As of April 2008, Assistant Professor Dept of Systems Biology, Harvard Medical School
Gene expression in metazoans is controlled by the interaction among cis-regulatory elements (sometimes called enhancers), silencers, insulators, chromatin structure and core promoters. The vast majority of gene specific spatial and temporal information is contained in cis-regulatory elements, which are collections of binding sites for sequence specific DNA-binding transcription factors.My current work is focused on two parallel questions. First, how do collections of transcription factor binding sites integrate information to produce gene expression patterns? And second, how do cis-regulatory elements and their associated expression patterns evolve?
I focus on the early development of multiple Drosophila species, and integrate a wide variety of experimental and computational approaches. The early development of Drosophila melanogaster is directed by an extremely well characterized transcriptional network, giving a large number of known transcription factors and regulatory elements to work with.Twelve Drosophila species have recently been sequenced, and more genomic resources are on the way. The relatively simple geometry of the early embryo has allowed us to develop quantitative imaging techniques that yield gene expression information for every cell in the entire embryo over time. Together, these resources give us the opportunity to bring a quantitative system-wide approach to evolutionary developmental biology.
Eisen Lab Publications:
Fowlkes, C.C., Eckenrode, K.B., Bragdon, M.D., Meyer, M., Wunderlich, Z., Simirenko, L., Luengo Hendriks, C.L., Keränen, S.V.E., Henriquez, C., Knowles, D.W., Biggin, M.D., Eisen, M.B., DePace, A.H.. (2011) A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genetics, 7(10): e1002346. doi:10.1371/journal.pgen.1002346
Fowlkes CC, Hendriks CL, Ker&aumel;nen SV, Weber GH, R&uumel;bel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18;133(2):364-74
Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin MD, Knowles DW. (2006) Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006;7(12):R123