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Transcription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol

ABSTRACT: Transcription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol

PROVIDER: PRJEB30078 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2976750.fastq.gz	Fastqsanger.gz
	ERR2976751.fastq.gz	Fastqsanger.gz
	ERR2976752.fastq.gz	Fastqsanger.gz
	ERR2976753.fastq.gz	Fastqsanger.gz
	ERR2976746.fastq.gz	Fastqsanger.gz

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Transcription start site mapping of Saccharomyces cerevisiae grown in YPD media using the nAnTi-iCAGE protocol

Project description:We used nAnT-iCAGE – unbiased single-nucleotide resolution method for genome-wide transcription start site (TSS) capture, to produce libraries from Saccharomyces cerevisiae total RNA. Our goal was to investigate S. cerevisiae core-promoters and assess the rules of transcription initiation in BY4741 strain grown in YPD media.

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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.

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