ArticleNucleic acids research2019
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 43 citations in OpenAlex.
- Establishing MS2-MCP-based single-molecule RNA visualization in Schizosaccharomyces pombe.Journal of cell science · 2026Article
- Establishing MS2-MCP-based single-molecule RNA visualization inbioRxiv : the preprint server for biology · 2026Article
- RNase III cleavage sites spread across splice junctions enforce sequential snoRNA processing.EMBO reports · 2025Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- Article
- POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology.ACS synthetic biology · 2024Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.Science advances · 2023Article
- Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis.Nucleic acids research · 2023Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.bioRxiv : the preprint server for biology · 2023Article
- Review
- Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation.Molecular and cellular biology · 2023Article
- Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance.Nature structural & molecular biology · 2022Article
- Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle.Human genomics · 2022Article
- Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms.STAR protocols · 2021Article
- Article
- The origin and evolution of a distinct mechanism of transcription initiation in yeasts.Genome research · 2021Article
- The RNA exosome shapes the expression of key protein-coding genes.Nucleic acids research · 2020Article
- Article
- Characterization ofThe Plant cell · 2020Article
- Organismal benefits of transcription speed control at gene boundaries.EMBO reports · 2020Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent on accurate annotation of transcription start sites (TSSs). However, comprehensive genome-wide maps of TSSs and their usage across commonly applied laboratory conditions and treatments for S. pombe are lacking. To this end, we profiled TSS activity genome-wide in S. pombe cultures exposed to heat shock, nitrogen starvation, hydrogen peroxide and two commonly applied media, YES and EMM2, using Cap Analysis of Gene Expression (CAGE). CAGE-based annotation of TSSs is substantially more accurate than existing PomBase annotation; on average, CAGE TSSs fall 50-75 bp downstream of PomBase TSSs and co-localize with nucleosome boundaries. In contrast to higher eukaryotes, dispersed TSS distributions are not common in S. pombe. Our data recapitulate known S. pombe stress expression response patterns and identify stress- and media-responsive alternative TSSs. Notably, alteration of growth medium induces changes of similar magnitude as some stressors. We show a link between nucleosome occupancy and genetic variation, and that the proximal promoter region is genetically diverse between S. pombe strains. Our detailed TSS map constitutes a central resource for S. pombe gene regulation research.
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