Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: The Saccharomyces cerevisiae TRAMP4 and TRAMP5 complexes, which consist of the poly(A) polymerase Trf4 or Trf5, respectively, the zinc knuckle proteins Air1 or Air2, and the RNA helicase Mtr4, play a critical role in nuclear RNA surveillance. Although it is known to enhance the nuclease activity of the exosome, relatively little is known about the exact mechanism and specificity of TRAMP. To better define the specificities of the TRAMP complexes, we used phenotypic analysis and RNA deep-sequencing technology to measure differences in global RNA polyadenylation in air mutants, revealing specific requirements for each Air protein in the regulation of the levels of non-coding and coding RNAs. These findings reveal differential functions for Air proteins in eukaryotic RNA metabolism and indicate that they control the substrate specificity of the RNA exosome. Poly(A)+ RNA from WT, rrp6-M-NM-^T, air1-M-NM-^T rrp6-M-NM-^T and air2-M-NM-^T rrp6-M-NM-^T was sequenced using ABI SOLiD platform, in duplicate.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: J. Scott Butler 

PROVIDER: E-GEOD-42231 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance.

Schmidt Karyn K   Xu Zhenjiang Z   Mathews David H DH   Butler J Scott JS  

RNA (New York, N.Y.) 20120824 10


RNA surveillance systems function at critical steps during the formation and function of RNA molecules in all organisms. The RNA exosome plays a central role in RNA surveillance by processing and degrading RNA molecules in the nucleus and cytoplasm of eukaryotic cells. The exosome functions as a complex of proteins composed of a nine-member core and two ribonucleases. The identity of the molecular determinants of exosome RNA substrate specificity remains an important unsolved aspect of RNA surve  ...[more]

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