Mounting an effective host immune response without incurring inflammatory injury requires the precise regulation of cytokine expression. To achieve this, cytokine mRNAs are post-transcriptionally regulated by diverse RNA-binding proteins and microRNAs (miRNAs) targeting their 3' untranslated regions (UTRs). Zcchc11 (zinc-finger, CCHC domain-containing protein 11) contains RNA-interacting motifs, and has been implicated in signalling pathways involved in cytokine expression. The nature of the Zcchc11 protein and how it influences cytokine expression are unknown. Here we show that Zcchc11 directs cytokine expression by uridylating cytokine-targeting miRNAs. Zcchc11 is a ribonucleotidyltransferase with a preference for uridine and is essential for maintaining the poly(A) tail length and stability of transcripts for interleukin-6 (IL-6) and other specific cytokines. The miR-26 family of miRNAs targets IL-6, and the addition of terminal uridines to the miR-26 3' end abrogates IL-6 repression. Whereas 78% of miR-26a sequences in control cells contained 1-3 uridines on their 3' ends, less than 0.1% did so in Zcchc11-knockdown cells. Thus, Zcchc11 fine tunes IL-6 production by uridylating miR-26a, which we propose is an enzymatic modification of the terminal nucleotide sequence of mature miRNA as a means to regulate gene expression.
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"RNAs less stable (Scott and Norbury, 2013). In mammalian cells, ZCCHC11, a terminal uridyltransferase also known as TUT4, mediates terminal uracil additions of miR-26a, thereby abolishing its function, albeit its relative abundance appears unaffected (Jones et al., 2009). Enrichment of 3 0 uridylated "
[Show abstract][Hide abstract] ABSTRACT: Functional biomolecules, including small noncoding RNAs (ncRNAs), are released and transmitted between mammalian cells via extracellular vesicles (EVs), including endosome-derived exosomes. The small RNA composition in cells differs from exosomes, but underlying mechanisms have not been established. We generated small RNA profiles by RNA sequencing (RNA-seq) from a panel of human B cells and their secreted exosomes. A comprehensive bioinformatics and statistical analysis revealed nonrandomly distributed subsets of microRNA (miRNA) species between B cells and exosomes. Unexpectedly, 3' end adenylated miRNAs are relatively enriched in cells, whereas 3' end uridylated isoforms appear overrepresented in exosomes, as validated in naturally occurring EVs isolated from human urine samples. Collectively, our findings suggest that posttranscriptional modifications, notably 3' end adenylation and uridylation, exert opposing effects that may contribute, at least in part, to direct ncRNA sorting into EVs.
"The addition of non-templated nucleotides to the 3′ ends of RNA molecules is a widespread mechanism for their regulation. Beyond the familiar long poly(A) tails of messenger RNAs, short 3′ tailing of uridine [1-4] and adenosine [5-7] nucleotides to noncoding RNAs is gathering increasing appreciation. These simple oligonucleotide additions (one to ~20 identical bases) can alter the stability, binding partners or activity of the enzymatic reactions in which these RNAs participate. "
[Show abstract][Hide abstract] ABSTRACT: Post-transcriptional 3[prime] end processing is a key component of RNA regulation. The abundant and essential RNA subunit of RNase MRP has been proposed to function in three distinct cellular compartments and therefore may utilize this mode of regulation. Here we employ 3[prime] RACE coupled with high-throughput sequencing to characterize the 3[prime] terminal sequences of human MRP RNA and other noncoding RNAs that form RNP complexes.
The 3[prime] terminal sequence of MRP RNA from HEK293T cells has a distinctive distribution of genomically encoded termini (including an assortment of U residues) with a portion of these selectively tagged by oligo(A) tails. This profile contrasts with the relatively homogenous 3[prime] terminus of an in vitro transcribed MRP RNA control and the differing 3[prime] terminal profiles of U3 snoRNA, RNase P RNA, and telomerase RNA (hTR).
3[prime] RACE coupled with deep sequencing provides a valuable framework for the functional characterization of 3[prime] terminal sequences of noncoding RNAs.
"In addition to miRNA precursors, mature small RNAs can also be uridylated, with different consequences on their stability. In mammals, uridylation can abrogate miRNA activity without affecting miRNA stability (7,8). However, uridylation can also trigger the degradation of miRNA and siRNA as shown in Caenorhabditis elegans, zebrafish, Chlamydomonas reinhardtii or Arabidopsis (9–13). "
[Show abstract][Hide abstract] ABSTRACT: Degradation of mRNAs is usually initiated by deadenylation, the shortening of long poly(A) tails to oligo(A) tails of 12–15
As. Deadenylation leads to decapping and to subsequent 5′ to 3′ degradation by XRN proteins, or alternatively 3′ to 5′ degradation
by the exosome. Decapping can also be induced by uridylation as shown for the non-polyadenylated histone mRNAs in humans and
for several mRNAs in Schizosaccharomyces pombe and Aspergillus nidulans. Here we report a novel role for uridylation in preventing 3′ trimming of oligoadenylated mRNAs in Arabidopsis. We show that
oligo(A)-tailed mRNAs are uridylated by the cytosolic UTP:RNA uridylyltransferase URT1 and that URT1 has no major impact on
mRNA degradation rates. However, in absence of uridylation, oligo(A) tails are trimmed, indicating that uridylation protects
oligoadenylated mRNAs from 3′ ribonucleolytic attacks. This conclusion is further supported by an increase in 3′ truncated
transcripts detected in urt1 mutants. We propose that preventing 3′ trimming of oligo(A)-tailed mRNAs by uridylation participates in establishing the
5′ to 3′ directionality of mRNA degradation. Importantly, uridylation prevents 3′ shortening of mRNAs associated with polysomes,
suggesting that a key biological function of uridylation is to confer 5′ to 3′ polarity in case of co-translational mRNA decay.
Full-text · Article · Jun 2013 · Nucleic Acids Research