Bio

• Ph.D. Physics University of Illinois, Chicago - 2002
• M.S. Physics Univesity of Illinois, Chicago - 1997
• B.S. Physics Truman State University - 1995

Research Overview

We are working to understand how our genomes are expressed and repaired while being tightly compacted into chromatin. We currently are focused on three research programs. The first program is to determine how histone post-translational modifications in structured regions of the nucleosome alter chromatin structure and dynamics. The second program is to determine how DNA mismatches are recognized and repaired in chromatin. The third program is to understand how the mechanical properties of DNA is important for DNA-protein interactions. We use an interdisciplinary approach that combines biochemical and biophysical techniques, which includes: restriction enzyme studies, cyclization experiments, nucleosome mapping, steady state Fluorescence Resonance Energy Transfer measurements (FRET), stopped flow FRET, fluorescence correlation spectroscopy, single molecule force and twist measurements with magnetic tweezers and single molecule FRET measurements. Because of our interdisciplinary nature, collaborations are essential for our success. We have developed close collaborations with the Ottesen Lab, the Fishel Lab and the Bundschuh Lab.

Nucleosome Structure and Function

Histones function to organize and compact our genomic DNA into nucleosomes and chromatin while histone modifications function to facilitate and regulate biological process that involve DNA-protein interactions, such as RNA transcription and DNA repair. The nucleosome contains 2 of each core histone protein: H2A, H2B, H3 and H4, and 147 base pairs of DNA This structure is densely repeated along our genomic DNA so that our chromosomes contain about 20 million nucleosomes, and creates long chromatin fibers. There are over 100 known post-translational histone modifications; however the molecular functions of most of these modifications are not well understood. Histone modifications are thought to function in one of two ways: (i) to create a protein binding site and (ii) to directly modify the structure and/or dynamics of chromatin. A majority of modifications are located on histone tails, which are unstructured regions of the nucleosome and emanate from the nucleosome core making the tails accessible for protein binding. However, recent mass spectrometry studies have revealed that there are over 30 modifications in the structured region of the nucleosome and 15 of them are located within the DNA-histone interface of the nucleosome. My lab is focused on four histone H3 modifications that are positioned within structured regions of the nucleosome. We are experimentally investigating models of how histone modifications function while buried within the DNA histone interface of the nucleosomes. We collaborate with Prof. Jennifer Ottesen (OSU), who constructs homogeneously modified histone H3 proteins using Expressed Protein Ligation, which is a powerful technique for the introduction of chemical modifications into one region of a protein. We are investigating molecular models of PMT function with a multidisciplinary approach that includes the restriction enzyme kinetics method, nucleosome mapping, histone binding affinity measurements, steady state Fluorescence Resonance Energy Transfer measurements (FRET), stopped flow FRET, fluorescence correlation spectroscopy, single molecule force and twist measurements with magnetic tweezers, and single molecule FRET measurements.

DNA Mismatch Repair

DNA mismatch repair occurs by excision of the mispair-containing DNA strand and resynthesis of the resulting gap using the remaining DNA strand as a template In eukaryotes, mismatch repair must occur while the DNA is packaged into chromatin, yet little is known about how MMR proceeds within chromatin and the molecular roles post-translational modifications play in mismatch repair. We are working with Prof. Richard Fishel (OSU) to understand the recognition of MMR in chromatin. This work naturally builds on our work on histone modifications and is a key step in understanding the molecular basis by which DNA mismatches are repaired in our cells.

Recent Publications

Wong Ng J, Poirier MG, Chatenay D, and  Robert J. Plasmid copy number noise in monoclonal populations of bacteria. (2010) Phys Rev E. Epub 2010 Jan 14.

Javaid S, Manohar M, Punja N, Mooney A, Ottesen JJ, Poirier MG, and Fishel R. Nucleosome remodeling catalyzed by hMSH2-hMSH6. Mol Cell. 2009 Dec 24;36(6):1086-94.

Poirier, M.G., Oh, E., Tims, H. and Widom, J. Dynamics and Function of Compact Nucleosome Arrays. Nat Struct Mol Bio. 2009 Sep;16(9):938-44. Epub 2009 Aug 23.

Manohar, M., Mooney, A.M., North, J.A., Nakkula, R.J., Picking, J.W., Edon, A. , Fishel, R, Poirier, M.G., and Ottesen, J.J. Acetylation of Histone H3 at the Nucleosome Dyad Alters DNA-Histone Binding. J Biol Chem. 2009 Aug 28;284(35):23312-21. Epub 2009 Jun 11

Forties RA, Bundschuh R, Poirier MG. The flexibility of locally melted DNA. Nucleic Acids Res. 2009 Aug;37(14):4580-6. Epub 2009 May 31

Shen HM, Poirier MG, Allen MJ, North J, Lai R, Widom J, Storb U. The Activation Induced Cytidine Deaminase (AID) Efficiently Targets DNA in Nucleosomes, But Only During Transcription. J Exp Med. 2009 May 11;206(5):1057-71

Poirier MG, Bussiek M, Langowski J, Widom J. Spontaneous access to DNA target sites in folded chromatin fibers. J Mol Biol. 2008 Jun 13;379(4):772-86. Epub 2008 Apr 16.

Poirier MG, Marko JF. Micromechanical studies of mitotic chromosomes. Curr Top Dev Biol. 2003;55:75-141.

Marko JF, Poirier MG. Micromechanics of chromatin and chromosomes. Biochem Cell Biol. 2003 Jun;81(3):209-20.

Poirier MG, Marko JF. Abstract Micromechanical studies of mitotic chromosomes. J Muscle Res Cell Motil. 2002;23(5-6):409-31.

Poirier MG, Marko JF. Free in PMC Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold. Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15393-7. Epub 2002 Nov 18.
Commentary by A.S. Belmont; Mitotic chromosome scaffold structure: New approaches to an old controversy Proc. Natl. Acad. Sci. USA 99, 15855-7 (2002)

Sarkar A, Eroglu S, Poirier MG, Gupta P, Nemani A, Marko JF. Dynamics of chromosome compaction during mitosis. Exp Cell Res. 2002 Jul 1;277(1):48-56.

Poirier MG, Marko JF. Effect of internal friction on biofilament dynamics. Phys Rev Lett. 2002 Jun 3;88(22):228103. Epub 2002 May 16.

Poirier MG, Eroglu S, Marko JF. The bending rigidity of mitotic chromosomes. Mol Biol Cell. 2002 Jun;13(6):2170-9.

Poirier MG, Monhait T, Marko JF. Reversible hypercondensation and decondensation of mitotic chromosomes studied using combined chemical-micromechanical techniques. J Cell Biochem. 2002;85(2):422-34.

Poirier MG, Nemani A, Gupta P, Eroglu S, Marko JF. Probing chromosome structure with dynamic force relaxation. Phys Rev Lett. 2001 Jan 8;86(2):360-3.

Poirier M, Eroglu S, Chatenay D, Marko JF. Reversible and irreversible unfolding of mitotic newt chromosomes by applied force. Mol Biol Cell. 2000 Jan;11(1):269-76.