Dataset Information

Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal.

ABSTRACT: The Xenopus laevis alpha-tubulin gene X alpha T14 produces two mRNAs of 1.7 and 2.15 kb and we have shown that this is due to the use, at approximately equal frequency, of alternative 3' processing sites. Unusually, the hexanucleotide polyadenylation signal responsible for use of the downstream site, pA2, is CAUAAA in contrast to the consensus AAUAAA used at the upstream site, pA1. Since such a variant hexanucleotide would normally be expected to reduce drastically the efficiency of 3' processing, we have examined the 3' flanking sequences involved in pA2 usage in injected oocytes. In deletion mutants with 40 bp or 440 bp of 3' flanking DNA use of pA2 was almost totally abolished whereas when 770 bp of the natural flank was present pA2 was used normally. This polyadenylation signal therefore requires an unexpectedly large amount of flanking DNA and we have identified in the required region a member of a novel family of 450 bp interspersed repeats that we have termed Pir elements. We speculate that because of the variant hexanucleotide efficient use of pA2 has to be potentiated by the Pir element, perhaps through an effect on transcriptional pausing or termination.

SUBMITTER: Rabbitts KG

PROVIDER: S-EPMC312421 | biostudies-other | 1992 Jun

REPOSITORIES: biostudies-other

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Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal.

Rabbitts K G KG Morgan G T GT

Nucleic acids research 19920601 12

The Xenopus laevis alpha-tubulin gene X alpha T14 produces two mRNAs of 1.7 and 2.15 kb and we have shown that this is due to the use, at approximately equal frequency, of alternative 3' processing sites. Unusually, the hexanucleotide polyadenylation signal responsible for use of the downstream site, pA2, is CAUAAA in contrast to the consensus AAUAAA used at the upstream site, pA1. Since such a variant hexanucleotide would normally be expected to reduce drastically the efficiency of 3' processin ...[more]

PMID: 1620589

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Project description:BACKGROUND:Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3' untranslated regions (3'UTRs). Given the increasing importance of UTRs in the understanding of RNA metabolism, and the growing interest in alternative polyadenylation especially in the nervous system, we aimed at identifying the alternative isoforms of odorant receptor mRNAs generated through 3'UTR variation. RESULTS:We implemented a dedicated pipeline using IsoSCM instead of Cufflinks to analyze RNA-Seq data from whole olfactory mucosa of adult mice and obtained an extensive description of the 3'UTR isoforms of odorant receptor mRNAs. To validate our bioinformatics approach, we exhaustively analyzed the 3'UTR isoforms produced from 2 pilot genes, using molecular approaches including northern blot and RNA ligation mediated polyadenylation test. Comparison between datasets further validated the pipeline and confirmed the alternative polyadenylation patterns of odorant receptors. Qualitative and quantitative analyses of the annotated 3' regions demonstrate that 1) Odorant receptor 3'UTRs are longer than previously described in the literature; 2) More than 77% of odorant receptor mRNAs are subject to alternative polyadenylation, hence generating at least 2 detectable 3'UTR isoforms; 3) Splicing events in 3'UTRs are restricted to a limited subset of odorant receptor genes; and 4) Comparison between male and female data shows no sex-specific differences in odorant receptor 3'UTR isoforms. CONCLUSIONS:We demonstrated for the first time that odorant receptor genes are extensively subject to alternative polyadenylation. This ground-breaking change to the landscape of 3'UTR isoforms of Olfr mRNAs opens new avenues for investigating their respective functions, especially during the differentiation of olfactory sensory neurons.

Dataset Information

Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal.

Publications

Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal.

Similar Datasets

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