Journal
Elife
Publication Date
2022
Volume
11
First Page
e70344
Document Type
Open Access Publication
DOI
10.7554/eLife.70344
Rights and Permissions
eLife 2022;11:e70344 DOI: 10.7554/eLife.70344. © 2022, Gutierrez et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Recommended Citation
Gutierrez, J. Ignacio; Brittingham, Gregory P.; Karadeniz, Yonca; Tran, Kathleen D.; Dutta, Arnob; Holehouse, Alex S.; Peterson, Craig L.; and Holt, Liam J., "SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence." Elife. 11, e70344 (2022).
https://digitalcommons.wustl.edu/open_access_pubs/11474
figure and figure supplement.pdf (10378 kB)
elife-70344-supp1-v2.xlsx (34 kB)
Supplementary file 1 Sequences of glutamine-rich low-complexity sequences (QLCs) in the Saccharomyces cerevisiae genome. All S. cerevisiae QLCs identified using the parameters optimized in Figure 1—figure supplement 2 are included in this summary table.
elife-70344-supp2-v2.xlsx (10 kB)
Supplementary file 2 Comparison of sequence properties of SNF5 N-terminal intrinsically disordered regions (IDRs). Comparison of the IDRs of SNF5 orthologues from Ascomycete fungi, with the number of glutamines and histidines indicated.
elife-70344-supp3-v2.xlsx (25 kB)
Supplementary file 3 Transcription factors enriched in each gene group from RNA-seq analysis. The YEASTRACT server used to find transcription factors enriched within the promoters of each of four gene sets defined by hierarchical clustering of genes significantly regulated upon carbon starvation (see Figure 4E). YEASTRACT search settings were DNA binding plus expression evidence; TF acting as either activator or inhibitor.
elife-70344-supp4-v2.xlsx (9 kB)
Supplementary file 4 SNF5 subregions examined by all-atom Monte Carlo simulations.
elife-70344-supp5-v2.xlsx (9 kB)
Supplementary file 5 Parameters used for all-atom Monte Carlo simulations.
elife-70344-supp6-v2.xlsx (11 kB)
Supplementary file 6 Yeast strains used in this study.
elife-70344-supp7-v2.xlsx (9 kB)
Supplementary file 7 Plasmids used in this study.
elife-70344-sa2-fig1-v2.jpg (17 kB)
elife-70344-transrepform1-v2.pdf (321 kB)
Transparent reporting form
elife-70344-supp1-v2.xlsx (34 kB)
Supplementary file 1 Sequences of glutamine-rich low-complexity sequences (QLCs) in the Saccharomyces cerevisiae genome. All S. cerevisiae QLCs identified using the parameters optimized in Figure 1—figure supplement 2 are included in this summary table.
elife-70344-supp2-v2.xlsx (10 kB)
Supplementary file 2 Comparison of sequence properties of SNF5 N-terminal intrinsically disordered regions (IDRs). Comparison of the IDRs of SNF5 orthologues from Ascomycete fungi, with the number of glutamines and histidines indicated.
elife-70344-supp3-v2.xlsx (25 kB)
Supplementary file 3 Transcription factors enriched in each gene group from RNA-seq analysis. The YEASTRACT server used to find transcription factors enriched within the promoters of each of four gene sets defined by hierarchical clustering of genes significantly regulated upon carbon starvation (see Figure 4E). YEASTRACT search settings were DNA binding plus expression evidence; TF acting as either activator or inhibitor.
elife-70344-supp4-v2.xlsx (9 kB)
Supplementary file 4 SNF5 subregions examined by all-atom Monte Carlo simulations.
elife-70344-supp5-v2.xlsx (9 kB)
Supplementary file 5 Parameters used for all-atom Monte Carlo simulations.
elife-70344-supp6-v2.xlsx (11 kB)
Supplementary file 6 Yeast strains used in this study.
elife-70344-supp7-v2.xlsx (9 kB)
Supplementary file 7 Plasmids used in this study.
elife-70344-sa2-fig1-v2.jpg (17 kB)
elife-70344-transrepform1-v2.pdf (321 kB)
Transparent reporting form
