TY - JOUR
T1 - Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
AU - Brouwer, Ineke
AU - Kerklingh, Emma
AU - van Leeuwen, Fred
AU - Lenstra, Tineke L.
N1 - Funding Information: We thank the Holstege laboratory (Prinses Maxima Centrum, Utrecht, the Netherlands) for strains. We thank A. Balwierz (the Netherlands Cancer Institute, Oncode Institute), L. Joosen (the Netherlands Cancer Institute, Oncode Institute), J. Haarhuis (the Netherlands Cancer Institute), H. Teunissen (the Netherlands Cancer Institute), L. Willems (the Netherlands Cancer Institute) and R. van der Weide (the Netherlands Cancer Institute) for assistance with MNase-seq experiments, W. Pomp (the Netherlands Cancer Institute) for assistance with the analysis software, and J. Meeussen (the Netherlands Cancer Institute) and T. van Welsem (the Netherlands Cancer Institute) for assistance with western blotting. We thank the Research High Performance Computing Facility and the Genomics Core Facility of the NKI for assistance. We thank the members of the T.L.L. and F.v.L. laboratories for helpful discussions and E. de Wit (the Netherlands Cancer Institute) and members of the T.L.L. laboratory for the critical reading of the manuscript. This work was supported by an institutional grant of the Dutch Cancer Society and of the Dutch Ministry of Health, Welfare and Sport, the Netherlands Organization for Scientific Research (NWO, 016.Veni.192.071 (I.B.), ZonMW-TOP 91218022 (F.v.L.) and gravitation program CancerGenomiCs.nl (T.L.L.)), Oncode Institute (T.L.L.), which is partly financed by the Dutch Cancer Society, and the European Research Council (Starting Grant 755695 BURSTREG (T.L.L.)). Funding Information: We thank the Holstege laboratory (Prinses Maxima Centrum, Utrecht, the Netherlands) for strains. We thank A. Balwierz (the Netherlands Cancer Institute, Oncode Institute), L. Joosen (the Netherlands Cancer Institute, Oncode Institute), J. Haarhuis (the Netherlands Cancer Institute), H. Teunissen (the Netherlands Cancer Institute), L. Willems (the Netherlands Cancer Institute) and R. van der Weide (the Netherlands Cancer Institute) for assistance with MNase-seq experiments, W. Pomp (the Netherlands Cancer Institute) for assistance with the analysis software, and J. Meeussen (the Netherlands Cancer Institute) and T. van Welsem (the Netherlands Cancer Institute) for assistance with western blotting. We thank the Research High Performance Computing Facility and the Genomics Core Facility of the NKI for assistance. We thank the members of the T.L.L. and F.v.L. laboratories for helpful discussions and E. de Wit (the Netherlands Cancer Institute) and members of the T.L.L. laboratory for the critical reading of the manuscript. This work was supported by an institutional grant of the Dutch Cancer Society and of the Dutch Ministry of Health, Welfare and Sport, the Netherlands Organization for Scientific Research (NWO, 016.Veni.192.071 (I.B.), ZonMW-TOP 91218022 (F.v.L.) and gravitation program CancerGenomiCs.nl (T.L.L.)), Oncode Institute (T.L.L.), which is partly financed by the Dutch Cancer Society, and the European Research Council (Starting Grant 755695 BURSTREG (T.L.L.)). Publisher Copyright: © 2023, The Author(s).
PY - 2023/5
Y1 - 2023/5
N2 - Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in Saccharomyces cerevisiae to measure how bursting changes upon combined perturbations of chromatin remodelers, the transcription factor Gal4 and preinitiation complex components. Using dynamic epistasis analysis, we reveal how the remodeling of different nucleosomes regulates transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC and Gal4 binding synergistically facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. At canonical TATA boxes, the nucleosomes are displaced by TBP binding to allow for transcription activation even in the absence of remodelers. Overall, our results reveal how promoter nucleosome remodeling together with Gal4 and preinitiation complex binding regulates transcriptional bursting.
AB - Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in Saccharomyces cerevisiae to measure how bursting changes upon combined perturbations of chromatin remodelers, the transcription factor Gal4 and preinitiation complex components. Using dynamic epistasis analysis, we reveal how the remodeling of different nucleosomes regulates transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC and Gal4 binding synergistically facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. At canonical TATA boxes, the nucleosomes are displaced by TBP binding to allow for transcription activation even in the absence of remodelers. Overall, our results reveal how promoter nucleosome remodeling together with Gal4 and preinitiation complex binding regulates transcriptional bursting.
UR - http://www.scopus.com/inward/record.url?scp=85154583797&partnerID=8YFLogxK
U2 - https://doi.org/10.1038/s41594-023-00981-1
DO - https://doi.org/10.1038/s41594-023-00981-1
M3 - Article
C2 - 37127821
SN - 1545-9993
VL - 30
SP - 692
EP - 702
JO - Nature structural & molecular biology
JF - Nature structural & molecular biology
IS - 5
ER -