Survey of cryptic unstable transcripts in yeast
Jessica M Vera1, Robin D Dowell2,3
1Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA.
BMC Genomics
|April 27, 2016
Summary
Cryptic unstable transcripts (CUTs) are pervasive in yeast. Conserved CUT expression suggests functional roles in gene regulation, with specific configurations impacting gene expression levels.
Area of Science:
- Molecular Biology
- Genomics
- Yeast Genetics
Background:
- Cryptic unstable transcripts (CUTs) are nuclear exosome-degraded, non-coding RNAs in budding yeast.
- The functional role of CUT transcription is debated, with possibilities including functional regulation or transcriptional noise.
Purpose of the Study:
- To investigate the extent of conserved CUT expression across different Saccharomyces yeast strains.
- To characterize the nature of CUT expression and its potential regulatory functions.
Main Methods:
- RNA sequencing (RNA-seq) of wild-type (WT) and rrp6Δ mutant transcriptomes from four yeast strains (S.cerevisiae and S.paradoxus).
- Utilized a hidden Markov model for CUT annotation and a four-way genomic alignment to identify conserved CUTs.
- Analyzed gene-CUT pair configurations (divergent and convergent) and their correlation with gene expression.
Main Results:
- Identified a significant population of CUTs with conserved syntenic expression across all four strains.
- Observed distinct gene expression trends associated with specific gene-CUT pair configurations.
- Divergent gene-CUT pairs correlated with increased gene expression, while convergent pairs correlated with reduced gene expression.
Conclusions:
- RNA-seq analysis significantly expanded CUT annotations in S.cerevisiae, revealing pervasive unstable transcription.
- Provided the first assessment of conserved CUT expression in yeast.
- Demonstrated potential modes of CUT-based gene expression regulation.
