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Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

ABSTRACT: Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

PROVIDER: PRJNA435437 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6760800.fastq.gz	Fastqsanger.gz
	SRR6760791.fastq.gz	Fastqsanger.gz
	SRR6760801.fastq.gz	Fastqsanger.gz
	SRR6760792.fastq.gz	Fastqsanger.gz
	SRR6760802.fastq.gz	Fastqsanger.gz

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Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

Project description:Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent of accurate annotation of genes and in particular Transcription Start Sites (TSSs) and thereby core promoters. However, comprehensive genome-wide maps of TSS and their usage across commonly applied laboratorial conditions and treatments for S. pombe are lacking. To this end, we have applied Cap Analysis of Gene Expression (CAGE) to profile TSSs activity in S. pombe cultures exposed to heat shock, nitrogen starvation, peroxide and two commonly applied media, YES and EMM. CAGE allows for nucleotide resolution detection of TSS, which we show is substantially more accurate than existing PomBase annotation. On gene expression levels, we recapitulate known S. pombe stress response patterns, but our data also allowed us to detect many alternative TSSs within gene bodies that are changing their activity between conditions. Some of these have the potential to change the functions of encoded proteins due to coding sequence exclusion. We show that the immediate region around TSSs is almost as conserved as coding sequence across S. pombe strains, but the upstream promoter which houses transcription factor binding sites linked to stress response show high diversity. Our data constitute a central resource for S. pombe transcriptional regulation research.

2018-03-14 | GSE110976 | GEO

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.

Project description: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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Transcription profiling of fission yeast grown in an enriched media was vs the same strain grown in minimal media

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Chromatin architectures at fission yeast transcriptional promoters and replication origins

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Project description:The fission yeast Schizosaccharomyces pombe

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