Chromatin Remodeling Enzyme CHD7 Negatively Regulate Hematopoietic Stem Cell Function

ATP-dependent chromatin remodeling enzymes alter histone/DNA interactions, and are involved in the regulation of transcription, chromosome segregation, DNA replication and repair. We identified Chromodomain Helicase DNA binding protein 7 (CHD7) as a negative regulator of hematopoietic stem cell function. Autosomal dominant CHD7 mutations are associated with CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth and/or development, Genital and/or urinary abnormalities, and Ear abnormalities and deafness). Although several cases of T and B cell immunodeficiency in a subset of CHARGE syndrome patients have been reported, no previous role for CHD7 in hematopoiesis had been proposed.

We show that morpholino knockdown of Chd7 in zebrafish embryos results in an increased number of runx1 and c-myb expressing hematopoietic stem and progenitor cells in the aorta/gonad/mesonephros (AGM) region, and this effect is cell autonomous as determined by blastula transplantation. Heterozygous germline Chd7 deletion in mice also results in an increased number of phenotypic hematopoietic stem and progenitor cells (Runx1⁺c-kit⁺CD31⁺) in the AGM region. Downstream lineages such as myeloid and erythroid cells are expanded in zebrafish, and similarly conditional pan-hematopoietic deletion of Chd7 in mice with Vav1-Cre results in myeloid lineage expansion and increased granulocyte/monocyte progenitors. Consistent with these results, microarray analysis of murine CD48^- CD150⁺ Lin^- Sca-1⁺ c-kit⁺ (SLAM LSK) phenotypic long term repopulating HSCs shows up-regulation of genes in several subclasses of the myeloid lineages. Interestingly, although CHD7 deficient mouse bone marrow had a normal frequency of SLAM LSK cells, it had a two-fold higher frequency of functional LT-HSCs as determined by whole bone marrow, purified LSK and SLAM LSK limiting dilution transplants. ChIP-seq performed in human CD34+ hematopoietic stem and progenitor cells show CHD7 localizes to genes encoding many key hematopoietic transcription factors including MYB and RUNX1. The most abundant transcription factor motif under CHD7 genomic binding sites is a RUNX motif, indicating that CHD7 and Runx1 function together. We show CHD7, Runx1 and c-Myb interact both physically and genetically. CHD7 function in hematopoietic stem cells is dependent on both Runx1 and c-Myb since the increase in hematopoiesis in fish upon morpholino knockdown of Chd7 is abolished when either Runx1 or c-Myb is mutated. In summary, our study identifies CHD7 as a novel evolutionarily conserved negative epigenetic regulator of HSCs and progenitors through its interaction with Runx1 and c-Myb.