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Updated: Jan 5, 2026
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
Published on: December 21, 2017
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Transcript Profiling Analysis Through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Reveals
Yani Kang1, Hong Sain Ooi2, Xiaodong Zhao3
1School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China.
Methods in Molecular Biology (Clifton, N.J.)
|October 12, 2019
Summary
This study precisely mapped yeast gene boundaries and untranslated regions using paired-end ditag sequencing. The findings reveal extensive transcript diversity and offer a valuable resource for yeast genomics research.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Genome annotation is challenging, with yeast gene boundaries and untranslated regions (UTRs) remaining poorly defined despite extensive transcriptome analysis.
- Understanding these elements is crucial for deciphering gene regulation and evolution.
Purpose of the Study:
- To accurately define the boundaries and UTRs of yeast genes.
- To identify novel transcripts and characterize 3' end heterogeneity.
- To provide a robust protocol applicable to various organisms.
Main Methods:
- Utilized a paired-end ditag (PET) approach combined with deep sequencing.
- Analyzed 562,133 PET sequences to identify gene structures.
- Investigated transcript profiling to characterize UTRs and novel transcripts.
Main Results:
- Accurately defined boundaries and UTRs for 3,409 open reading frames (ORFs).
- Identified multiple transcription start sites (TSSs) for many yeast genes.
- Discovered 85 uncharacterized transcripts and revealed extensive 3' end heterogeneity.
- Identified a novel putative motif for polyadenylation.
Conclusions:
- The study provides a comprehensive map of yeast gene boundaries and UTRs.
- Findings highlight significant complexity in yeast transcription and regulation.
- The developed protocol is adaptable for transcriptomic studies in diverse species, including mammals.
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