The disassembly and reassembly of nucleosomes by histone chaperones is an essential activity during eukaryotic transcription elongation. This highly conserved process maintains chromatin integrity by transiently removing nucleosomes as barriers and then restoring them in the wake of transcription. While transcription elongation requires multiple histone chaperones, there is little understanding of how most of them function and why so many are required. Here, we show that the histone chaperone Spt6 acts through its acidic, intrinsically disordered N-terminal domain (NTD) to bind histones and control chromatin structure. The Spt6 NTD is essential for viability, and its histone-binding activity is conserved between yeast and humans. The essential nature of the Spt6 NTD can be bypassed by changes in another histone chaperone, FACT, revealing a close functional connection between the two. Our results have led to a mechanistic model for dynamic cooperation between multiple histone chaperones during transcription elongation.

Department of Genetics Blavatnik Institute Harvard Medical School Boston MA 02115 USA

Institute of Organic Chemistry and Biochemistry of the CAS Prague 16000 Czech Republic

Institute of Organic Chemistry and Biochemistry of the CAS Prague 16000 Czech Republic; Department of Cell Biology Faculty of Science Charles University Prague 12800 Czech Republic

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bioRxiv. 2024 Nov 25:2024.11.25.625227. doi: 10.1101/2024.11.25.625227. PubMed

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Luger K, Rechsteiner TJ, and Richmond TJ (1999). Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol Biol 119, 1–16. 10.1385/1-59259-681-9:1. PubMed DOI

Kornberg RD, and Lorch Y (2020). Primary Role of the Nucleosome. Mol Cell 79, 371–375. 10.1016/j.molcel.2020.07.020. PubMed DOI

Kujirai T, Ehara H, Sekine SI, and Kurumizaka H (2023). Structural Transition of the Nucleosome during Transcription Elongation. Cells 12. 10.3390/cells12101388. PubMed DOI PMC

Farnung L (2024). Chromatin Transcription Elongation - A structural perspective. J Mol Biol, 168845. 10.1016/j.jmb.2024.168845. PubMed DOI PMC

Robert F, and Jeronimo C (2023). Transcription-coupled nucleosome assembly. Trends Biochem Sci 48, 978–992. 10.1016/j.tibs.2023.08.003. PubMed DOI

Hammond CM, Stromme CB, Huang H, Patel DJ, and Groth A (2017). Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol 18, 141–158. 10.1038/nrm.2016.159. PubMed DOI PMC

Warren C, and Shechter D (2017). Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 429, 2401–2426. 10.1016/j.jmb.2017.06.005. PubMed DOI PMC

Ray-Gallet D, and Almouzni G (2022). H3-H4 histone chaperones and cancer. Curr Opin Genet Dev 73, 101900. 10.1016/j.gde.2022.101900. PubMed DOI

Ehara H, Kujirai T, Shirouzu M, Kurumizaka H, and Sekine SI (2022). Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. Science 377, eabp9466. 10.1126/science.abp9466. PubMed DOI

Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, and Farnung L (2024). Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Mol Cell 84, 3423–3437 e3428. 10.1016/j.molcel.2024.08.022. PubMed DOI PMC

Kemble DJ, McCullough LL, Whitby FG, Formosa T, and Hill CP (2015). FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs. Mol Cell 60, 294–306. 10.1016/j.molcel.2015.09.008. PubMed DOI PMC

Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D’Arcy S, and Luger K (2020). FACT caught in the act of manipulating the nucleosome. Nature 577, 426–431. 10.1038/s41586-019-1820-0. PubMed DOI PMC

Formosa T, and Winston F (2020). The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 48, 11929–11941. 10.1093/nar/gkaa912. PubMed DOI PMC

Jeronimo C, and Robert F (2022). The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 13, 16–38. 10.1080/21541264.2022.2069995. PubMed DOI PMC

Clark-Adams CD, and Winston F (1987). The SPT6 gene is essential for growth and is required for delta-mediated transcription in Saccharomyces cerevisiae. Mol Cell Biol 7, 679–686. 10.1128/mcb.7.2.679-686.1987. PubMed DOI PMC

