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High-Resolution Profiling of NMD Targets in Yeast
Feng He1, Alper Celik1, Richard Baker1
1Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States.
Methods in Enzymology
|December 4, 2018
Summary
Researchers identified nearly 900 transcripts regulated by the nonsense-mediated decay (NMD) pathway in yeast using RNA-sequencing. This study details methods for analyzing transcript changes in biological states, advancing our understanding of gene regulation.
Area of Science:
- Molecular Biology
- Genomics
- Yeast Genetics
Background:
- High-throughput sequencing, like RNA-Seq, enables systematic transcriptomic analysis.
- The nonsense-mediated decay (NMD) pathway plays a crucial role in regulating gene expression.
- Understanding NMD targets is vital for comprehending cellular responses to various biological states.
Purpose of the Study:
- To describe methods for applying RNA-Seq to identify NMD-regulated transcripts in Saccharomyces cerevisiae.
- To define the set of transcripts influenced by the NMD pathway in yeast.
Main Methods:
- Culturing wild-type and NMD-deficient yeast strains.
- Isolating RNA, depleting ribosomal RNA (rRNA), and preparing RNA-Seq libraries.
- Utilizing bioinformatics software for sequence read analysis.
Main Results:
- Identification of approximately 900 transcripts commonly upregulated upon NMD pathway inactivation.
- Characterization of transcriptomic changes associated with NMD deficiency in yeast.
Conclusions:
- The described methods provide a robust framework for transcriptomic profiling of regulatory pathways.
- This work elucidates a significant portion of the yeast transcriptome regulated by NMD.
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