Open AccessIdentification of Genomic Sites That Bind the Drosophila Suppressor of Hairy-wing Insulator Protein
Author(s) -
Timothy J. Parnell,
Emily J. Kuhn,
Brian L. Gilmore,
Cecilia Helou,
Marc S. Wold,
Pamela Geyer
Publication year - 2006
Publication title -
molecular and cellular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.14
H-Index - 327
eISSN - 1067-8824
pISSN - 0270-7306
DOI - 10.1128/mcb.00698-06
Subject(s) - biology , enhancer , genetics , chromatin immunoprecipitation , gene , genome , consensus sequence , genomic dna , regulatory sequence , chromatin , drosophila melanogaster , conserved sequence , transcription factor , computational biology , gene expression , promoter , peptide sequence
Eukaryotic genomes are divided into independent transcriptional domains by DNA elements known as insulators. Thegypsy insulator, a 350-bp element isolated from theDrosophila gypsy retrovirus, contains twelve degenerate binding sites for the Suppressor of Hairy-wing [Su(Hw)] protein. Su(Hw) associates with over 500 non-gypsy genomic sites, the functions of which are largely unknown. Using a bioinformatics approach, we identified 37p utativeS u(Hw)i nsulators (pSIs) that represent regions containing clustered matches to thegypsy insulator Su(Hw) consensus binding sequence. The majority of these pSIs contain fewer than four Su(Hw) binding sites, with only seven showing in vivo Su(Hw) association, as demonstrated by chromatin immunoprecipitation. To understand the properties of the pSIs, these elements were tested for enhancer-blocking capabilities using a transgene assay system. In a complementary set of experiments, effects of the pSIs on transcriptional regulation of genes at the natural genomic location were determined. Our data suggest that pSIs have complex genomic functions and, in some cases, establish insulators. These studies provide the first direct evidence that the Su(Hw) protein contributes to the regulation of gene expression in theDrosophila genome through the establishment of endogenous insulators.