Fischbeck JA, Kraemer SM, and Stargell LA (2002). SPN1, a conserved gene identified by suppression of a postrecruitment-defective yeast TATA-binding protein mutant. Genetics 162, 1605–1616. 10.1093/genetics/162.4.1605. PubMed DOI PMC

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, et al. (2020). The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443. 10.1038/s41586-020-2308-7. PubMed DOI PMC

Neigeborn L, Celenza JL, and Carlson M (1987). SSN20 is an essential gene with mutant alleles that suppress defects in SUC2 transcription in Saccharomyces cerevisiae. Molecular and Cellular Biology 7, 672–678. 10.1128/mcb.7.2.672. PubMed DOI PMC

Swanson MS, Malone EA, and Winston F (1991). SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat. Mol Cell Biol 11, 3009–3019. 10.1128/mcb.11.6.3009-3019.1991. PubMed DOI PMC

Wittmeyer J, and Formosa T (1997). The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein. Mol Cell Biol 17, 4178–4190. 10.1128/MCB.17.7.4178. PubMed DOI PMC

Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, and Winston F (2018). Spt6 Is Required for the Fidelity of Promoter Selection. Mol Cell 72, 687–699 e686. 10.1016/j.molcel.2018.09.005. PubMed DOI PMC

Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dolken L, Schlosser A, Erhard F, Baluapuri A, and Wolf E (2021). Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell 81, 3110–3127 e3114. 10.1016/j.molcel.2021.06.016. PubMed DOI PMC

Zumer K, Maier KC, Farnung L, Jaeger MG, Rus P, Winter G, and Cramer P (2021). Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Mol Cell 81, 3096–3109 e3098. 10.1016/j.molcel.2021.05.028. PubMed DOI

Zumer K, Ochmann M, Aljahani A, Zheenbekova A, Devadas A, Maier KC, Rus P, Neef U, Oudelaar AM, and Cramer P (2024). FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo. Mol Cell 84, 2053–2069 e2059. 10.1016/j.molcel.2024.05.003. PubMed DOI

Reim NI, Chuang J, Jain D, Alver BH, Park PJ, and Winston F (2020). The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 48, 10241–10258. 10.1093/nar/gkaa745. PubMed DOI PMC

Henriques T, Scruggs BS, Inouye MO, Muse GW, Williams LH, Burkholder AB, Lavender CA, Fargo DC, and Adelman K (2018). Widespread transcriptional pausing and elongation control at enhancers. Genes Dev 32, 26–41. 10.1101/gad.309351.117. PubMed DOI PMC

Shetty A, Kallgren SP, Demel C, Maier KC, Spatt D, Alver BH, Cramer P, Park PJ, and Winston F (2017). Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation. Mol Cell 66, 77–88 e75. 10.1016/j.molcel.2017.02.023. PubMed DOI PMC

Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, and Sekine SI (2019). Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science 363, 744–747. 10.1126/science.aav8912. PubMed DOI

Farnung L, Ochmann M, Engeholm M, and Cramer P (2021). Structural basis of nucleosome transcription mediated by Chd1 and FACT. Nat Struct Mol Biol 28, 382–387. 10.1038/s41594-021-00578-6. PubMed DOI PMC

Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, and Cramer P (2018). Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 560, 607–612. 10.1038/s41586-018-0440-4. PubMed DOI

Vos SM, Farnung L, Linden A, Urlaub H, and Cramer P (2020). Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Nat Struct Mol Biol 27, 668–677. 10.1038/s41594-020-0437-1. PubMed DOI

Vos SM, Farnung L, Urlaub H, and Cramer P (2018). Structure of paused transcription complex Pol II-DSIF-NELF. Nature 560, 601–606. 10.1038/s41586-018-0442-2. PubMed DOI PMC

Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, and Kurumizaka H (2023). Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA. J Biol Chem 299, 105477. 10.1016/j.jbc.2023.105477. PubMed DOI PMC

Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, et al. (2021). A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science 374, 1113–1121. 10.1126/science.abe2913. PubMed DOI PMC

