People

Alexander J. Ruthenburg, PhD

The unifying theme of my lab is the elucidation of molecular mechanisms underlying management chromatin, the physiological form of the genome. In particular, we are interested in how post translational modifications to histones, newly appreciated DNA modifications and noncoding RNA can control chromatin structure. Our research spans several traditional disciplines, ranging from discovery biochemistry and genome-scale measurements to mechanistic characterization with biophysical methods coupled with X-Ray structure to address fundamental questions in chromatin biology. We have pioneered new technologies to make quantitative local measurements of chromatin components. Projects ideally will transition from discovery biology to detailed molecular and structural investigation.

Rockefeller University
New York, NY
Postdoctoral Fellow - Chromatin biochemsitry and epigenetics
2010

Harvard University
Cambridge, MA
Ph.D. - Chemical and Structural biology
2005

Carleton College
Northfield, MN
B.A. - Chemistry
1999

Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia.
Richter WF, Shah RN, Ruthenburg AJ. Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia. Elife. 2021 07 15; 10.
PMID: 34263728

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads.
Shah RN, Ruthenburg AJ. Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads. PLoS Comput Biol. 2021 04; 17(4):e1008926.
PMID: 33872311

Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription.
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. 2020 07 13; 11(1):3491.
PMID: 32661239

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq.
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. 2020 02; 16(2):e1007119.
PMID: 32040509

Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications.
Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc. 2019 12; 14(12):3275-3302.
PMID: 31723301

A Mutation in Histone H2B Represents a New Class of Oncogenic Driver.
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. 2019 10; 9(10):1438-1451.
PMID: 31337617

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies.
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. 2018 10 04; 72(1):162-177.e7.
PMID: 30244833

Regulated Capture of V? Gene Topologically Associating Domains by Transcription Factories.
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 V? Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 2018 08 28; 24(9):2443-2456.
PMID: 30157436

Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy.
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. 2018 11; 8(11):1376-1389.
PMID: 30115703

Facile target validation in an animal model with intracellularly expressed monobodies.
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. 2018 09; 14(9):895-900.
PMID: 30013062

View All Publications

New Scholar in Aging
Ellison Medical Foundation
2013 - 2017

Kavli Fellow
National Academy of Sciences
2011

Neubauer Family Foundation Assistant Professor
University of Chicago
2010 - 2015

Junior Investigator
Chicago Biomedical Consortium
2010 - 2012

Irvington Institute Research Fellowship
Cancer Research Institute
2007 - 2010

National Science Foundation Graduate Research Fellow
Harvard University
2000 - 2004