List of Selected Publications
Krishnaraj A*, Wei X*, Thakral R*, Guo W, Subramanian SB, Zhang X, Alley KR, Feng A, Hoy A, Kung D, Tiwari PB, Uren A, Maillard R, DeRose V, Nair SJ (2025) Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs. https://www.biorxiv.org/content/10.64898/2025.12.20.694502v1. *Co-first authors.
Wang S, Suter T, Gamliel A, Kim Y, Nair SJ, Oh S, Yang F, Ohgi KA, Wagner T, Gan S, Rosenfeld MG (2025) Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During Ligand-Mediated Transcriptional Burst Events, eLife14:RP108726. PMID: 40894578.
Krishnaraj A and Nair SJ. Quantifying Intracellular Platinum Accumulation Using Inductively Coupled Mass Spectrometry. Current Protocols. 2024 Sep;4(9): e70012. doi: 10.1002/cpz1.70012. PMID:39240240
Wagner T#, Priyanka P#, Micheletti R#, Friedman MJ*, Nair SJ*, Gamliel A*, Taylor H*, Song X*, Cho M*, Oh S, Li W, Han J, Ohgi KA, Abrass M, D'Antonio-Chronowska A, D'Antonio M, Hazuda H, Duggirala R, Blangero J, Ding S, Guzmann C, Frazer KA, Aggarwal AK, Zemljic-Harpf AE, Rosenfeld MG, Suh Y. Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription. bioRxiv. 2024 May. doi:0.1101/2024.05.17.594600.PMID: 38798402. #Co-first authors, *Equal contributions.
Tan Y, Yao L, Gamliel A, Nair SJ, Taylor H, Ohgi K, Aggarwal AK, Rosenfeld MG. Signal-induced Enhancer Activation Requires Ku70 to Read Topoisomerase1-DNA Covalent Complexes. Nature Structural & Molecular Biology. 2023 Feb;30(2):148-158. doi: 10.1038/s41594-022-00883-8.
Gamliel A@, Meluzzi D, Oh S, Jiang N, Destici E, Rosenfeld MG@, Nair SJ@. Long-distance association of topological boundaries through nuclear condensates. Proceedings of the National Academy of Sciences 119 (32) e2206216119. (@Corresponding authors).
Nair SJ@, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG@. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends in Genetics: 38(10):1019-1047. PMID:35811173 (@Corresponding authors). Cover article.
Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee J, Nair SJ, Yang F, Ohgi K, Frazer K, Zhang Z, Li W, Rosenfeld MG. Enhancer Release and Retargeting Activates Disease Susceptibility Genes. Nature, 2021Jul 595(7869):735-740. DOI:10.1038/s41586-021-03577-1 PMID: 34040254.
Pre-2021
Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I (2020) “Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells.” Cell Reports, 31(3):107532
Nair SJ@, Yang Lu, Meluzzi D, Oh S, Yang F, Friedman M, Wang S, Suter T, Alshareedah I, Gamliel A, Ma Q, Zhang J, Hu Y, Tan Y, Ohgi K, Jayani RS, Banerjee PR, Aggarwal, AK, Rosenfeld MG@ (2019) “Ligand-Induced Enhancer Cooperation by Localization in a Phase-separated Structure Dictates Functional Robustness”, Nature Structural & Molecular Biology, 26(3): 193-203 (@Corresponding authors). Recommended by F1000,
Commentaries on this article: ERa Condensates: Chronic Stimulation is Hard to Ignore, Nature Structural & Molecular
Biology, 26(3):
Koch, L (2019). Enhancer Assemble, Nature Reviews Genetics, 20(3)
Zhang X*, Chiang H-C*, Wang Y*, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R (2017) “Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis”. Nature Communications: 8:15908
Nair SJ*, Zhang X*, Chiang H-C*, Wang Y, Jahid, Md J, Wang Y, Garza P, April C, Salathia N, Banerjee T, Alenazi FS, Ruan J, Fan J-B, Parvin JD, Jin VX, Hu Y, Li R (2016) “Genetic Suppression Reveals DNA Repair-independent Antagonism Between BRCA1 and COBRA1 in Mammary Gland Development”. Nature Communications: 7:10913. * Co-first author.
Chiang H-C*, Nair SJ*, Ghosh S, Sun L, Santillan-Gomez A, Yeh I-T, Hu Y, Elledge R, Li R (2012) “Association of Radiotherapy with Preferential Depletion of Luminal Epithelial Cells in a BRCA1 Mutation Carrier”. Exp Hematol Oncol: 1(1):31. * Co-first author.
Sun JS, Pan H, Lei C, Yuan B, Nair SJ, April C, Parameswaran B, Klotzle B, Fan J-B, Ruan J, Li R (2011) “Genetic and Genomic Analyses of RNA Polymerase II Pausing Factor in Regulation of Mammalian Transcription and Cell Growth”. J Biol Chem: 286(42): 36248-57.
Amleh A, Nair SJ*, Sun J, Sutherland A, Hasty P, Li R (2009) “Mouse Cofactor of BRCA1 (Cobra1) Is Required for Early Embryogenesis” Plos One:4(4):e5034. * Co-first author.