Pre-printed versions:

2023

Ajay Larkin, Colin Kunze, Melissa Seman, Alexander Levashkevich, Justin Curran, Ahmad Khail* and Kaushik Ragunathan*, “Mapping the dynamics of epigenetic adaptationdoi.org/10.1101/2023.07.10.548368 (bioRxiv)- in revision, Developmental Cell

Basila Moochickal Assainar, Kaushik Ragunathan* and Ryan Baldridge*, “Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERADdoi.org/10.1101/2023.06.20.545802 (bioRxiv)- accepted, Nature Communications

Melissa Seman, Alexander Levashkevich, Ajay Larkin, Fengting Huang and Kaushik Ragunathan*, “Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenancedoi.org/10.1101/2023.04.30.538869 (bioRxiv)- accepted, Cell Reports

Ziyuan Chen, Melissa Seman, Ali Farhat, Yekaterina Fyodorova, Saikat Biswas, Alexander Levashkevich, Peter L. Freddolino, Julie S. Biteen*, and Kaushik Ragunathan*, “Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactionsdoi.org/10.1101/2023.03.08.531771 (bioRxiv)- in revision, Nucleic Acids Research

Jessica F. Williams, Ivan V. Surovtsev, Sarah M. Schreiner, Ziyuan Chen, GulzhanRaiymbek, Hang Nguyen, Yan Hu, Julie S. Biteen, Simon G.J. Mochrie, Kaushik Ragunathan*, Megan C. King*, “The condensation of HP1-α/Swi6 imparts nuclear stiffness” doi.org/10.1101/2020.07.02.184127 (bioRxiv)

Amanda Ames, Melissa Seman, Ajay Larkin, Gulzhan Raiymbek, Ziyuan Chen, AlexLevashkevich, Julie Suzanne Biteen, Kaushik Ragunathan*, “Identification of a novel, tunable interface in the S.pombe HP1 protein, Swi6, that underpins epigenetic inheritance” doi.org/10.1101/2023.11.28.569027, (bioRxiv)

Published versions:

2023

Melissa Seman, Alexander Levashkevich, Ajay Larkin, Fengting Huang and Kaushik Ragunathan*, “Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance” Cell Reports, 42(11), 2023 doi.org/10.1016/j.celrep.2023.113428

2022

Saikat Biswas, Joshua D. Karslake, Ziyuan Chen, Ali Farhat, Amanda Ames, Gulzhan Raiymbek, Peter L. Freddolino*, Julie S. Biteen*, and Kaushik Ragunathan*, “HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization Science Advances (link)

Kehan Bao, Chun-Min Shan, Xiao Chen, Gulzhan Raiymbek, Jeremy G. Monroe, Yimeng Fang, Takenori Toda, Kristin S. Koutmou, Kaushik Ragunathan, Chao Lu, Luke E. Berchowitz, Songtao Jia, “The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly” PLOS Genetics (2022) doi.org/10.1371/journal.pgen.1010049

Lindsay Moritz et al., “Single residue substitution in protamine 1 disrupts sperm genome packaging and embryonic development in mice” in revision, Nature Structural and Molecular Biology (bioRxiv)

2021

Ajay Larkin*, Amanda Ames*, Melissa Seman* and Kaushik Ragunathan, “Investigating mitotic inheritance of histone modifications using tethering strategies” Methods in Molecular Biology, Springer-Nature series: Histone methyltransferases: Methods and Protocols (accepted)

2020

Raiymbek G, An S, Khurana N, Gopinath S, Larkin, A, Biswas, S, Trievel R, Cho US, Ragunathan K, “An H3K9 methylation dependent protein interaction regulates the non-enzymatic function of a putative histone demethylase” eLife 2020;9:e53155 (PDF) #labinthetimeofcovid-19

2017

Abeysirigunawardena SC, Kim H, Lai J, Ragunathan, K Rappé MC, Luthey-Schulten Z, Ha T, Woodson SA. “Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes” Nat Commun. 8;8(1):492 (2017)

2015

Ragunathan, K., G.Jih and D.Moazed “Epigenetic inheritance uncoupled from sequence specific recruitment” Science 348(6230), 1258699 (2015)

2014

S.Kim , K. Ragunathan , J. Park , C. Joo , D. Kim , and T. Ha “Cooperative conformational transitions keep RecA filament active during ATPase cycle” J. Am. Chem. Soc., 136 (42), pp 14796–14800 (2014)

H. Kim,  S.C. Abeysirigunawarden,  K. Chen,  M. Mayerle,  K. Ragunathan,  Z. Luthey-Schulten,  T. Ha , S.A. Woodson, “Protein-guided RNA dynamics during early ribosome assembly”, Nature 506, 334–338 (2014)

News and Views: Kathleen B. Hall “Molecular biology: Protein binding cannot subdue a lively RNA” 

2012

Ragunathan,K., C. Liu and T.Ha, “RecA filament sliding on DNA facilitates homology search”, eLife 1:e00067 (2012)

Commentary – B.Gibb and E.Greene, “Sliding to the rescue of damaged DNA” 

H.Koh, M.Kidwell, K. Ragunathan, J.Doudna and S.Myong “ATP-independent diffusion of double stranded RNA binding proteins”, Proc.Natl.Acad.Sci 110(1) 151-156 (2012)

2011

Ragunathan,K., C. Joo and T.Ha, “Real time observation of strand exchange reaction with high spatiotemporal resolution”, Structure 19(8) 1064-73 (2011)            

Commentary – C.Wyman, “Mechanistic insight from Chaos: How RecA Mediates DNA Strand Exchange”
Evaluated at F1000 biology

Jain, A., R.Liu, B.Ramani, E.Aruaz, Y.Ishitsuka, K. Ragunathan, J. Park, J. Chen, Y. Xiang and T.Ha, “Probing cellular protein complexes using single-molecule pull-down”, Nature 473, 484-488 (2011)

2010

Lee, J., S. Lee, K. Ragunathan, C. Joo, T. Ha and S. Hohng, “Single-molecule four-color FRET”, Angew. Chem. Int. Ed. 49(51), 9922-9925 (2010)