Transcription factor FoxA (HNF3) on a nucleosome at an enhancer complex in liver chromatin.
Nucleosome-like particles and acetylated histones occur near active promoters and enhancers, and certain transcription factors can recognize their target sites on the surface of a nucleosome in vitro; yet it has been unclear whether transcription factors can occupy target sites on nucleosomes in native chromatin. We developed a method for sequential chromatin immunoprecipitation of distinct nuclear proteins that are simultaneously cross-linked to nucleosome-sized genomic DNA segments. We find that core histone H2A co-occupies, along with the FoxA (hepatocyte nuclear factor-3) transcription factor, DNA for the albumin transcriptional enhancer in native liver chromatin, where the enhancer is active. Because histone H2A on nuclear DNA is only known to exist in nucleosomes, we conclude that transcription factors can form a stable complex on nucleosomes at an active enhancer element in vivo.
Chaya
D
D
Cell and Developmental Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.
Hayamizu
T
T
Bustin
M
M
Zaret
K S
KS
D000818:Animals; D015139:Blotting, Southern; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000096:biosynthesis* / Q000737:chemistry*; D004742:Enhancer Elements, Genetic; D051542:Hepatocyte Nuclear Factor 3-beta; D006657:Histones / Q000737:chemistry; D008099:Liver / Q000378:metabolism*; D008297:Male; D051379:Mice; D008809:Mice, Inbred C3H; D009687:Nuclear Proteins / Q000096:biosynthesis* / Q000737:chemistry*; D009707:Nucleosomes / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011233:Precipitin Tests; D011485:Protein Binding; D011487:Protein Conformation; D014157:Transcription Factors; D014158:Transcription, Genetic
D002843:Chromatin; D004268:DNA-Binding Proteins; C496503:Foxa2 protein, mouse; D006657:Histones; D009687:Nuclear Proteins; D009707:Nucleosomes; D014157:Transcription Factors; D051542:Hepatocyte Nuclear Factor 3-beta