1. Identification and characterization of Hoxa9 binding sites in hematopoietic cells
- Author
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Jay L. Hess, Kajal V. Sitwala, Joel Bronstein, Gordon Robertson, Monisha Dandekar, Yongsheng Huang, Martin Hirst, Steven J.M. Jones, James W. MacDonald, Thomas Zeng, Timothee Cezard, Daniel S. Sanders, Cailin Collins, Misha Bilenky, Nina Thiessen, Alfred O. Hero, and Yongjun Zhao
- Subjects
Epigenomics ,Chromatin Immunoprecipitation ,Hematopoiesis and Stem Cells ,Blotting, Western ,Immunology ,Bone Marrow Cells ,Enhancer RNAs ,Biology ,Real-Time Polymerase Chain Reaction ,Biochemistry ,Mice ,Biomarkers, Tumor ,Animals ,MYB ,RNA, Messenger ,Myeloid Ecotropic Viral Integration Site 1 Protein ,Hox gene ,Enhancer ,Transcription factor ,Oligonucleotide Array Sequence Analysis ,Homeodomain Proteins ,Genetics ,Binding Sites ,Leukemia ,Gene Expression Regulation, Leukemic ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Acetylation ,Cell Biology ,Hematology ,Hematopoiesis ,Neoplasm Proteins ,Mice, Inbred C57BL ,Enhancer Elements, Genetic ,Histone ,biology.protein ,Female ,Chromatin immunoprecipitation ,Transcription Factors - Abstract
The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.
- Published
- 2012