RuthenLab

Publications

2026

Kainth AS

Sirjoosingh P

Werner, MS

, Koide, A, Koide, S,

Ruthenburg AJ

. Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state. Molecular Cell. doi:10.64898/2026.05.25.727590.

Bogdanović JV

, Galeota-Sprung J,

Kainth AS

, Medhanie F, Budhathoki A, Pappas V, Banani SF, Spille J,

Ruthenburg AJ

. Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes. bioRxiv. doi:10.64898/2026.05.25.727590.

Keplinger AJ

, Cropley TC, Ortiz-Pacheco J,

Srinivasan PA

, Ueberheide BM,

Ruthenburg AJ

. Bound for the nucleus: defining the molecular principles of cargo selection by importin 9. bioRxiv. doi:10.1016/j.molcel.2026.08.008.

2025

Keplinger AJ*

Srinivasan PA*

, Christensen SM, Suarez C,

Ruthenburg AJ

. A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding. Journal of Biological Chemistry. doi:10.1016/j.jbc.2025.111123. *Contributed equally.

Memişoğlu G

, Bohn S, Krogan NJ, Haber JE,

Ruthenburg AJ

. The Mediator Kinase Module regulates cell cycle re-entry and transcriptional response following DNA damage. bioRxiv. doi: 10.1101/2023.02.26.530133.

2024

Elias J

Rosin JJ

Keplinger AJ

Ruthenburg AJ

. The N-terminus of YY1 regulates DNA and RNA binding affinity for both the zinc-fingers and an unexpected nucleic acid binding domain. bioRxiv. doi: 10.1101/2024.10.04.616721.

Gaurav N, Kanai A, Lachance C, Cox KL, Liu J,

Grzybowski AT

, Saksouk N, Klein BJ, Komata Y, Asada S,

Ruthenburg AJ

, Poirier MG, Côté J, Yokohama A, Kutateladze TG. Guiding the HBO1 complex function through the JADE subunit. Nat. Struct. Mol. Biol. 1-11.

2023

Kainth AS*

Haddad GA*

, Hall JM,

Ruthenburg AJ

. Merging short and stranded long reads improves transcript assembly. PLOS Comput. Biol. 19: e1011576 *Contributed equally.

2021

Shah RN*

Grzybowski AT*

Elias J*

Chen Z

, Hattori T, Lechner CC, Lewis PW, Koide S, Fierz B,

Ruthenburg AJ

. Re-evaluating the role of nucleosomal bivalency in early development. bioRxiv. doi: 10.1101/2021.09.09.458948. *Contributed equally.

Richter WF

Shah RN

Ruthenburg AJ

. Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia. eLife. 10: e64960.

Shah RN

Ruthenburg AJ

. Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads. PLOS Comput. Biol. 17: e1008926.

2020

Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V, O'Doherty A, Falk E, Sporniak M, D'Santos C, Franklin VNR, Kishore K, Bradshaw CR, Keane D, Freour T, David L,

Grzybowski AT

Ruthenburg AJ

, Gurdon J, Jullien J. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nat. Commun. 11: 3491.

Sun X, Wang Z, Hall JM, Perez-Cervantes C,

Ruthenburg AJ

, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PLOS Comput. Biol. 16: e1007119.

2019

Grzybowski AT*

Shah RN*

Richter WF

Ruthenburg AJ

. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat. Protoc. 14: 3275-3302. *Contributed equally.

Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP,

Grzybowski AT

, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL,

Ruthenburg AJ

, Liphardt J, Licht JD. A Mutation in Histone H2B Represents a New Class of Oncogenic Driver. Cancer Discov. 9: 1438-1451.

2018

Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Yockell-Lelièvre J, Battaion HL, Khan ST, Howard JP, Li Y,

Grzybowski AT

, Sabri E,

Ruthenburg AJ

, Dilworth FJ, Perkins TJ, Sabloff M, Ito CY, Stanford WL. Targeting the MTF2–MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy. Cancer Discov. 8: 1376-1389.

Shah RN

Grzybowski AT

, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC,

Ruthenburg AJ

. Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. Mol. Cell. 72: 162-177.

Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A,

Ruthenburg AJ

, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat. Chem. Biol. 14: 895-900.

Karki S, Kennedy DE, Mclean K,

Grzybowski AT

, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H,

Ruthenburg AJ

, Clark MR. Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 24: 2443-2456.

Chen Z

, Notti RQ, Ueberheide B,

Ruthenburg AJ

. Quantitative and Structural Assessment of Histone Methyllysine Analogue Engagement by Cognate Binding Proteins Reveals Affinity Decrements Relative to Those of Native Counterparts. Biochemistry. 57: 300-304.

2017

Yang XH, Nadadur RD, Hilvering CR, Bianchi V,

Werner M

, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W,

Ruthenburg AJ

, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. eLife. 6: e31638.

Werner MS

Sullivan MA

Shah RN

, Nadadur RD,

Grzybowski AT

, Galat V, Moskowitz IP,

Ruthenburg AJ

. Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat. Struct. Mol. Biol. 24: 596-603.

2016

Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM,

Grzybowski AT

, Koide A, Krajewski K, Strahl BD, Kelleher NL,

Ruthenburg AJ

, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc. Natl. Acad. Sci. U S A. 113: 2092-2097.

2015

Werner MS

Ruthenburg AJ

. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Rep. 12:1089-98.

Rothbart SB, Dickson BM, Raab JR,

Grzybowski AT

, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR,

Ruthenburg AJ

, Strahl BD. An Interactive Database for the Assessment of Histone Antibody Specificity. Mol. Cell. 59:502.

Gryzbowski AT

Chen Z

Ruthenburg AJ

. Calibrating ChIP-seq with nucleosomal internal standards to measure histone modification density genome-wide. Mol. Cell. 58: 866.

2014

Chen Z

Gryzbowski A

, and

Ruthenburg AJ

. Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks. ChemBioChem. 15: 2071-2075.

2013

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A,

Ruthenburg AJ

, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nat. Methods.10:992-5.

2012

Malecek K

Ruthenburg AJ

. Validation of histone-binding partners by peptide pull-downs and isothermal titration calorimetry. Methods in Enzymology. 512: 187-220.

Mohrig JR, Beyer BG, Fleischhacker AS,

Ruthenburg AJ

, John SG, Snyder DA, Nyffeler PT, Noll RJ, Penner ND, Phillips LA, Hurley HLS, Jacobs JS, Treitel C, James TL, Montgomery MP. 2012. Does Activation of the Anti Proton, Rather than Concertedness, Determine the Stereochemistry of Base-Catalyzed 1,2-Elimination Reactions? Anti Stereospecificity in E1cB Eliminations of beta-3-Trifluoromethylphenoxy Esters, Thioesters, and Ketones. J. Org. Chem. 77: 2819–2828.

2011

Werner M

Ruthenburg AJ

. The United States of Histone Ubiquitylation and Methylation. Mol. Cell., 43: 5-7.

Ruthenburg AJ

, Li H, Milne TA, Dou Y, McGinty RK, Yuen M, Ueberheide B, Muir TW, Patel DJ, Allis CD. Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions. Cell. 145: 1-15.

2010

Milne TA, Kim J, Wang GG, Whitcomb SJ, Basrur V,

Ruthenburg AJ

, Elenitoba-Johnson KS, Roeder RG, Allis CD. Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Mol. Cell. 38:853-863.

2007

Ruthenburg AJ

, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8: 983-994. With accompanying poster: "Readout of histone marks by chromatin binding modules."

Taverna SD, Li H,