficiently repressed by microRNAs in vivo, arguing against a major role for the poly(A) tail in microRNA-mediated silencing. These results provide new insights into how transcripts that lack poly(A) tails are stabilized and regulated and suggest that RNA triple-helical structures likely have key regulatory functions in vivo.
    Genes & development 10/2012; 26(21). DOI:10.1101/gad.204438.112 · 10.80 Impact Factor
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    • "Intragenic ERV integrants could introduce targets for heterochromatin formation that could disrupt full-length transcription in cis. Other possibilities also are plausible (Wilusz and Spector 2010). We identified about 100 intronic ERV candidates that may trigger premature transcriptional termination at a distance (Table 2), out of approximately 1025 genes displaying evidence for premature termination. "
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