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*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

61 Downloads (Pure)

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.
Original languageEnglish
Article numbergky1227
JournalNucleic acids research
Volume47
Issue number4
Pages (from-to)1671-1691
Number of pages21
ISSN0305-1048
DOIs
Publication statusPublished - 2019

Cite this

Thodberg, M., Thieffry, A., Bornholdt, J., Boyd, M., Holmberg, C., Azad, A., ... Sandelin, A. (2019). Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. Nucleic acids research, 47(4), 1671-1691. [gky1227]. https://doi.org/10.1093/nar/gky1227
Thodberg, Malte ; Thieffry, Axel ; Bornholdt, Jette ; Boyd, Mette ; Holmberg, Christian ; Azad, Ajuna ; Workman, Christopher T. ; Chen, Yun ; Ekwall, Karl ; Nielsen, Olaf ; Sandelin, Albin. / Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. In: Nucleic acids research. 2019 ; Vol. 47, No. 4. pp. 1671-1691.
@article{bbdb019128d94a069bc47ae30b9c2042,
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",
year = "2019",
doi = "10.1093/nar/gky1227",
language = "English",
volume = "47",
pages = "1671--1691",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "4",

}

Thodberg, M, Thieffry, A, Bornholdt, J, Boyd, M, Holmberg, C, Azad, A, Workman, CT, Chen, Y, Ekwall, K, Nielsen, O & Sandelin, A 2019, 'Comprehensive profiling of the fission yeast transcription start site activity during stress and media response', Nucleic acids research, vol. 47, no. 4, gky1227, pp. 1671-1691. https://doi.org/10.1093/nar/gky1227

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. / Thodberg, Malte; Thieffry, Axel; Bornholdt, Jette; Boyd, Mette; Holmberg, Christian; Azad, Ajuna; Workman, Christopher T.; Chen, Yun; Ekwall, Karl; Nielsen, Olaf; Sandelin, Albin.

In: Nucleic acids research, Vol. 47, No. 4, gky1227, 2019, p. 1671-1691.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

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

Y1 - 2019

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.

U2 - 10.1093/nar/gky1227

DO - 10.1093/nar/gky1227

M3 - Journal article

VL - 47

SP - 1671

EP - 1691

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 4

M1 - gky1227

ER -