*And member, Lawrence Berkeley Laboratory, Life Sciences Division
My lab studies how the genomic sequences that control gene expression function and evolve. We are driven by a desire to understand the molecular basis of organismal diversity, and the belief that many differences in physiology, morphology and behavior arise from changes in gene regulation. Our ultimate goal is to be able to interpret the regulatory information encoded in genomic DNA, so that we can routinely identify regulatory sequences, discern their function, predict the consequences of their perturbation, and reconstruct how they evolved.
We are a hybrid computational and experimental lab who couple genome-scale computational and experimental analysis of gene regulation in Drosophila melanogaster and Saccharomyces cerevisiae with extensive analysis of comparative sequence data and experimental analysis of species closely related to these model systems. We focus on short evolutionary timescales where it is possible to couple specific changes in genome sequences with alterations in gene regulation and expression.
Experimental characterization of gene regulation in D. melanogaster embryos
To provide a solid experimental foundation for our evolutionary studies, we are working with several other labs in Berkeley to systematically dissect gene expression and regulation in the early D. melanogaster embryo. For each of the approximately 40 transcription factors critical in shaping anterior-posterior and dorsal-ventral patterns, our goals are to: 1) measure the factor’s in vitro affinity to each of its potential target sequences, 2) identify the genomic regions bound by each factor in living embryos, 3) determine the expression pattern of the factor and its targets in three-dimensions at cellular resolution. I and members of my lab are actively involved in the experimental portions of the project and are carrying out the analyses of these data.
Modeling the evolutionary constraints on eukaryotic regulatory sequences
We now have extensive comparative sequence data for fruitflies (12 Drosophila genomes) and yeasts (many fungal genomes), and are using these data to characterize how the individual building blocks of regulatory sequences (transcription factor binding sites) and higher order structures (e.g. developmental enhancers) evolve. We are particularly interested in understanding how selection to maintain transcription factor binding sites affects the evolution of target sequences, and how the extensive plasticity seen in the organization of developmental enhancers is related to their function.
Characterization and modeling of the transcriptional network variation within and between Drosophila species
My lab is applying the high-resolution fluorescent imaging methods developed for D. melanogaster to systematically analyze gene expression, and dissect regulatory networks, in other Drosophila species and in several inbred lines of D. melanogaster. The detailed experimental data we are generating for D. melanogaster, and the genome sequences of 12 Drosophila species are a tremendous resource for studying the evolution of gene regulation. However, it is difficult to study changes in sequence without understanding the context in which these sequences exist and how those changes affect function. While it is impractical to repeat every experiment done in D. melanogaster in every other strain and species, we are extending several classes of experiment to selected strains and species so that we can better understand regulatory variation at each of its multiple levels: how sequence variation affects binding, how binding variation affects expression, and how expression variation affects phenotype.
Using regulatory sequence evolution to elucidate the mechanisms of gene regulation
To take advantage of sequence diversity outside of the genus Drosophila, we are sequencing developmentally important loci from several non-Drosophilid fly families to provide insights into the underlying principles of gene regulation. We are particularly interested in regulatory sequences that have undergone extensive rearrangements in their binding site repertoires without altering their function. Although extensive rearrangements are observed among Drosophla regulatory sequences, there must be limits to this plasticity. Over time, regulatory sequences will accumulate only those changes in their binding site repertoires that are compatible with the complex biochemical events required to produce their specific regulatory output. We therefore believe that collecting and characterizing regulatory sequences with similar functions but diverse sequences will ultimately lead to a better understanding of the biochemical principles that relate the composition and organization of regulatory sequences to their function. To perform such an analysis, we are currently sequencing 20 targeted loci from 6 species each in the families Sepsidae (ensign flies), Tephritidae (true fruit flies) and Diopsidae (stalk-eyed flies). We chose these taxa, which diverged from Drosophila between 100 and 150 million years ago, to provide the optimal balance between sequence divergence and functional divergence. We are complementing the sequence analysis with experimental analysis of development in select species from each taxa, examination of the activity of enhancers from these species in D. melanogaster embryos, and extensive testing of hypotheses regarding regulatory sequence function and evolution.
[copies of all papers are available at rana.lbl.gov]
Pollard DA, Moses AM, Iyer VN and Eisen MB (2006). Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genetics 2(10):e173.
Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB (2006). Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Computational Biology 2(10):e130.
Pollard DA, Moses AM, Iyer VN and Eisen MB. Detecting the limits of regulatory element conservation and divergence estimation using multiple pairwise and multiple alignments. BMC Bioinformatic 7(1):376.
Chiang DY, Nix DA, Shultzaberger RK, Gasch AP, Eisen MB (2006). Flexible promoter architecture requirements for coactivator recruitment. BMC Molecular Biology 7(1):16.
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M and Eisen MB (2004). Conservation and evolution of cis-regulatory systems in Ascomycete fungi. PLoS Biology 2(12):e398.
Moses AM, Chiang DY, Pollard DA, Iyer VN and Eisen MB (2004). MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biology 5(12):R98.
Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB and Celniker SE (2004). Computational identification of developmental enhancers: conservation and function of transcription factor binding-sites clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology 5(9):R61.
Moses AM, Chiang DY, Kellis M, Lander ES and Eisen MB (2003). Position specific variation in the rate of evolution in transcription factor binding sites BMC Evolutionary Biology 3(19).
Berman BP, Nubu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM and Eisen MB (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA 99, 757-62.
Last Updated 2007-02-27