Genome-wide mapping of in vivo targets of the Drosophila transcription factor Kruppel.
Krüppel (Kr), a member of the gap class of Drosophila segmentation genes, encodes a DNA binding zinc finger-type transcription factor. In addition to its segmentation function at the blastoderm stage, Krüppel also plays a critical role in organ formation during later stages of embryogenesis. To systematically identify in vivo target genes of Krüppel, we isolated DNA fragments from the Krüppel-associated portion of chromatin and used them to find and map Krüppel-dependent cis-acting regulatory sites in the Drosophila genome. We show that Krüppel binding sites are not enriched in Krüppel-associated chromatin and that the clustering of Krüppel binding sites, as found in the cis-acting elements of Krüppel-dependent segmentation genes used for in silico searches of Krüppel target genes, is not a prerequisite for the in vivo binding of Krüppel to its regulatory elements. Results obtained with the newly identified target gene ken and barbie (ken) indicate that Krüppel represses transcription and thereby restricts the spatial expression pattern of ken during blastoderm and gastrulation.
Matyash
Alexey
A
Max-Planck-Institut für biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie, D-37070 Göttingen, Germany.
Chung
Ho-Ryun
HR
Jäckle
Herbert
H
D000818:Animals; D015139:Blotting, Southern; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D002874:Chromosome Mapping; D003001:Cloning, Molecular; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000502:physiology*; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000737:chemistry; D015723:Gene Library; D017344:Genes, Insect; D016678:Genome; D005982:Glutathione Transferase / Q000378:metabolism; D006720:Homozygote; D017403:In Situ Hybridization; D007438:Introns; D051741:Kruppel-Like Transcription Factors; D008957:Models, Genetic; D009154:Mutation; D016133:Polymerase Chain Reaction; D011233:Precipitin Tests; D011485:Protein Binding; D012313:RNA / Q000737:chemistry; D012097:Repressor Proteins; D014157:Transcription Factors / Q000235:genetics* / Q000502:physiology*; D019076:Transgenes; D016335:Zinc Fingers
D002843:Chromatin; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; C497244:Kr protein, Drosophila; D051741:Kruppel-Like Transcription Factors; D012097:Repressor Proteins; D014157:Transcription Factors; D012313:RNA; D004247:DNA; D005982:Glutathione Transferase