Lopez-Rivera F, Chuang J, Spatt D, Gopalakrishnan R, and Winston F (2022). Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae. Genetics 222. 10.1093/genetics/iyac125. PubMed DOI PMC

Viktorovskaya O, Chuang J, Jain D, Reim NI, Lopez-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, and Winston F (2021). Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev 35, 698–712. 10.1101/gad.348431.121. PubMed DOI PMC

Geisberg JV, Moqtaderi Z, and Struhl K (2024). Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate. Proc Natl Acad Sci U S A 121, e2405827121. 10.1073/pnas.2405827121. PubMed DOI PMC

Li S, Edwards G, Radebaugh CA, Luger K, and Stargell LA (2022). Spn1 and Its Dynamic Interactions with Spt6, Histones and Nucleosomes. J Mol Biol 434, 167630. 10.1016/j.jmb.2022.167630. PubMed DOI

Malone EA, Clark CD, Chiang A, and Winston F (1991). Mutations in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae. Mol Cell Biol 11, 5710–5717. 10.1128/mcb.11.11.5710-5717.1991. PubMed DOI PMC

Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, and Winston F (2008). Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol 6, e277. 10.1371/journal.pbio.0060277. PubMed DOI PMC

Jeronimo C, Poitras C, and Robert F (2019). Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep 28, 1206–1218 e1208. 10.1016/j.celrep.2019.06.097. PubMed DOI

Jeronimo C, Watanabe S, Kaplan CD, Peterson CL, and Robert F (2015). The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell 58, 1113–1123. 10.1016/j.molcel.2015.03.030. PubMed DOI PMC

van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, and Nislow C (2013). A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet 9, e1003479. 10.1371/journal.pgen.1003479. PubMed DOI PMC

Diebold ML, Koch M, Loeliger E, Cura V, Winston F, Cavarelli J, and Romier C (2010). The structure of an Iws1/Spt6 complex reveals an interaction domain conserved in TFIIS, Elongin A and Med26. EMBO J 29, 3979–3991. 10.1038/emboj.2010.272. PubMed DOI PMC

McDonald SM, Close D, Xin H, Formosa T, and Hill CP (2010). Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. Mol Cell 40, 725–735. 10.1016/j.molcel.2010.11.014. PubMed DOI PMC

Miller CLW, Warner JL, and Winston F (2023). Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability. Trends Genet 39, 858–872. 10.1016/j.tig.2023.06.008. PubMed DOI PMC

Bortvin A, and Winston F (1996). Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272, 1473–1476. 10.1126/science.272.5267.1473. PubMed DOI

Kasiliauskaite A, Kubicek K, Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, and Stefl R (2022). Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res 50, 5961–5973. 10.1093/nar/gkac451. PubMed DOI PMC

McCullough L, Connell Z, Petersen C, and Formosa T (2015). The Abundant Histone Chaperones Spt6 and FACT Collaborate to Assemble, Inspect, and Maintain Chromatin Structure in Saccharomyces cerevisiae. Genetics 201, 1031–1045. 10.1534/genetics.115.180794. PubMed DOI PMC

Close D, Johnson SJ, Sdano MA, McDonald SM, Robinson H, Formosa T, and Hill CP (2011). Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain. J Mol Biol 408, 697–713. 10.1016/j.jmb.2011.03.002. PubMed DOI PMC

Markert JW, Soffers JH, and Farnung L (2025). Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription. Science 387, 528–533. 10.1126/science.adn6319. PubMed DOI PMC

Swanson MS, Carlson M, and Winston F (1990). SPT6, an essential gene that affects transcription in Saccharomyces cerevisiae, encodes a nuclear protein with an extremely acidic amino terminus. Mol Cell Biol 10, 4935–4941. 10.1128/mcb.10.9.4935-4941.1990. PubMed DOI PMC

Lyons H, Veettil RT, Pradhan P, Fornero C, De La Cruz N, Ito K, Eppert M, Roeder RG, and Sabari BR (2023). Functional partitioning of transcriptional regulators by patterned charge blocks. Cell 186, 327–345 e328. 10.1016/j.cell.2022.12.013. PubMed DOI PMC

