Stephen Small

Stephen Small

Director of PhD Program; Professor of Biology
Ph.D. 1988 (developmental biology), Cincinnati; B.A. 1973, Thomas More College.

Office Address:
New York University
Department of Biology
1009 Silver Center
100 Washington Square East
New York, NY 10003-6688

Email:
Phone: (212) 998-8244
Fax: (212) 995-4015
List of Publications from Pubmed

Research

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Our main goal is to understand the molecular mechanisms that establish the body plans of multi-cellular animals. In the fruit fly Drosophila melanogaster, many genes that control body form have been genetically identified in the last twenty years. Most of these genes encode transcription factors that are localized in patterns in the early embryo. We have concentrated our efforts on the regulation of the pair-rule genes, which are expressed in patterns of stripes in the early embryo (Figure 1). By studying how these patterns are established, we hope to understand the molecular mechanisms involved in position-specific activation and repression of transcription. Since many of the transcription factors we study in fruit flies are evolutionarily similar to factors in higher eukaryotes, understanding how they work in Drosophila should provide us with profound insights into developmental mechanisms in higher animals and man.

Current Projects:

1. Mechanisms of stripe formation.
The focus of much of the work in the lab is on the transcriptional regulation of the pair-rule gene even-skipped (eve). eve is a pair-rule gene that encodes a homeobox transcription factor. eve is expressed in a pattern of seven evenly spaced stripes in the precellular embryo. By analyzing the eve promoter, we and others have discovered that individual stripes are controlled by discrete regions of the promoter. These regions act as enhancer elements that individually control one or two stripes of expression. Thus the whole seven stripe pattern is the result of the summation of the effects of the individual enhancers.

We are studying the regulation of two stripe enhancers in detail (Figure 2). The stripe 2 and stripe 3+7 enhancers are each about 500 bp in length. Genetic experiments have identified numerous transcription factors, some of which are involved in activating transcription through these enhancers. Other factors act as repressors that form the stripe borders. We have used DNase I footprint studies to show that these transcription factors can bind directly to several sites within the enhancers. We then test the role these sites play in stripe regulation in vivo by mutating individual sites in vitro, and testing whether enhancers bearing these mutations are still able to make a stripe in transgenic flies.

Many of the identified binding sites in the enhancers are arranged in clusters, suggesting that activation may involve cooperative binding to neighboring sites. Furthermore, repression may involve competition for DNA-binding, or protein-protein interactions between activators and repressors. We are currently using biochemical approaches to test these hypotheses. We are also using genetic and biochemical approaches to identify other factors that may be important for stripe regulation. These experiments have identified new proteins involved in repression and activation. By studying these in detail, we hope to understand the complexities of enhancer-mediated transcription.

2. Targeted misexpression of segmentation genes.
The segmentation genes we study are distributed in asymmetric expression domains along the anterior-posterior axis. Individual domains may act as sources for protein gradients that regulate target genes based on their concentration. To test this, we create ectopic domains of gene expression. Our approach is to use enhancers that are active early in development and the yeast FLP-FRT recombination system to control the position and timing of misexpression. For example, we have used the eve stripe 2 enhancer to misexpress the gap gene knirps (kni) (Figure 3). The kni protein is an orphan steroid hormone receptor normally involved in regulating development in the abdominal region of the embryo. Misexpressing kni under the control of the stripe 2 enhancer creates an ectopic domain in more anterior regions, and causes significant changes in the expression patterns of many genes.

We have currently extended these experiments to test the role of other segmentation genes, including the gap genes giant (gt), hunchback (hb), and Kruppel (Kr), as well as several other segmentation genes. These experiments will continue to shed light on the mechanisms by which these genes control cell fate choices during development.

This work is funded by grants from the NIH and the NSF.

Biosketch

I received my Ph. D. in developmental biology in 1988 from the University of Cincinnati. For my thesis, I worked with Dr. Richard Akeson on the structure and function of different NCAM polypeptides in rat development. NCAMs are cell adhesion molecules t hat may be important for establishing connectivity in the developing nervous system. From 1989-1993, I worked as a post-doctoral fellow at Columbia University and at U. C. San Diego with Dr. Michael Levine on the formation of embryonic pattern that estab lishes the body plan in Drosophila. I joined NYU's biology department in 1993 as an assistant professor. In my lab, we are continuing to study how genes control the establishment of different body forms.

Teaching

I am involved in teaching both undergraduate and graduate students. At the undergraduate level, I teach an upper level course in Developmental Biology with Dr. Benfey, and participate in core courses such as Principles of Biology and Molecular and Cell Biology, which are team-taught. At the graduate level, I am the organizer of Molecular Genetics, a rigorous course designed for Ph.D. students. I also teach several lectures in Foundations of Developmental Genetics I and II, and organize a journal club entitled Special Topics in Developmental Biology.

At present, there are two postdoctoral fellows, one Ph.D. student, a full-time technician, and three undergraduate students working in the laboratory.

Areas of Research/Interest

Spatial control of gene transcription during early Drosophila development

External Affiliations

Genetics Society of America, American Association for Advancement of Science.

Fellowships/Honors

National Institutes of Health Research Grant, 1996-2001; National Science Foundation Research Grant, 1995-1998; National Institutes of Health Postdoctoral Fellowship, 1991-1993.

Publications