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Global view of mRNA uridylation in Arabidopsis

ABSTRACT: To obtain a global view of mRNA uridylation in Arabidopsis, we generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant. The TAIL-seq protocol was recently developed to deep-sequence the 3' ends of RNAs (Chang et al., 2014).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE72457 | GEO | 2016/03/11

SECONDARY ACCESSION(S): PRJNA294090

REPOSITORIES: GEO

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Global view of mRNA uridylation in Arabidopsis

Project description:To obtain a global view of mRNA uridylation in Arabidopsis, we generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant. The TAIL-seq protocol was recently developed to deep-sequence the 3' ends of RNAs (Chang et al., 2014). We generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant.

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Uridylation by TUT4 and TUT7 marks mRNA for degradation [TAIL-Seq]

Project description:Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. In cells depleted of TUT4/7, the vast majority of mRNAs lose the U tails, and their half-lives are extended. Suppression of mRNA decay factors leads to the accumulation of uridylated mRNAs. In line with this, microRNA induces uridylation of its targets, and TUT4/7 is required for enhanced decay of microRNA targets. Our study explains the mechanism underlying selective uridylation of deadenylated mRNAs, and demonstrates a fundamental role of the U tail as a molecular mark for global mRNA decay. Thirteen separate sets of TAIL-seq experiments were performed. Each set includes a negative control for transfection, immunoprecipitation, or knockout cell generation. Experimental samples were treated with various conditions including siRNA transfection, transdominant negative protein expression, TALEN-based gene knockout, or immunoprecipitation. The 'README-TAIL-seq.txt' include detailed information about structure of seq entries in FASTQ files and of processed data for 3' end modifications.

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Project description:Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications, such as 3’ uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we have discovered that a nonfunctional target site unable to base pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. This Tail-U-Mediated Repression (TUMR) is abolished in cells lacking the uridylation enzymes TUT4 and TUT7, indicating that uridylation alters miRNA function by modulating target recognition. We identified a set of non-canonical targets in human cells that are specifically regulated by uridylated miR-27a. We provide evidence that TUMR expands the targets of other endogenous miRNAs. Our study reveals a function for uridylated isomiRs in regulating non-canonical miRNA targets.

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