Prather D, Krogan NJ, Emili A, Greenblatt JF, and Winston F (2005). Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol Cell Biol 25, 10122–10135. 10.1128/MCB.25.22.10122-10135.2005. PubMed DOI PMC

Mayer A, Lidschreiber M, Siebert M, Leike K, Soding J, and Cramer P (2010). Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol 17, 1272–1278. 10.1038/nsmb.1903. PubMed DOI

Kujirai T, Kato J, Yamamoto K, Hirai S, Fujii T, Maehara K, Harada A, Negishi L, Ogasawara M, Yamaguchi Y, et al. (2025). Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis. Nat Commun 16, 4724. 10.1038/s41467-025-59580-x. PubMed DOI PMC

Dronamraju R, Kerschner JL, Peck SA, Hepperla AJ, Adams AT, Hughes KD, Aslam S, Yoblinski AR, Davis IJ, Mosley AL, and Strahl BD (2018). Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction. Cell Rep 25, 3476–3489 e3475. 10.1016/j.celrep.2018.11.089. PubMed DOI PMC

Gopalakrishnan R, and Winston F (2021). The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions. J Biol Chem 297, 101205. 10.1016/j.jbc.2021.101205. PubMed DOI PMC

Evrin C, Serra-Cardona A, Duan S, Mukherjee PP, Zhang Z, and Labib KPM (2022). Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II. EMBO J 41, e109783. 10.15252/embj.2021109783. PubMed DOI PMC

Crickard JB, Lee J, Lee TH, and Reese JC (2017). The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome. Nucleic Acids Res 45, 6362–6374. 10.1093/nar/gkx220. PubMed DOI PMC

Ellison MA, Namjilsuren S, Shirra MK, Blacksmith MS, Schusteff RA, Kerr EM, Fang F, Xiang Y, Shi Y, and Arndt KM (2023). Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae. Nucleic Acids Res 51, 4814–4830. 10.1093/nar/gkad180. PubMed DOI PMC

Jonas F, Vidavski M, Benuck E, Barkai N, and Yaakov G (2023). Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding. Nucleic Acids Res 51, 8496–8513. 10.1093/nar/gkad615. PubMed DOI PMC

Nyamugenda E, Cox AB, Pierce JB, Banning RC, Huynh ML, May C, Marshall S, Turkal CE, and Duina AA (2018). Charged residues on the side of the nucleosome contribute to normal Spt16-gene interactions in budding yeast. Epigenetics 13, 1–7. 10.1080/15592294.2017.1418132. PubMed DOI PMC

Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, et al. (2024). Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500. 10.1038/s41586-024-07487-w. PubMed DOI PMC

Goswami I, Sandlesh P, Stablewski A, Toshkov I, Safina AF, Magnitov M, Wang J, and Gurova K (2022). FACT maintains nucleosomes during transcription and stem cell viability in adult mice. EMBO Rep 23, e53684. 10.15252/embr.202153684. PubMed DOI PMC

Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, and Robert F (2021). FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell 81, 3542–3559 e3511. 10.1016/j.molcel.2021.07.010. PubMed DOI PMC

Martin BJE, Chruscicki AT, and Howe LJ (2018). Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes in Saccharomyces cerevisiae. Genetics 210, 869–881. 10.1534/genetics.118.301349. PubMed DOI PMC

McCauley MJ, Morse M, Becker N, Hu Q, Botuyan MV, Navarrete E, Huo R, Muthurajan UM, Rouzina I, Luger K, et al. (2022). Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes. Cell Rep 41, 111858. 10.1016/j.celrep.2022.111858. PubMed DOI PMC

Valieva ME, Armeev GA, Kudryashova KS, Gerasimova NS, Shaytan AK, Kulaeva OI, McCullough LL, Formosa T, Georgiev PG, Kirpichnikov MP, et al. (2016). Large-scale ATP-independent nucleosome unfolding by a histone chaperone. Nat Struct Mol Biol 23, 1111–1116. 10.1038/nsmb.3321. PubMed DOI PMC

