Genetic reconstruction of a functional transcriptional regulatory network - PubMed (original) (raw)
Comparative Study
doi: 10.1038/ng2012. Epub 2007 Apr 8.
Affiliations
- PMID: 17417638
- DOI: 10.1038/ng2012
Comparative Study
Genetic reconstruction of a functional transcriptional regulatory network
Zhanzhi Hu et al. Nat Genet. 2007 May.
Abstract
Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstruct a functional regulatory network. First, we profiled transcriptional responses in S. cerevisiae strains with individual deletions of 263 transcription factors. Then we used directed-weighted graph modeling and regulatory epistasis analysis to identify indirect regulatory relationships between these transcription factors, and from this we reconstructed a functional transcriptional regulatory network. The enrichment of promoter motifs and Gene Ontology annotations provide insight into the biological functions of the transcription factors.
Similar articles
- Transcriptional regulatory networks in Saccharomyces cerevisiae.
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Lee TI, et al. Science. 2002 Oct 25;298(5594):799-804. doi: 10.1126/science.1075090. Science. 2002. PMID: 12399584 - Statistical methods in integrative analysis for gene regulatory modules.
Zeng L, Wu J, Xie J. Zeng L, et al. Stat Appl Genet Mol Biol. 2008;7(1):Article 28. doi: 10.2202/1544-6115.1369. Epub 2008 Oct 10. Stat Appl Genet Mol Biol. 2008. PMID: 18976224 - Transcriptional networks: reverse-engineering gene regulation on a global scale.
Chua G, Robinson MD, Morris Q, Hughes TR. Chua G, et al. Curr Opin Microbiol. 2004 Dec;7(6):638-46. doi: 10.1016/j.mib.2004.10.009. Curr Opin Microbiol. 2004. PMID: 15556037 Review. - Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast.
Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B. Kainth P, et al. Methods. 2009 Jul;48(3):258-64. doi: 10.1016/j.ymeth.2009.02.015. Epub 2009 Mar 6. Methods. 2009. PMID: 19269327 - [Analysis of the transcriptional regulatory network in the model organisms: yeast and sea urchin].
Takamatsu K, Takeda T. Takamatsu K, et al. Tanpakushitsu Kakusan Koso. 2004 Dec;49(17 Suppl):2742-50. Tanpakushitsu Kakusan Koso. 2004. PMID: 15669249 Review. Japanese. No abstract available.
Cited by
- Position-dependent function of human sequence-specific transcription factors.
Duttke SH, Guzman C, Chang M, Delos Santos NP, McDonald BR, Xie J, Carlin AF, Heinz S, Benner C. Duttke SH, et al. Nature. 2024 Jul;631(8022):891-898. doi: 10.1038/s41586-024-07662-z. Epub 2024 Jul 17. Nature. 2024. PMID: 39020164 Free PMC article. - Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships.
Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH. Kudron M, et al. bioRxiv [Preprint]. 2024 Jan 20:2024.01.18.576242. doi: 10.1101/2024.01.18.576242. bioRxiv. 2024. PMID: 38293065 Free PMC article. Preprint. - Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach.
Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Raja R, et al. Biophys J. 2024 Jan 16;123(2):221-234. doi: 10.1016/j.bpj.2023.12.010. Epub 2023 Dec 15. Biophys J. 2024. PMID: 38102827 - Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae.
Vande Zande P, Siddiq MA, Hodgins-Davis A, Kim L, Wittkopp PJ. Vande Zande P, et al. PLoS Genet. 2023 Dec 13;19(12):e1011078. doi: 10.1371/journal.pgen.1011078. eCollection 2023 Dec. PLoS Genet. 2023. PMID: 38091349 Free PMC article. - Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.
Zhang Z, Ruf-Zamojski F, Zamojski M, Bernard DJ, Chen X, Troyanskaya OG, Sealfon SC. Zhang Z, et al. Nucleic Acids Res. 2024 Jan 25;52(2):572-582. doi: 10.1093/nar/gkad1166. Nucleic Acids Res. 2024. PMID: 38084892 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases