A refined Saccharomyces cerevisiae reference transcriptome from Direct RNA Sequencing, with a reusable pipeline for UTR annotation updates

Clicks: 15
ID: 329500
2026
Free PDF
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This article has not been analysed, so there is no overall score — reader engagement is measured and shown alongside.
AI Quality Assessment
Not analyzed
Readership in this journal
Emerging

Ranked #42 of 47 articles by views in fems yeast research

Most read Least read

Bar heights use a square-root scale.

Mint this article as an NFT
Not yet minted

Create a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.

5 SUSD one-off · no wallet required
Sign in to mint
Abstract
Untranslated regions (UTRs) flanking the coding sequence govern mRNA translation, localisation, and decay, making accurate UTR boundaries essential for quantitative RNA sequencing and the study of post-transcriptional control. Reference transcriptomes built from short-read sequencing have been invaluable to the yeast community, yet in a genome as gene-dense as that of Saccharomyces cerevisiae, short reads cannot be assigned to a single transcript of origin, leaving roughly one quarter of transcripts without a defined UTR. Here we use Direct RNA Sequencing (DRS), in which native polyadenylated molecules are sequenced without fragmentation or amplification, to reduce this ambiguity and deliver two complementary resources. First, an updated S. cerevisiae S288C reference: change-point segmentation of per-gene DRS coverage defined boundaries for 5 682 of the 6 607 genes in the backbone model, and a merge-max rule retaining the longer UTR from each source ensures no gene loses existing annotation. The result adds previously absent UTRs to 1 213 (5') and 1 220 (3') of the genes that the earlier short-read annotation left unannotated, and extends 28.9% of 5' and 19.4% of 3' boundaries among comparable genes. Second, the complete, documented pipeline so that the transcriptome can be rebuilt from any DRS data. Validation on two independent datasets shows improved mapping rates, reduced soft-clipping, and metagene profiles consistent with genuine transcript signal.
Reference Key
openalex_W7166432915 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Orlane Rossini, Alice Cleynen, Nikolay E. Shirokikh
Journal fems yeast research
Year 2026
DOI
10.1093/femsyr/foag052
URL
https://doi.org/10.1093/femsyr/foag052
Keywords Keywords not found

Citations

No citations found. To add a citation, contact the admin at info@scimatic.org

Comments

No comments yet. Be the first to comment on this article.