Faculty

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 biochemistry and epigenetics
2010

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

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

Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state.
Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state. Mol Cell. 2026 Sep 17; 86(18):3740-3758.e9.
PMID: 42673957

Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.
Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes. bioRxiv. 2026 May 25.
PMID: 42244752

Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state.
Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state. bioRxiv. 2026 May 22.
PMID: 42239275

Bound for the nucleus: defining the molecular principles of cargo selection by importin 9.
Bound for the nucleus: defining the molecular principles of cargo selection by importin 9. bioRxiv. 2026 May 14.
PMID: 42182196

A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure.
A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure. Nat Cardiovasc Res. 2026 Feb; 5(2):96-117.
PMID: 41731058

A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding.
A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding. J Biol Chem. 2026 Feb; 302(2):111123.
PMID: 41478570

A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding.
A revised model of nuclear actin import: Importin 9 competes with cofilin, profilin, and RanGTP for actin binding. bioRxiv. 2025 Sep 26.
PMID: 41040170

The Mediator Kinase Module regulates cell cycle re-entry and transcriptional responses following DNA damage.
The Mediator Kinase Module regulates cell cycle re-entry and transcriptional responses following DNA damage. bioRxiv. 2025 May 20.
PMID: 40475552

Binding mode-guided development of high-performance antibodies targeting site-specific posttranslational modifications.
Binding mode-guided development of high-performance antibodies targeting site-specific posttranslational modifications. Proc Natl Acad Sci U S A. 2025 Jan 07; 122(1):e2411720121.
PMID: 39793060

Guiding the HBO1 complex function through the JADE subunit.
Guiding the HBO1 complex function through the JADE subunit. Nat Struct Mol Biol. 2024 Jul; 31(7):1039-1049.
PMID: 38448574

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