Publications

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*Equal contribution; ^#Corresponding author; Bold – lab members

2026

• Jeffrey N. Dudley, Joel E. Berends, Chayan K. De, Tongchen He, Giovana B. Veronezi, Benedict Abdon, Anjali Sengar, Matthias C. Truttmann, Mats Ljungman, Lanbo Xiao, Srinivas Ramachandran, Sethuramasundaram Pitchiaya. Divergent condensates tune transcriptional responses during stress. bioRxiv [Preprint]. 2026.02.12.705659. doi: https://doi.org/10.64898/2026.02.12.705659

2025

• La V, Trouth A, Ramani V, Ramachandran S^#. Rotational settings quantize nucleosome movement by chromatin regulators. bioRxiv [Preprint]. 2025 Dec 12: 2025.12.12.693854. doi: https://doi.org/10.64898/2025.12.12.693854
• Silveria S, Peeters JG, Vickery J, Veronezi GMB, Ramachandran S, DuPage M. Epigenetically regulated p53 activity maintains intestinal regulatory T cell identity to prevent inflammation. bioRxiv [Preprint]. 2025 Sep 3:2025.08.29.673118. doi: 10.1101/2025.08.29.673118.
• Kelnhofer-Millevolte LE, Smith JR, Nguyen DH, Wilson LS, Lewis HC, Arnold EA, Brinkley MR, Shin K, Ahn JH, Kim ET, Kulej K, Geballe AP, Ramachandran S, Avgousti DC. Human cytomegalovirus induces neuronal gene expression through IE1 for viral maturation. Nat Commun. 2025 Aug 8;16(1):7316. doi: 10.1038/s41467-025-61915-7.

Preprint

• Han AL, Vinod-Paul K, Rao S, Brechbuhl HM, Sartorius CA, Ramachandran S^#, Kabos P^#. Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha. J Biol Chem. 2025 Apr 9:108499. doi: 10.1016/j.jbc.2025.108499.

Preprint

• Trouth A*, Ravichandran K*, Gafken P, Martire S, Boyle GE, Veronezi GMB, La V, Namciu SJ, Banaszynski LA, Sarthy JF, Ramachandran S^#. The length of the G1 phase is an essential determinant of H3K27me3 landscapes across diverse cell types. PLoS Biol. 2025 Apr 17;23(4):e3003119. doi: 10.1371/journal.pbio.3003119

Preprint

• Tonsager AJ, Zukowski A, Radebaugh CA, Weirich A, Stargell LA^#, Ramachandran S^#. The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames. G3 (Bethesda). 2025 Apr 17;15(4):jkaf032. doi: 10.1093/g3journal/jkaf032

Preprint

2024

• Brechbuhl HM, Han A, Paul KV, Nemkov T, Ramachandran S, Ward A, Jacobsen BM, Hansen K, Sartorius CA, D’Alessandro A, Kabos P. Metabolic Switch in Endocrine Resistant Estrogen Receptor Positive Breast Cancer. bioRxiv [Preprint]. 2024 Dec 29:2024.12.28.630631. doi: 10.1101/2024.12.28.630631.
• Peeters JGC, Silveria S, Ozdemir M, Ramachandran S^#, DuPage M^#. Hyperactivating EZH2 to augment H3K27me3 levels in regulatory T cells enhances immune suppression by driving early effector differentiation. Cell Reports 2024 Sep 11;43(9):114724 doi: 10.1016/j.celrep.2024.114724

Preprint

• Tonsager AJ, Zukowski A, Radebaugh CA, Weirich A, Stargell LA^#, Ramachandran S^#. The Histone Chaperone Spn1 Preserves Subnucleosomal Structures at Promoters and Nucleosome Positioning in Open Reading Frames. bioRxiv 2024.03.14.585010. doi: 10.1101/2024.03.14.585010
• Ingersoll S*, Trouth A*, Luo X, Espinoza A, Wen J, Tucker J, Astatike K, Phiel CJ, Kutateladze TG, Wu TP, Ramachandran S^#, Ren X^#. Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes. bioRxiv 2024.02.05.578969
• Zhao H, Li J, Xiang Y, Malik S, Vartak S, Veronezi GMB, Young N, Ryner M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R & Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Molecular Cell 2024 Jul 25;84(14): 2648-2664.e10. doi: 10.1016/j.molcel.2024.06.006
• Veronezi GMB, Ramachandran S^#. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Reports 2024 Apr 11;43(4):114090. doi: 10.1016/j.celrep.2024.114090

