Genomics

Dataset Information

52

Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough


ABSTRACT: Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. Consistent with this, tiling array and RNAPII binding data revealed 3’ extended mRNA and snoRNA transcripts in the absence of Npl3. This reflected transcriptional readthrough by RNAPII, and extension and stabilization of cryptic unstable transcript (CUT) long noncoding RNAs. Transcription readthrough was widespread, often resulting in down-regulation of neighboring genes. We conclude that Npl3 is required for the formation of a termination-competent RNA, affecting both coding and noncoding RNAs. Overall design: We assessed the role of Npl3 in transcription termination, by examining the RNA binding profile of Npl3, Nab3 and Rpo21in WT yeast, as well as Nab3 and Rpo21 in npl3∆ yeast. We have included replicates of each sample as well as an untagged 'BY' negative control

INSTRUMENT(S): Illumina HiSeq 2000 (Saccharomyces cerevisiae)

ORGANISM(S): Saccharomyces Cerevisiae

SUBMITTER: Rebecca Katharine Holmes  

PROVIDER: GSE70191 | GEO | 2015-12-03

SECONDARY ACCESSION(S): PRJNA287824

REPOSITORIES: GEO

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Publications

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.

Holmes Rebecca K RK   Tuck Alex C AC   Zhu Chenchen C   Dunn-Davies Hywel R HR   Kudla Grzegorz G   Clauder-Munster Sandra S   Granneman Sander S   Steinmetz Lars M LM   Guthrie Christine C   Tollervey David D  

PLoS genetics 20151222 12


Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of Npl3 include transcription elongation, splicing and RNA 3' end processing. We used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites, and strand-specific tiling arrays to look at the effects of loss of Npl3 on all transcripts across the genome. We found that Npl3 binds diverse RNA species, both coding and non-coding, at sites indic  ...[more]

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