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Size selected NET‐Seq reveals a conserved architecture of transcription units around yeast genes.
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  • Jane Mellor,
  • Shidong Xi,
  • Struan Murray,
  • Philipp Lorenz
Jane Mellor
University of Oxford Department of Biochemistry

Corresponding Author:[email protected]

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Shidong Xi
University of Oxford Department of Biochemistry
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Struan Murray
University of Oxford Department of Biochemistry
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Philipp Lorenz
University of Oxford Department of Biochemistry
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Abstract

Genomes from yeast to human are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but experimentally is can be hard to distinguish from background signals. Size selected native elongating transcript sequencing (ssNET-Seq) was developed to precisely map transcription units (TU) independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes define the expected reference pattern for a TU. Bioinformatic pattern matching to the reference identified 9542 TU in Saccharomyces cerevisiae, of which 47% are coding and 53% are non-coding. 3113 (33%) are newly identified unannotated non-coding TU. Anchoring all TU to the TSS or polyadenylation site (PAS) of annotated coding regions reveals distinctive architectures of linked pairs of divergent TU approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS-60nt) non-coding TU co-occurs with a downstream (TSS+150nt) coding TU and supports nucleosome depletion in the generation of the pervasive nascent transcriptome. The potential for extensive transcriptional interference is evident from low abundance unannotated TUs with variable TSS (median-240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.
31 Oct 2023Submitted to Yeast
31 Oct 2023Submission Checks Completed
31 Oct 2023Assigned to Editor
31 Oct 2023Review(s) Completed, Editorial Evaluation Pending
02 Nov 2023Reviewer(s) Assigned
30 Jan 2024Review(s) Completed, Editorial Evaluation Pending
30 Jan 2024Submission Checks Completed
30 Jan 2024Assigned to Editor
31 Jan 2024Editorial Decision: Revise Minor
08 Feb 20242nd Revision Received
08 Feb 2024Submission Checks Completed
08 Feb 2024Assigned to Editor
08 Feb 2024Review(s) Completed, Editorial Evaluation Pending
09 Feb 2024Editorial Decision: Accept