Transcriptomics

Dataset Information

65

Transcription profiling of S. cerevisiae Nab3 and Nrd1 mutants


ABSTRACT: Nrd1 and Nab3 are two yeast RNA binding proteins which have been shown to be involved in transcription termination of non poly(A) genes. We have used expression profiling of a Nab3 mutant to discover novel RNA targets of the Nrd1 and Nab3 transcription termination pathway. Failure to terminate RNA polymerase II by Nab3 leads to continued transcription well beyond the correct termination sites, altering the expression of adjacent downstream genes. Using this concept, our microarray uncovered the up-regulation of numerous genes that are located downstream of “cryptic unstable transcripts”, transcripts that are transcribed, terminated and rapidly degraded by Nrd1, Nab3, and the nuclear exosome. Experiment Overall Design: Four yeast total RNA samples where analyzed in this study. These RNAs come from two separate strains of yeast, each strain at either the permissive temperature (25C) or the non-permissive temperature (37C). One of these strains is a wild type strain of yeast used as a control. The other strain has a mutation in the Nab3 protein that confers temperature sensitivity at the non-permissive temperature of 37C. After two hours at the non-permissive temperature, we observe disruptions in the Nrd1/Nab3 transcription termination pathway and this is the scheme that we followed for our microarray experiment. Our goal was to observe the global expression changes after 2 hours without Nab3 function.

ORGANISM(S): Saccharomyces cerevisiae  

SUBMITTER: Jeff L. Corden 

PROVIDER: E-GEOD-4657 | ArrayExpress | 2008-06-13

SECONDARY ACCESSION(S): GDS2079GSE4657PRJNA95303

REPOSITORIES: GEO, ArrayExpress

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Publications

Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3.

Arigo John T JT   Eyler Daniel E DE   Carroll Kristina L KL   Corden Jeffry L JL  

Molecular cell 20060901 6


Studies of yeast transcription have revealed the widespread distribution of intergenic RNA polymerase II transcripts. These cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome. Yeast RNA binding proteins Nrd1 and Nab3 direct termination of sn/snoRNAs and recently have also been implicated in premature transcription termination of the NRD1 gene. In this paper, we show that Nrd1 and Nab3 are required for transcription termination of CUTs. In nrd1 and nab3 mutants, we ob  ...[more]

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