Alex Ruthenburg, PhD Alex Ruthenburg
Chromatin Biochemistry and Structure

Associate Professor, Molecular Genetics and Cell Biology,
Biochemistry and Molecular Biology

B.A. Department of Chemistry, Carleton College, Northfield, MN (1999)
PhD Chemistry (NSF Fellow), Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA (2005)


Research Summary

Chromatin is the physiologic form of the genome. Rather than mere packaging, chromatin structure appears to serve as the master regulator of underlying DNA function. Local chromatin structure may be stable for decades, yet is sufficiently dynamic to respond to signaling pathways, potentiating transcriptional program changes in development. Indeed cellular identity and changes thereof are intimately connected to chromatin states -- keeping a neuron a neuron and not a liver cell. What are the molecular mechanisms of factors that control chromatin structure?

The unifying theme of our lab is the elucidation of molecular mechanisms underlying genome management using the toolkits of biochemistry, chemical and structural biology; 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. Projects ideally will transition from discovery biology to detailed molecular and structural investigation.

Selected Publications

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide.
Jun, 4 2015 • Mol Cell (PubMed)

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.
Aug, 18 2015 • Cell Rep (PubMed)

An Interactive Database for the Assessment of Histone Antibody Specificity.
Aug, 6 2015 • Mol Cell (PubMed)

Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks.
Sep, 22 2014 • Chembiochem (PubMed)

Recombinant antibodies to histone post-translational modifications.
2013 • Nat Methods (PubMed)

Validation of histone-binding partners by peptide pull-downs and isothermal titration calorimetry.
2012 • Methods Enzymol (PubMed)

Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions.
May, 27 2011 • Cell (PubMed)

The United States of histone ubiquitylation and methylation.
Jul, 8 2011 • Mol Cell (PubMed)

Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark.
Jan, 12 2007 • Mol Cell (PubMed)

Multivalent engagement of chromatin modifications by linked binding modules.
2007 • Nat Rev Mol Cell Biol (PubMed)


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