Xin H, Takahata S, Blanksma M, McCullough L, Stillman DJ, and Formosa T (2009). yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. Mol Cell 35, 365–376. 10.1016/j.molcel.2009.06.024. PubMed DOI PMC

McCullough LL, Pham TH, Parnell TJ, Connell Z, Chandrasekharan MB, Stillman DJ, and Formosa T (2019). Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae. Genetics 211, 877–892. 10.1534/genetics.118.301853. PubMed DOI PMC

Burgos-Bravo F, Tong AB, Li C, Diaz-Celis C, Kaplan CD, LeRoy G, Reinberg D, and Bustamante C (2025). FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate. Mol Cell. 10.1016/j.molcel.2025.05.002. PubMed DOI PMC

Li Y, and Huang H (2023). Structural basis for H2A-H2B recognitions by human Spt16. Biochem Biophys Res Commun 651, 85–91. 10.1016/j.bbrc.2023.02.016. PubMed DOI

Li S, Almeida AR, Radebaugh CA, Zhang L, Chen X, Huang L, Thurston AK, Kalashnikova AA, Hansen JC, Luger K, and Stargell LA (2018). The elongation factor Spn1 is a multi-functional chromatin binding protein. Nucleic Acids Res 46, 2321–2334. 10.1093/nar/gkx1305. PubMed DOI PMC

Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, et al. (2024). Parental histone transfer caught at the replication fork. Nature. 10.1038/s41586-024-07152-2. PubMed DOI

Clark-Adams CD, Norris D, Osley MA, Fassler JS, and Winston F (1988). Changes in histone gene dosage alter transcription in yeast. Genes Dev 2, 150–159. 10.1101/gad.2.2.150. PubMed DOI

Swanson MS, and Winston F (1992). SPT4, SPT5 and SPT6 interactions: effects on transcription and viability in Saccharomyces cerevisiae. Genetics 132, 325–336. 10.1093/genetics/132.2.325. PubMed DOI PMC

De La Cruz N, Pradhan P, Veettil RT, Conti BA, Oppikofer M, and Sabari BR (2024). Disorder-mediated interactions target proteins to specific condensates. Mol Cell 84, 3497–3512 e3499. 10.1016/j.molcel.2024.08.017. PubMed DOI PMC

Jones DT, and Cozzetto D (2015). DISOPRED3: precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31, 857–863. 10.1093/bioinformatics/btu744. PubMed DOI PMC

Fassler JS, and Winston F (1988). Isolation and analysis of a novel class of suppressor of Ty insertion mutations in Saccharomyces cerevisiae. Genetics 118, 203–212. 10.1093/genetics/118.2.203. PubMed DOI PMC

Klein DC, Troy K, Tripplehorn SA, and Hainer SJ (2023). The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. BMC Genomics 24, 201. 10.1186/s12864-023-09287-4. PubMed DOI PMC

Langmead B, and Salzberg SL (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359. 10.1038/nmeth.1923. PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079. 10.1093/bioinformatics/btp352. PubMed DOI PMC

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, and Li H (2021). Twelve years of SAMtools and BCFtools. Gigascience 10. 10.1093/gigascience/giab008. PubMed DOI PMC

Quinlan AR, and Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842. 10.1093/bioinformatics/btq033. PubMed DOI PMC

Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dundar F, and Manke T (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44, W160–165. 10.1093/nar/gkw257. PubMed DOI PMC

Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, et al. (2012). Fiji: an open-source platform for biological-image analysis. Nat Methods 9, 676–682. 10.1038/nmeth.2019. PubMed DOI PMC

Lima DB, de Lima TB, Balbuena TS, Neves-Ferreira AGC, Barbosa VC, Gozzo FC, and Carvalho PC (2015). SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. J Proteomics 129, 51–55. 10.1016/j.jprot.2015.01.013. PubMed DOI

Lima DB, Melchior JT, Morris J, Barbosa VC, Chamot-Rooke J, Fioramonte M, Souza T, Fischer JSG, Gozzo FC, Carvalho PC, and Davidson WS (2018). Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins. Nat Protoc 13, 431–458. 10.1038/nprot.2017.113. PubMed DOI

Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, and Ferrin TE (2021). UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci 30, 70–82. 10.1002/pro.3943. PubMed DOI PMC

Winston F, Dollard C, and Ricupero-Hovasse SL (1995). Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11, 53–55. 10.1002/yea.320110107. PubMed DOI

Rose MD, Winston F, and Hieter P (1990). Methods in Yeast Genetics (Cold Spring Harbor Laboratory Press; ).

