Holehouse, A. S. & Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered protein regions. Nat. Rev. Mol. Cell Biol. 25, 187–211 (2024).

Article  CAS  PubMed  Google Scholar 

van der Lee, R. et al. Classification of intrinsically disordered regions and proteins. Chem. Rev. 114, 6589–6631 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Xue, B., Dunker, A. K. & Uversky, V. N. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. J. Biomol. Struct. Dyn. 30, 137–149 (2012).

Article  CAS  PubMed  Google Scholar 

Du, M. & Chen, Z. J. DNA-induced liquid phase condensation of cGAS activates innate immune signaling. Science 361, 704–709 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wright, P. E. & Dyson, H. J. Intrinsically disordered proteins in cellular signalling and regulation. Nat. Rev. Mol. Cell Biol. 16, 18–29 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corden, J. L. RNA polymerase II C-terminal domain: tethering transcription to transcript and template. Chem. Rev. 113, 8423–8455 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Quintero-Cadena, P., Lenstra, T. L. & Sternberg, P. W. RNA Pol II length and disorder enable cooperative scaling of transcriptional bursting. Mol. Cell 79, 207–220.e8 (2020).

Article  CAS  PubMed  Google Scholar 

Gibbs, E. B. et al. Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain. Nat. Commun. 8, 15233 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Portz, B. et al. Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain. Nat. Commun. 8, 15231 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Venkat Ramani, M. K., Yang, W., Irani, S. & Zhang, Y. Simplicity is the ultimate sophistication-crosstalk of post-translational modifications on the RNA polymerase II. J. Mol. Biol. 433, 166912 (2021).

Article  CAS  PubMed  Google Scholar 

Cermakova, K. et al. A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science 374, 1113–1121 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van Roey, K. et al. Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chem. Rev. 114, 6733–6778 (2014).

Article  PubMed  Google Scholar 

Sharma, S. et al. Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation. Proc. Natl Acad. Sci. USA 115, E7053–E7062 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lyons, H. et al. Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 186, 327–345 e28 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sabari, B. R., Dall’Agnese, A. & Young, R. A. Biomolecular condensates in the nucleus. Trends Biochem. Sci. 45, 961–977 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mittag, T. & Pappu, R. V. A conceptual framework for understanding phase separation and addressing open questions and challenges. Mol. Cell 82, 2201–2214 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

Article  CAS  PubMed  Google Scholar 

Keogh, M. C. et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593–605 (2005).

Article  CAS  PubMed  Google Scholar 

Joshi, A. A. & Struhl, K. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell 20, 971–978 (2005).

Article  CAS  PubMed  Google Scholar 

Wiren, M. et al. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J. 24, 2906–2918 (2005).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jelinic, P., Pellegrino, J. & David, G. A novel mammalian complex containing Sin3B mitigates histone acetylation and RNA polymerase II progression within transcribed loci. Mol. Cell. Biol. 31, 54–62 (2011).

Article  CAS  PubMed  Google Scholar 

Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007).

Article  CAS  PubMed  Google Scholar 

Govind, C. K. et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol. Cell 39, 234–246 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, B. et al. Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316, 1050–1054 (2007).

Article  CAS  PubMed  Google Scholar 

Guan, H. et al. Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S. Nature 620, 669–675 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, Y. et al. Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Cell Res. 33, 971–974 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, W., Cui, H., Lu, Z. & Wang, H. Structure of histone deacetylase complex Rpd3S bound to nucleosome. Nat. Struct. Mol. Biol. 30, 1893–1901 (2023).

Article  CAS  PubMed  Google Scholar 

Markert, J. W., Vos, S. M. & Farnung, L. Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Nat. Commun. 14, 8128 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chu, Y., Sutton, A., Sternglanz, R. & Prelich, G. The BUR1 cyclin-dependent protein kinase is required for the normal pattern of histone methylation by SET2. Mol. Cell. Biol. 26, 3029–3038 (2006).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee, K. Y., Ranger, M. & Meneghini, M. D. Combinatorial genetic control of Rpd3S through histone H3K4 and H3K36 methylation in budding yeast. G3 (Bethesda) 8, 3411–3420 (2018).

Article  CAS