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

Malte Thodberg; Axel Thieffry; Jette Bornholdt; Mette Boyd; Christian Holmberg; Ajuna Azad; Christopher T Workman; Yun Chen; Karl Ekwall; Olaf Nielsen; Albin Sandelin

doi:10.1093/nar/gky1227

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

Malte Thodberg, Axel Thieffry, Jette Bornholdt, Mette Boyd, Christian Holmberg, Ajuna Azad, Christopher T Workman, Yun Chen, Karl Ekwall, Olaf Nielsen, Albin Sandelin

14 Citationer (Scopus)

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.

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
Vol/bind	47
Udgave nummer	4
Sider (fra-til)	1671-1691
Antal sider	21
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gky1227
Status	Udgivet - 28 feb. 2019

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10.1093/nar/gky1227

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title = "Comprehensive profiling of the fission yeast transcription start site activity during stress and media response",

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.",

author = "Malte Thodberg and Axel Thieffry and Jette Bornholdt and Mette Boyd and Christian Holmberg and Ajuna Azad and Workman, {Christopher T} and Yun Chen and Karl Ekwall and Olaf Nielsen and Albin Sandelin",

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doi = "10.1093/nar/gky1227",

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T1 - Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

AU - Thodberg, Malte

AU - Thieffry, Axel

AU - Bornholdt, Jette

AU - Boyd, Mette

AU - Holmberg, Christian

AU - Azad, Ajuna

AU - Workman, Christopher T

AU - Chen, Yun

AU - Ekwall, Karl

AU - Nielsen, Olaf

AU - Sandelin, Albin

PY - 2019/2/28

Y1 - 2019/2/28

N2 - 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.

AB - 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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DO - 10.1093/nar/gky1227

M3 - Journal article

C2 - 30566651

SN - 0305-1048

VL - 47

SP - 1671

EP - 1691

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 4

ER -

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

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