Alan Tackett Ph.D.

Assistant Professor

Ph.D. University of Arkansas for Medical Science

The Systems Biology of Unique Chromatin Structures

DNA is packaged with histones to form nucleosomes, which in turn become condensed into higher order structures that constitute chromatin.  Chromatin is generally classified into two categories which are either condensed and thus transcriptionally inactive (heterochromatin) or less condensed and transcriptionally active (euchromatin).  Heterochromatic regions are interspersed within euchromatin, thus necessitating a unique classification of chromatin that will define the transition areas between the transcriptionally silent and active regions (i.e., boundary chromatin).  Without these boundary regions, the barrier between heterochromatin and euchromatin is breached and the silent region propagates into more transcriptionally active areas.  In some cases, certain proteins have been implicated as having a role in maintaining these boundary zones; however, the exact composition of the boundary chromatin or the regions just proximal (i.e., the protein complexes and histone modification states) has not been fully described.  Furthermore, the mechanism by which these transition regions are established, maintained and replicated is not understood.  My laboratory is interested in identifying, localizing and functionally characterizing the proteins and protein complexes that maintain boundary chromatin in S. cerevisiae. We plan to utilize this information to build towards a comprehensive mechanism(s) of maintenance of all types of boundary regions. 

We utilize a systems biology approach to functionally analyze boundary chromatin.  This multi-faceted or systems approach is composed of an array of tools which include rapid isolations of protein complexes in their natural state, focused proteomic identification of protein complex components, isotopic differentiation of real complex members (i.e., I-DIRT technology), mass spectrometric analysis of post-translational modifications, yeast genetics and high resolution microarray analysis.  For our proteomic applications, we have a MALDI-based prOTOF mass spectrometer (PerkinElmerSciex) and a MALDI-based LTQ ion trap mass spectrometer (Thermo Electron) that we use for accurate measurements of peptide m/z values and efficient peptide sequencing by fragmentation.   

By applying this systems approach, we have identified novel protein complexes that bind to and maintain boundary chromatin (Tackett et al, 2005, J. Cell Biol., 169, 35-47).  Furthermore, we have positioned these proteins throughout the chromosomes and identified their preferential histone binding state.  We are currently exploring the detailed boundary activity mechanisms for three of these proteins: Yta7, Isw2, Itc1.  Additionally, we are using proteomic techniques to search for new protein complexes involved in boundary chromatin maintenance.

Selected Publications

Tackett, A.J., Dilworth, D.J., Davey, M.J., O'Donnell, M.D., Aitchison, J.D., Rout, M.P. and Chait, B.T. (2005) Proteomic and genomic characterization of chromatin complexes at a boundary. J. Cell Biol., 169, 35-47. [Abstract]

Dou, Y., Milne, T.A., Tackett, A.J., Smith, E.R., Fukuda, A., Wysocka, J., Allis, C.D., Chait, B.T., Hess, J.L. and Roeder, R.G. (2005) Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF. Cell, 121, 873-885. [Abstract]

Tackett, A.J., DeGrasse, J.A., Oeffinger, M., Rout, M.P. and Chait, B.T. (2005) I-DIRT, A General Method for Distinguishing Between Specific and Non-specific Protein Interactions. J. Proteome Res., 4, 1752-6. [Abstract]

Pubmed link to additional publications