Unknown

Dataset Information

0

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


ABSTRACT: 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 indicative of roles in both early pre-mRNA processing and 3' end formation. Tiling arrays and RNAPII mapping data revealed 3' extended RNAPII-transcribed RNAs in the absence of Npl3, suggesting that defects in pre-mRNA packaging events result in termination readthrough. Transcription readthrough was widespread and frequently resulted in down-regulation of neighboring genes. We conclude that the absence of Npl3 results in widespread 3' extension of transcripts with pervasive effects on gene expression.

SUBMITTER: Holmes RK 

PROVIDER: S-EPMC4687934 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

altmetric image

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]

Similar Datasets

2015-12-03 | GSE70191 | GEO
2015-12-02 | E-MTAB-3642 | biostudies-arrayexpress
| S-EPMC3510044 | biostudies-literature
| S-EPMC2677966 | biostudies-literature
| S-EPMC2214835 | biostudies-literature
2008-12-31 | GSE11491 | GEO
| S-EPMC2538588 | biostudies-literature
2008-12-30 | E-GEOD-11491 | biostudies-arrayexpress
2022-11-26 | GSE160709 | GEO
| S-EPMC8417969 | biostudies-literature