Publications

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

Abby Trouth*, Kamesh Ravichandran*, Philip Gafken, Sara Martire, Stephanie J Namciu, Laura A Banaszynski, Jay F Sarthy, Srinivas Ramachandran^#. G1 length dictates heterochromatin landscape. bioRxiv 2023.12.05.570186
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

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

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

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

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

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

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

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
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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

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

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

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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