Publications

2023

Wille, C.K.,  Neumann, E.N., Deshpande, A.J. and Sridharan, R. (2023) DOT1L interaction partner AF10 controls patterning of H3K79 methylation and RNA polymerase II to maintain cell identity. Stem Cell Reports 2023 Dec 12;18(12):2451-2463. doi: 10.1016/j.stemcr.2023.10.017. Epub 2023 Nov 22. PMID: 37995701; PMCID: PMC10724070.

Wille, C.K. *,  Zhang, X. *, Haws, S.A., Denu, J.M. and Sridharan, R. (2023)  DOT1L is a barrier to histone acetylation during reprogramming to pluripotency. Science Advances * co-first authors- Nov 15;9(46):eadf3980PMID: 37976354; PMCID: PMC10656071

Salamon RJ, McKeon MC, Bae J, Zhang X, Paltzer WG, Wanless KN, Schuett AR, Nuttall DJ, Nemr SA, Sridharan R, Lee Y, Kamp TJ, Mahmoud AI. LRRC10 regulates mammalian cardiomyocyte cell cycle during heart regeneration. NPJ Regen Med. (2023) Jul 28;8(1):39. doi: 10.1038/s41536-023-00316-0. PMID: 37507410; PMCID: PMC10382521.

Dillingham, C.M , Cormaty, H., Morgan, E., Esgdaille, D., Boutz, P., and Sridharan, R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. bioRxiv [Preprint]. 2023 Jun 1:2023.05.31.543088. doi: 10.1101/2023.05.31.543088. PMID: 37398291; PMCID: PMC10312572

Zhang, S., Pyne, S., Pietrzak, S., Halberg, S., McCalla, S.G., Siahpirani, A.F., Sridharan, R., Roy, S. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun. 2023 May 27;14(1):3064.PMID: 37244909; PMCID: PMC10224950.

2022

Lo, J.H., Edwards, M., Langerman, J., Sridharan, R., Plath, K., Smale, S.T. Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cells. Genes Dev. 2022 Oct 1;36(19-20):1079-1095. doi: 10.1101/gad.350113.122. Epub 2022 Nov 23. PMID: 36418052; PMCID: PMC9744233.

Siahpirani, A.F., Knaack, S., Chasman, D., Seirup, M., Sridharan, R., Stewart, R., Thomson, J., Roy, S. Dynamic regulatory module networks for inference of cell type-specific transcriptional networks. Genome Res. 2022 Jul;32(7):1367-1384. doi: 10.1101/gr.276542.121. Epub 2022 Jun 15. PMID: 35705328; PMCID: PMC9341506

Wille C.K., Sridharan, R. Connecting the DOTs on Cell Identity. Front Cell Dev Biol. 2022 Jun 6;10:906713. doi: 10.3389/fcell.2022.906713. PMID: 35733849; PMCID: PMC9207516.

Wille CK, Sridharan R. DOT1L inhibition enhances pluripotency beyond acquisition of epithelial identity and without immediate suppression of the somatic transcriptome. Stem Cell Reports. 2022 Feb 8;17(2):384-396. doi: 10.1016/j.stemcr.2021.12.004. Epub 2022 Jan 6. PMID: 34995500; PMCID: PMC8828533.

2020

Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res. 2020 Dec 16;48(22):12660-12674. doi: 10.1093/nar/gkaa1091. PMID: 33237287; PMCID: PMC7736818.

Lee H, Lee YS, Harenda Q, Pietrzak S, Oktay HZ, Schreiber S, Liao Y, Sonthalia S, Ciecko AE, Chen YG, Keles S, Sridharan R, Engin F. Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes. Cell Metab. 2020 Apr 7;31(4):822-836.e5. doi: 10.1016/j.cmet.2020.03.002. Epub 2020 Mar 26.PMID: 32220307

Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, Liu WH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM. Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence. Mol Cell. 2020 Apr 16;78(2):210-223.e8. doi: 10.1016/j.molcel.2020.03.004. Epub 2020 Mar 23.PMID: 32208170

2019

Tran KA, Dillingham CM, Sridharan R. Coordinated removal of repressive epigenetic modifications during induced reversal of cell identity. EMBO J. 2019 Nov 15;38(22):e101681. doi: 10.15252/embj.2019101681. Epub 2019 Oct 4.PMID: 31583744

Tran KA, Pietrzak SJ, Zaidan NZ, Siahpirani AF, McCalla SG, Zhou AS, Iyer G, Roy S, Sridharan R. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency. Cell Rep. 2019 May 7;27(6):1726-1741.e5. doi: 10.1016/j.celrep.2019.04.056.PMID: 31067459

Tran KA, Dillingham CM, Sridharan R. The role of α-ketoglutarate-dependent proteins in pluripotency acquisition and maintenance. J Biol Chem. 2019 Apr 5;294(14):5408-5419. doi: 10.1074/jbc.TM118.000831. Epub 2018 Sep 4.PMID: 30181211 

2018

Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, et al. Compartmentalization of HP1 proteins in pluripotency acquisition and maintenance. Stem cell reports. Elsevier; 2018 Jan 19.

2017

Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating protein-DNA interactions in human alphoid chromatin via hybridization capture and mass spectrometry.J Proteome Res. 2017 Sep 1;16(9):3433-3442. doi: 10.1021/acs.jproteome.7b00448. Epub 2017 Aug 4. PMID: 28704058

Roy S, Sridharan R. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Res. 2017 Jul;27(7):1250-1262.

2016

Jackson, S.A. *, Olufs, Z.P.G. *, Tran, K.A., Zaidan, N.Z., and Sridharan, R. Alternative routes to induced pluripotent stem cells revealed by reprogramming of neural lineage.  Stem Cell Reports 2016 Mar 8;6(3):302–11.* co-first authors.

2015

Roy, S. *, Siahpirani, A.F., Knaack, S., Stewart, R., Wilson, M., Sridharan, R. Predictive framework for cell-line specific enhancer-promoter interactions defines signatures of long and short range regulation. Nucleic Acids Research 43 (18): 8694-8712. * corresponding author.

Tran KA, Jackson SA, Olufs ZPG, Zaidan NZ, Leng N, Kendziorski C, et al. Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways. Nat Commun. Nature Publishing Group; 2015 Feb 4;6:6188.

2013

Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nature cell biology. Nature Research; 2013 Jul 1;15(7):872–82.

Britton L-MP, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, et al. Initial characterization of histone H3 serine 10 O-acetylation. Epigenetics. Landes Bioscience; 2013;8(10):1101–13.

Jackson SA, Sridharan R. The nexus of Tet1 and the pluripotency network. Cell stem cell. 2013 Apr;12(4):387–8.

Jackson SA, Sridharan R. Peering into the black box of reprogramming to the pluripotent state. Current Pathobiology Reports. Springer; 2013;1(2):129–36.