Publications

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

2024

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

Kelnhofer-Millevolte LE, Smith JR, Nguyen DH, Wilson LS, Lewis HC, Arnold EA, Brinkley MR, Geballe AP, Ramachandran S, Avgousti DC^#. Human cytomegalovirus induces neuronal gene expression for viral maturation. bioRxiv 2024.06.13.598910

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

Trouth A*, Ravichandran K*, Gafken P, Martire S, Boyle GE, Veronezi GMB, La V, Namciu SJ, Banaszynski LA, Sarthy JF, Ramachandran S^#. G1 length dictates H3K27me3 landscapes. bioRxiv 202.12.05.570186; doi: https://doi.org/10.1101/2023.12.05.570186

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

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

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

Han AL, Vinod-Paul K, Rao S, Brechbuhl HM, Sartorius CA, Ramachandran S^#, Kabos P^#. Estradiol (E2) concentration shapes the chromatin binding landscape of the estrogen receptor. biorXiv 2022 Sep 23

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

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

Commentary by Abdulhay and Ramani

Talk describing this work

2020

Zkowski 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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