Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell. 2023;83:373–92. https://doi.org/10.1016/j.molcel.2022.12.032.
Article CAS PubMed Google Scholar
Pelechano V, Chavez S, Perez-Ortin JE. A complete set of nascent transcription rates for yeast genes. PLoS ONE. 2010;5:e15442. https://doi.org/10.1371/journal.pone.0015442.
Article CAS PubMed PubMed Central Google Scholar
Miller C, Schwalb B, Maier K, Schulz D, Dumcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dolken L, et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol. 2011;7:458. https://doi.org/10.1038/msb.2010.112.
Article CAS PubMed PubMed Central Google Scholar
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000;11:4241–57.
Article CAS PubMed PubMed Central Google Scholar
Hahn S, Young ET. Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics. 2011;189:705–36. https://doi.org/10.1534/genetics.111.127019.
Article CAS PubMed PubMed Central Google Scholar
Rando OJ, Winston F. Chromatin and transcription in yeast. Genetics. 2012;190:351–87. https://doi.org/10.1534/genetics.111.132266.
Article CAS PubMed PubMed Central Google Scholar
Gaston K, Jayaraman PS. Transcriptional repression in eukaryotes: repressors and repression mechanisms. Cell Mol Life Sci. 2003;60:721–41. https://doi.org/10.1007/s00018-003-2260-3.
Article CAS PubMed PubMed Central Google Scholar
Arnosti DN. Soft repression and chromatin modification by conserved transcriptional corepressors. Enzymes. 2023;53:69–96. https://doi.org/10.1016/bs.enz.2023.08.001.
Gartenberg MR, Smith JS. The nuts and bolts of transcriptionally silent chromatin in Saccharomyces cerevisiae. Genetics. 2016;203:1563–99. https://doi.org/10.1534/genetics.112.145243.
Article CAS PubMed PubMed Central Google Scholar
Allshire RC, Madhani HD. Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol. 2018;19:229–44. https://doi.org/10.1038/nrm.2017.119.
Article CAS PubMed Google Scholar
Bi X. Heterochromatin structure: lessons from the budding yeast. IUBMB Life. 2014;66:657–66. https://doi.org/10.1002/iub.1322.
Article CAS PubMed Google Scholar
Kueng S, Oppikofer M, Gasser SM. SIR proteins and the assembly of silent chromatin in budding yeast. Annu Rev Genet. 2013;47:275–306. https://doi.org/10.1146/annurev-genet-021313-173730.
Article CAS PubMed Google Scholar
Grunstein M, Gasser SM. Epigenetics in Saccharomyces cerevisiae. Cold Spring Harb Perspect Biol. 2013;5. https://doi.org/10.1101/cshperspect.a017491.
Trojer P, Reinberg D. Facultative heterochromatin: is there a distinctive molecular signature? Mol Cell. 2007;28:1–13.
Article CAS PubMed Google Scholar
Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Genome regulation by Polycomb and trithorax: 70 years and counting. Cell. 2017;171:34–57. https://doi.org/10.1016/j.cell.2017.08.002.
Article CAS PubMed Google Scholar
Blackledge NP, Klose RJ. The molecular principles of gene regulation by polycomb repressive complexes. Nat Rev Mol Cell Biol. 2021;22:815–33. https://doi.org/10.1038/s41580-021-00398-y.
Article CAS PubMed PubMed Central Google Scholar
Uckelmann M, Davidovich C. Chromatin compaction by polycomb group proteins revisited. Curr Opin Struct Biol. 2024;86:102806. https://doi.org/10.1016/j.sbi.2024.102806.
Article CAS PubMed Google Scholar
Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev. 2020;12:387–400. https://doi.org/10.1007/s12551-020-00663-y.
Article PubMed PubMed Central Google Scholar
von Hippel PH. From simple DNA-protein interactions to the macromolecular machines of gene expression. Annu Rev Biophys Biomol Struct. 2007;36:79–105. https://doi.org/10.1146/annurev.biophys.34.040204.144521.
Biggin MD. Animal transcription networks as highly connected, quantitative continua. Dev Cell. 2011;21:611–26. https://doi.org/10.1016/j.devcel.2011.09.008.
Article CAS PubMed Google Scholar
Wagh K, Stavreva DA, Upadhyaya A, Hager GL. Transcription factor dynamics: one molecule at a time. Annu Rev Cell Dev Biol. 2023;39:277–305. https://doi.org/10.1146/annurev-cellbio-022823-013847.
Article CAS PubMed Google Scholar
Larson DR. What do expression dynamics tell us about the mechanism of transcription? Curr Opin Genet Dev. 2011;21:591–9. https://doi.org/10.1016/j.gde.2011.07.010.
Article CAS PubMed PubMed Central Google Scholar
Suter DM. Transcription factors and DNA play hide and seek. Trends Cell Biol. 2020;30:491–500. https://doi.org/10.1016/j.tcb.2020.03.003.
Article CAS PubMed Google Scholar
Jana T, Brodsky S, Barkai N. Speed-specificity trade-offs in the transcription factors search for their genomic binding sites. Trends Genet. 2021;37:421–32. https://doi.org/10.1016/j.tig.2020.12.001.
Article CAS PubMed Google Scholar
Carminati M, Vecchia L, Stoos L, Thoma NH. Pioneer factors: emerging rules of engagement for transcription factors on chromatinized DNA. Curr Opin Struct Biol. 2024;88:102875. https://doi.org/10.1016/j.sbi.2024.102875.
Article CAS PubMed Google Scholar
Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. Phase Sep Model Transcriptional Control Cell. 2017;169:13–23. https://doi.org/10.1016/j.cell.2017.02.007.
Weingarten-Gabbay S, Segal E. The grammar of transcriptional regulation. Hum Genet. 2014;133:701–11. https://doi.org/10.1007/s00439-013-1413-1.
Article CAS PubMed PubMed Central Google Scholar
Friedman N, Rando OJ. Epigenomics and the structure of the living genome. Genome Res. 2015;25:1482–90. https://doi.org/10.1101/gr.190165.115.
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