Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

  1. Julia Zeitlinger1,
  2. Robert P. Zinzen2,
  3. Alexander Stark3,4,
  4. Manolis Kellis3,4,
  5. Hailan Zhang5,
  6. Richard A. Young1,6, and
  7. Michael Levine2,7
  1. 1 Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA;
  2. 2 Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkeley, California 94720, USA;
  3. 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA;
  4. 4 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
  5. 5 Department of Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA;
  6. 6 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

Abstract

Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determined the genome-wide occupancy of the dorsoventral (DV) determinants Dorsal, Twist, and Snail in the Drosophila embryo using chromatin immunoprecipitation coupled with microarray analysis (ChIP–chip). The in vivo binding of these proteins correlate tightly with the limits of known enhancers. Our analysis predicts substantially more target genes than previous estimates, and includes Dpp signaling components and anteroposterior (AP) segmentation determinants. Thus, the ChIP–chip data uncover a much larger than expected regulatory network, which integrates diverse patterning processes during development.

Keywords

Footnotes

| Table of Contents

G&D Most Read

View all ...

Life Science Alliance