Srinivas Ramachandran, PhD

Publications

• 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. 2024 Dec 29. PubMed PMID: 39763830
• Trouth A, Veronezi GMB, Ramachandran S. The impact of cell states on heterochromatin dynamics. Biochem J. 2024 Nov 6;481(21):1519-1533. PubMed PMID: 39422321
• 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 Rep. 2024 Sep 24;43(9):114724. PubMed PMID: 39264807
• Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney 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. Mol Cell. 2024 Jul 25;84(14):2648-2664.e10. PubMed PMID: 38955181
• 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 Jun 13. PubMed PMID: 38915666
• Veronezi GMB, Ramachandran S. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Rep. 2024 Apr 23;43(4):114090. PubMed PMID: 38607915
• 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. bioRxiv. 2024 Jul 29. PubMed PMID: 38559248
• 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 Feb 5. PubMed PMID: 38370615
• Trouth A, Ravichandran K, Gafken PR, Martire S, Boyle GE, Veronezi GMB, La V, Namciu SJ, Banaszynski LA, Sarthy JF, Ramachandran S. G1 length dictates H3K27me3 landscapes. bioRxiv. 2024 Aug 26. PubMed PMID: 38106207
• Lewis HC, Kelnhofer-Millevolte LE, Brinkley MR, Arbach HE, Arnold EA, Sanders S, Bosse JB, Ramachandran S, Avgousti DC. HSV-1 exploits host heterochromatin for nuclear egress. J Cell Biol. 2023 Sep 4;222(9). PubMed PMID: 37516914
• 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. Mol Cell. 2022 Oct 6;82(19):3632-3645.e4. PubMed PMID: 36206739
• Rao S, Han AL, Zukowski A, Kopin E, Sartorius CA, Kabos P, Ramachandran S. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer. Sci Adv. 2022 Aug 26;8(34):eabm4358. PubMed PMID: 36001652
• Rao S, Ramachandran S. A computational pipeline to visualize DNA-protein binding states using dSMF data. STAR Protoc. 2022 Jun 17;3(2):101299. PubMed PMID: 35463472
• Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annu Rev Biochem. 2022 Jun 21;91:183-195. PubMed PMID: 35303789
• Rao S, Ahmad K, Ramachandran S. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Mol Cell. 2021 Apr 15;81(8):1651-1665.e4. PubMed PMID: 33705711
• Satyanarayan Rao*, Amy L. Han*, Alexis Zukowski, Etana Kopin, Carol A. Sartorius, Peter Kabos#, Srinivas Ramachandran#. Mapping Transcription Factor-Nucleosome Dynamics from Plasma cfDNA. bioRxiv 2021.04.14.439883; doi: https://doi.org/10.1101/2021.04.14.439883
• 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 TH, Happoldt C, O'Conner B, Janknecht R, Li CY, Marrack P, Kappler J, Leach S, Zhang G. JMJD5 couples with CDK9 to release the paused RNA polymerase II. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19888-19895. PubMed PMID: 32747552
• Zukowski A, Rao S, Ramachandran S. Phenotypes from cell-free DNA. Open Biol. 2020 Sep;10(9):200119. PubMed PMID: 32873154
• Jagannathan S, Ramachandran S, Rissland OS. Slow Down to Catch Up. Cell. 2019 Aug 8;178(4):774-776. PubMed PMID: 31398334
• Yee WB, Delaney PM, Vanderzalm PJ, Ramachandran S, Fehon RG. The CAF-1 complex couples Hippo pathway target gene expression and DNA replication. Mol Biol Cell. 2019 Nov 1;30(23):2929-2942. PubMed PMID: 31553691
• Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol. 2018;1832:159-168. PubMed PMID: 30073526
• Henikoff S, Ramachandran S. Pioneers Invade the Nucleosomal Landscape. Mol Cell. 2018 Jul 19;71(2):193-194. PubMed PMID: 30028998
• Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol. 2018 Feb 9;19(1):19. PubMed PMID: 29426353
• Kami Ahmad*, Steven Henikoff, Srinivas Ramachandran*. Managing the steady state chromatin landscape by nucleosome dynamics. Annual Reviews Biochemistry (in press)