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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...mechanisms and support the robustness of our findings.Our work opens other avenues for future studies. Many yeast TFs act in condition-specific ways, and the deletion of such TFs under log-phase growth in rich medium in some cases has no significant transcriptional effects. Therefore, one future direction...
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Research: Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
- Bingxiang Xu,
- Xiaomeng Gao,
- Xiaoli Li,
- Yan Jia,
- Feifei Li,
- and Zhihua Zhang
Genome Res. July 2022 32: 1285-1297; Published in Advance July 14, 2022, doi:10.1101/gr.276554.122
..., and the mechanism for heat shock (HS) response reported in the literature showed certain consensus patterns from yeasts to humans (Hartl et al. 2011). More specifically, cells globally repress their transcription (Vihervaara et al. 2018), RNA processing (Biamonti and Caceres 2009; Shalgi et al. 2014...
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Method: Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
- Sushmita Roy,
- Ilan Wapinski,
- Jenna Pfiffner,
- Courtney French,
- Amanda Socha,
- Jay Konieczka,
- Naomi Habib,
- Manolis Kellis,
- Dawn Thompson,
- and Aviv Regev
Genome Res. June 2013 23: 1039-1050; Published in Advance May 2, 2013, doi:10.1101/gr.146233.112
...Ilan Wapinski Roy Sushmita Socha, Amanda Thompson, Dawn Jay Konieczka, J C French Regev Courtney French Regev, A genome;gr.146233.112 1088-9051 10.1101/gr.146233.112 Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules Method Arboretum...
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Research: Determinants of nucleosome positioning and their influence on plant gene expression
- Ming-Jung Liu,
- Alexander E. Seddon,
- Zing Tsung-Yeh Tsai,
- Ian T. Major,
- Monique Floer,
- Gregg A. Howe,
- and Shin-Han Shiu
Genome Res. August 2015 25: 1182-1195; Published in Advance June 10, 2015, doi:10.1101/gr.188680.114
...-disfavoring sequence poly(dA/dT) around TF binding sites (TFBSs) significantly affects transcription in yeast (Raveh-Sadka et al. 2012), showing the importance of chromatin structure as a determinant of gene expression.In plants, -wide nucleosome positions have been determined for Arabidopsis thaliana (Chodavarapu et...
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Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
...into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The assay for transposase-accessible chromatin (ATAC)–seq, coupled with TF motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs -wide. Here, we propose methods for TRN...
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Research: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- David van Dijk,
- Eilon Sharon,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Eran Segal,
- and Lucas B. Carey
Genome Res. January 2017 27: 87-94; Published in Advance December 13, 2016, doi:10.1101/gr.212316.116
...TFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res 40: D169–D179. ↵Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11...
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Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
- Daniel Marbach,
- Sushmita Roy,
- Ferhat Ay,
- Patrick E. Meyer,
- Rogerio Candeias,
- Tamer Kahveci,
- Christopher A. Bristow,
- and Manolis Kellis
Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
...equally to this work. Abstract Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...responses to environmental stress in yeast have been studied, how the chromatin state changes and how those changes connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
...; Yanai and Hunter 2009; McManus et al. 2010; Goncalves et al. 2012; Shi et al. 2012; Combs et al. 2018). Whether this variation results from changes in condition-specific regulation or from differences in the capacity of the general transcriptional machinery remain unresolved. By generating a compendium...
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Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
- Yiming Kang,
- Nikhil R. Patel,
- Christian Shively,
- Pamela Samantha Recio,
- Xuhua Chen,
- Bernd J. Wranik,
- Griffin Kim,
- R. Scott McIsaac,
- Robi Mitra,
- and Michael R. Brent
Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
...and the transcriptional responses to direct TF perturbations. Systematic data sets of both types exist for yeast and human, but they rarely converge on a common set of direct, functional targets for a TF. Even the few genes that are both bound and responsive may not be direct functional targets. Our analysis shows...
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