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Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

ABSTRACT: During nuclear surveillance, the RNA exosome functions together with the TRAMP complexes, which include the RNA helicase Mtr4 together with a RNA binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions by TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. Comparison of the binding sites of TRAMP components with multiple nuclear RNA binding proteins revealed preferential colocalization of subsets of factors. On pre-mRNAs, ∆trf5 deletion caused reduced Mtr4 binding and RNA accumulation of Trf5 top targets.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE135526 | GEO | 2020/04/20

REPOSITORIES: GEO

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Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

Project description:During nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed coenrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduced Mtr4 recruitment and increased RNA abundance for mRNAs specifically showing high Trf5 binding.

2020-07-02 | PXD017114 | Pride

RNA-seq reveals that Air1 and Air2 control TRAMP substrate specificity for nuclear RNA surveillance

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2012-11-14 | E-GEOD-42231 | biostudies-arrayexpress

RNA-seq reveals that Air1 and Air2 control TRAMP substrate specificity for nuclear RNA surveillance

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Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-Î?98-117

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2016-06-29 | E-GEOD-83827 | biostudies-arrayexpress

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2014-08-09 | E-GEOD-60221 | biostudies-arrayexpress

Quality control of spliced mRNAs requires the shuttling SR-proteins Gbp2 and Hrb1

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2015-04-22 | PXD001908 | Pride

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