Benfey Lab

In collaboration with Dennis Shasha of the Courant Institute at NYU, Detlef Weigel of the Salk Institute and David Galbraith of the University of Arizona, we have recently undertaken a project whose long-term goal is to understand the transcriptional code in Arabidopsis. Analogous to the genetic code, the transcriptional code is the combinatorial relationship between the binding of transcription factors to DNA and the resulting production of RNA in the correct location and amounts.

The key to deciphering the transcriptional code in plants is to understand in detail the control of RNA expression. A first step in this direction is to determine the expression pattern of all genes at cellular resolution.
To accomplish this we are developing a new genomics approach that involves sorting cells from transgenic lines in which a fluorescent protein is used as a cell-specific marker.

The sorted cell populations are then used as a source of RNA that is hybridized to microarrays. Our preliminary results demonstrate the feasibility of this approach. We are also developing bioinformatics tools to identify transcription factor/cis-element relations based on genome-wide expression data. We have developed a simple new algorithm, cis/TF, that uses genome-wide expression data and the full genomic sequence to match transcription factors to their binding sites.
The algorithm has successfully identified experimentally-supported transcription factor-binding relationships in tests on several datasets from Saccharomyces cerevisiae (Birnbaum et al., 2001).

In addition, we are interested in collecting expression data from various sources in a single queriable database. We have developed a site that collects root gene expression data from multiple experiments (e.g. microarrays and in situs) and allows for specialized queries. This work is supported by the NSF Arabidopsis thaliana 2010 program and can be accessed at http://www.arexdb.org

The goal of the second genomics project in the Benfey lab is to identify genes involved in fruit development along evolutionary lineages in the coffee family (Rubiaceae) using a well-resolved phylogenetic framework. This work is being done in collaboration with New York University (NYU), Cold Spring Harbor Laboratory (CSHL), and the New York Botanical Garden (NYBG).

This effort takes advantage of the recently published complete genome sequence of Arabidopsis and the specific scientific approach is based on examples from prokaryotic genomic analysis, in which comparison of the genomes of closely related species has revealed candidate genes for the traits that differ between the species.
The first step in the plant comparative genomics project was to identify closely related, scientifically and commercially valuable species that differed in a small number of easily detectable traits of scientific and commercial value.

The Curators at NYBG assembled a list of candidate groups based on their systematics expertise and detailed knowledge of the plant species in question. Two proof-of-concept projects were selected. One addresses evolutionary, medicinal and developmental aspects of cycads which have been demonstrated to be the least specialized of extant seed plants and are considered to be the sister group to all other seed plants based upon morphological and molecular data. The second project seeks to identify transcriptional differences between closely related Rubiaceae species that may be responsible for their divergent fruit morphology.
.