Preprint

2023

• Lewis HC*, Kelnhofer-Millevolte L*, Brinkley MR, Arbach HE, Arnold EA, Sanders S, Bosse JB, Ramachandran S^#, Avgousti DC^#. HSV-1 exploits host heterochromatin for nuclear egress. Journal of Cell Biology 2023 Sep 4;222(9):e202304106

Preprint

2022

• Fong N, Sheridan RM, Ramachandran S, Bentley DL. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model. Molecular Cell 2022 Oct 6;82(19):3632-3645.e4
• Rao S*, Han AL*, Zukowski A, Kopin E, Sartorius CA, Kabos P^#, Ramachandran S^#. Mapping Transcription Factor-Nucleosome Dynamics from Plasma cfDNA. Science Advances 2022 Aug 26;8(34):eabm4358

Highlight by Jonathan Dennis

Preprint

• Rao S, Ramachandran S^#.  A computational pipeline to visualize DNA-protein binding states using dSMF data. STAR Protocols 2022 Apr 12;3(2):101299
• Ahmad K, Henikoff S,Ramachandran S.  Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annual Review of Biochemistry June 2022 Vol. 19

2021

• Rao S, Ahmad K, Ramachandran S^#. Cooperative Binding of Transcription Factors is a Hallmark of Active Enhancers. Molecular Cell 2021 Apr 15;81(8):1651-1665.e4. doi: 10.1016/j.molcel.2021.02.014. Epub 2021 Mar 1

Cover

Commentary by Abdulhay and Ramani

Preprint

Talk describing this work

2020

• Zukowski A*, Rao S*, Ramachandran S^#. Phenotypes from cell-free DNA. Open Biology 2020
  
  
• Liu H, Ramachandran S, Fong N, Phang T, Lee S, Parsa P, Liu X, Harmacek L, Danhorn T, Song T, Oh S, Zhang Q, Chen Z, Zhang Q, Tu T, Happoldt C, O’Conner B, Janknecht R, Li C, Marrack P, Kappler J, Leach S, Zhang G. JMJD5 couples with CDK9 to release the paused RNA polymerase II. Proceedings of the National Academy of Sciences of the USA 2020 Aug 3; 202005745

2019

• Yee WB, Delaney PM, Vanderzalm PJ, Ramachandran S^#, Fehon, RG^#. The CAF-1 Complex Couples Hippo Pathway Target Gene Expression and DNA Replication. Molecular Biology of the Cell 2019 Nov 1;30(23):2929-2942
• Jagannathan S, Ramachandran S, Rissland O. Slow down to catch up. Cell 2019 Aug 8; 178(4):774-776

2018

• Chereji R*, Ramachandran S*, Bryson TD,  Henikoff, S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biology 2018 Feb 9; 19(1):19
• Ramachandran S, and Henikoff S. MINCE-seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods in Molecular Biology 2018;1832:159-168
• Henikoff S, and Ramachandran S. Pioneers invade the nucleosome landscape. Molecular Cell 2018 Jul 19;71(2):193-194

2017

• Ramachandran S, Ahmad K,  Henikoff, S. Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Molecular Cell 2017 Dec 21; 68(6):1038-1053. pubmed journal
  
       Cover
  
       Featured in “Meet the Author”
• Warfield L*, Ramachandran S*, Baptista T, Devys D, Tora L, Hahn S. Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factior TFIID. Molecular Cell 2017 Oct 5; 68:1-12 pubmed journal
  
       Preview by Dylan Taatjes : The Continuing SAGA of TFIID and RNA Polymerase II Transcription
• Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: establishing chromatin specificity behind the replication fork. Bioessays 2016 pubmed

2016

• Ramachandran, S., Henikoff, S. “Transcriptional regulators compete with nucleosomes post-replication”, Cell, 165(3):580-92 (2016) pubmed  journal
  
       Science Spotlight at Fred Hutchinson Cancer Research Center
• Ramachandran S., and Henikoff, S. “Nucleosome dynamics during chromatin remodeling in vivo”, Nucleus 7(1):20-6 (2016)  pubmed    journal

2015

• Ramachandran, S., Zentner G. E., Henikoff, S. “Asymmetric nucleosomes flank promoters in the budding yeast genome”, Genome Research, 25(3):381-90 (2015) pubmed     journal
• Ramachandran, S., and Henikoff, S. “Replicating nucleosomes”, Science Advances 1, e1500587 (2015)  pubmed    journal

2014

• Henikoff, S, Ramachandran, S., Krassovsky K., Bryson, T. D., Brogaard, K., Widom, J., Wang, J-P. and Henikoff, J. G. “The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo”, eLife, e01861 (2014)  pubmed     journal
• Weber, C. M., Ramachandran, S., Henikoff, S. “Nucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase”, Molecular Cell, 53(5):819-30 (2014) pubmed journal
  
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