Interactions between the chromatin remodeller CHD1 and the spliceosome are critical for hematopoietic stem and progenitor cell emergence

Abstract

Defects in hematopoietic stem cells (HSCs) lead to hematological diseases, such as myelodysplastic syndromes (MDS) and leukemia. Recurrent mutations in spliceosomal components were recently identified in these diseases, suggesting an underappreciated role for splicing regulation in HSC biology. Based on this hypothesis, we explored the importance of splicing on hematopoietic stem and progenitor cell (HSPC) specification during zebrafish development. Zebrafish mutants in U2 snRNP components, specifically sf3a3hi1950 and sf3b1hi3394, have diminished runx1 expression within their aorta by 28 hours post fertilization (hpf), while expression of the endothelial marker flk1/kdrl is mostly unaffected, indicating a defect at the level of HSPC formation. Using these mutants, we defined chd1 as a genetic interaction partner with the spliceosome that is critical for HSPC emergence. CHD1 (Chromodomain Helicase DNA Binding Protein 1) is a chromatin remodeler that interacts with SF3A and SF3B spliceosomal complexes in human cells and is needed for their recruitment to actively transcribed genes. Transient morpholino-mediated knockdown of chd1 in zebrafish embryos has no effect on HSPC development. Similarly, embryos heterozygous for sf3a3hi1950 have no noticeable hematopoietic phenotype, however, in combination, diminished chd1 levels in sf3a3hi1950 heterozygotes leads to a significant decline in HSPC levels. These results demonstrate a clear in vivo connection between splicing and epigenetic regulation within HSPCs. As these two processes are the most frequently mutated in MDS, our data might also have implications for understanding the origins of MDS at the HSC level. Defects in hematopoietic stem cells (HSCs) lead to hematological diseases, such as myelodysplastic syndromes (MDS) and leukemia. Recurrent mutations in spliceosomal components were recently identified in these diseases, suggesting an underappreciated role for splicing regulation in HSC biology. Based on this hypothesis, we explored the importance of splicing on hematopoietic stem and progenitor cell (HSPC) specification during zebrafish development. Zebrafish mutants in U2 snRNP components, specifically sf3a3hi1950 and sf3b1hi3394, have diminished runx1 expression within their aorta by 28 hours post fertilization (hpf), while expression of the endothelial marker flk1/kdrl is mostly unaffected, indicating a defect at the level of HSPC formation. Using these mutants, we defined chd1 as a genetic interaction partner with the spliceosome that is critical for HSPC emergence. CHD1 (Chromodomain Helicase DNA Binding Protein 1) is a chromatin remodeler that interacts with SF3A and SF3B spliceosomal complexes in human cells and is needed for their recruitment to actively transcribed genes. Transient morpholino-mediated knockdown of chd1 in zebrafish embryos has no effect on HSPC development. Similarly, embryos heterozygous for sf3a3hi1950 have no noticeable hematopoietic phenotype, however, in combination, diminished chd1 levels in sf3a3hi1950 heterozygotes leads to a significant decline in HSPC levels. These results demonstrate a clear in vivo connection between splicing and epigenetic regulation within HSPCs. As these two processes are the most frequently mutated in MDS, our data might also have implications for understanding the origins of MDS at the HSC level.