Laughery MF, Hunter T, Brown A, Hoopes J, Ostbye T, Shumaker T, and Wyrick JJ (2015). New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. Yeast 32, 711–720. 10.1002/yea.3098. PubMed DOI PMC

Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, and Luger K (2004). Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol 375, 23–44. 10.1016/s0076-6879(03)75002-2. PubMed DOI

Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, et al. (2023). Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res 51, 10011–10025. 10.1093/nar/gkad674. PubMed DOI PMC

Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC, Ciferri C, and Dimitrova YN (2020). Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 A Resolution. Structure 28, 363–370 e363. 10.1016/j.str.2019.12.002. PubMed DOI PMC

Ruone S, Rhoades AR, and Formosa T (2003). Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. J Biol Chem 278, 45288–45295. 10.1074/jbc.M307291200. PubMed DOI

Laemmli UK (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685. 10.1038/227680a0. PubMed DOI

Renshaw PS, Veverka V, Kelly G, Frenkiel TA, Williamson RA, Gordon SV, Hewinson RG, and Carr MD (2004). Sequence-specific assignment and secondary structure determination of the 195-residue complex formed by the Mycobacterium tuberculosis proteins CFP-10 and ESAT-6. J Biomol NMR 30, 225–226. 10.1023/B:JNMR.0000048852.40853.5c. PubMed DOI

Veverka V, Lennie G, Crabbe T, Bird I, Taylor RJ, and Carr MD (2006). NMR assignment of the mTOR domain responsible for rapamycin binding. J Biomol NMR 36 Suppl 1, 3. 10.1007/s10858-005-4324-1. PubMed DOI

Moriwaki Y, Yamane T, Ohtomo H, Ikeguchi M, Kurita J, Sato M, Nagadoi A, Shimojo H, and Nishimura Y (2016). Solution structure of the isolated histone H2A-H2B heterodimer. Sci Rep 6, 24999. 10.1038/srep24999. PubMed DOI PMC

Lee W, Tonelli M, and Markley JL (2015). NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31, 1325–1327. 10.1093/bioinformatics/btu830. PubMed DOI PMC

Veverka V, Crabbe T, Bird I, Lennie G, Muskett FW, Taylor RJ, and Carr MD (2008). Structural characterization of the interaction of mTOR with phosphatidic acid and a novel class of inhibitor: compelling evidence for a central role of the FRB domain in small molecule-mediated regulation of mTOR. Oncogene 27, 585–595. 10.1038/sj.onc.1210693. PubMed DOI

Schanda P, Kupce E, and Brutscher B (2005). SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33, 199–211. 10.1007/s10858-005-4425-x. PubMed DOI

Gopalakrishnan R, and Winston F (2019). Whole-Genome Sequencing of Yeast Cells. Curr Protoc Mol Biol 128, e103. 10.1002/cpmb.103. PubMed DOI PMC

Ellison MA, Walker JL, Ropp PJ, Durrant JD, and Arndt KM (2020). MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations. G3 (Bethesda) 10, 3009–3014. 10.1534/g3.120.401396. PubMed DOI PMC

McKnight LE, Crandall JG, Bailey TB, Banks OGB, Orlandi KN, Truong VN, Donovan DA, Waddell GL, Wiles ET, Hansen SD, et al. (2021). Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms. STAR Protoc 2, 100486. 10.1016/j.xpro.2021.100486. PubMed DOI PMC

Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A, et al. (2006). A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Nature 439, 497–501. 10.1038/nature04384. PubMed DOI

Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, and Mesirov JP (2011). Integrative genomics viewer. Nat Biotechnol 29, 24–26. 10.1038/nbt.1754. PubMed DOI PMC