Differences in the chromatin structure and cis-element organization of the human and mouse GATA1 loci: implications for cis-element identification

Abstract

Cis-element identification is a prerequisite to understand transcriptional regulation of gene loci. From analysis of a limited number of conserved gene loci, sequence comparison has proved a robust and efficient way to locate ciselements. Human and mouse GATA1 genes encode a critical hematopoietic transcription factor conserved in expression and function. Proper control of GATA1 transcription is critical in regulating myeloid lineage specification and maturation. Here, we compared sequence and systematically mapped position of DNase I hypersensitive sites, acetylation status of histone H3/H4, and in vivo binding of transcription factors over approximately 120 kilobases flanking the human GATA1 gene and the corresponding region in mice. Despite lying in approximately 10 megabase (Mb) conserved syntenic segment, the chromatin structures of the 2 homologous loci are strikingly different. The 2 previously unidentified hematopoietic cis-elements, one in each species, are not conserved in position and sequence and have enhancer activity in erythroid cells. In vivo, they both bind the transcription factors GATA1, SCL, LMO2, and Ldb1. More broadly, there are both species-and regulatory elementspecific patterns of transcription factor binding. These findings suggest that some cis-elements regulating human and mouse GATA1 genes differ. More generally, mouse human sequence comparison may fail to identify all cis-elements. IntroductionGATA1 is a key hematopoietic transcription factor and a member of a conserved family of GATA factors that execute a program of differentiation in diverse cell types. 1 The precise pattern of GATA1 expression is critical for its function. Gain-of-function experiments demonstrate that GATA1 directs cell fate of myeloid progenitors in a manner dependent on the level of GATA1 expressed and that GATA1 expression has to be extinguished to allow neutrophil and macrophage differentiation. [2][3][4] Loss-of-function experiments show that GATA1 is required for terminal maturation of erythroid cells, megakaryocytes, eosinophils, and mast cells. [5][6][7][8] Moreover, reduction of GATA1 levels to 20% of normal is insufficient for erythroid maturation. 9 Lastly, rescue experiments in GATA1-mutant hematopoietic cells 10 and mice 11 and analysis of knock-in mice 12 show that GATA1 function is determined not just by specific GATA1 protein sequences (other GATA factors can, to a large extent, replace GATA1), but is also critically dependent on the precise pattern of GATA1 expression.Consistent with this function, in both human and mouse definitive hematopoiesis, GATA1 expression is detected at a low level in the common myeloid progenitor (CMP) 13,14 and is selectively maintained in erythroid cells, megakaryocytes, eosinophils, and mast cells (reviewed in Orkin 15 ) and repressed in neutrophils and monocytes. 4 Outside blood cells, GATA1 is expressed in testis where its role is unclear. Taken together, these observations argue that the time, place (cell-type), and level of GATA1 expression help regulate output...

The mediator complex functions as a coactivator for GATA-1 in erythropoiesis via subunit Med1/TRAP220

“…9A). GATA-1 is able to stimulate its own GATA-1 promoter activity (33); the GATA-1-binding sites could be systematically mapped on the GATA-1 gene locus (37). We confirmed the described GATA recruitment to GATA-1 gene enhancer elements and found a clear correlation with the presence of Mediator subunits Med1 and Med17, as well as polII.…”

Mast cell transcriptional networks

“…Similar results have been published previously for definitive erythroid hematopoiesis (84). We observed that hyperacetylated histone H3 and H4 generally associated with open chromatin(85) at the previously identified DNase I hypersensitive sites in both definitive (fetal liver) and primitive (yolk sac) erythroid cells ( figure 4C).…”

“…We observed that hyperacetylated histone H3 and H4 generally associated with open chromatin(85) at the previously identified DNase I hypersensitive sites in both definitive (fetal liver) and primitive (yolk sac) erythroid cells ( figure 4C). The DNase I hypersensitive sites represent erythroid and megakaryocyte enhancers of the GATA-1 locus (86)(87)(88)(89)). An unexpected result in one of the controls of our analysis, however, was the finding of hyperacetylated histone H3 and H4 chromatin in the GATA-1 large first intron in the M1 myeloid cell line (figure 4B).…”

Phylogenetic comparisons suggest that distance from the locus control region guides developmental expression of primate β-type globin genes

“…This difference in expression patterns probably results from the mouse's trans-acting environment being different from the human's. For example, GATA1, an erythroid transcription factor that interacts with the LCR, resides at a locus with marked differences in chromatin structure in mice and humans (51). Moreover, cis-elements in the GATA1 locus show greater binding affinity for trans-factors in mouse than in human erythroid cells (51).…”

“…For example, GATA1, an erythroid transcription factor that interacts with the LCR, resides at a locus with marked differences in chromatin structure in mice and humans (51). Moreover, cis-elements in the GATA1 locus show greater binding affinity for trans-factors in mouse than in human erythroid cells (51). If this pattern holds for embryonic erythroid cells as well, then the different trans-acting transcriptional environments that apparently exist in human and mouse may account for human ␥ 1 being a major embryonic gene in transgenic mice but only a minor embryonic gene in humans, where it is the major ␤-type globin fetal gene.…”