Identification of cell-type specific enhancers is important for understanding the regulation of programs controlling cellular development and differentiation. Recent studies utilizing genomic methodologies have shown that enhancers are frequently associated with biologically relevant and disease-associated genetic variants. Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups of cell-expressed transcription factors. We hypothesized that a unique set of enhancers regulate gene expression in human erythroid cells, a highly specialized cell type evolved to provide adequate amounts of oxygen throughout the body. Using chromatin immunoprecipitation followed by massively parallel sequencing, genome-wide maps of candidate enhancers were constructed for p300 and four transcription factors, GATA1, NF-E2, KLF1, and SCL, in primary human erythroid cells. These data were combined with parallel gene expression analyses and candidate enhancers identified. Cell and tissue-type specific enhancers act over distances of tens to hundreds of kilobases, thus bona fide erythroid enhancers are expected to be enriched in the genomic vicinity of genes expressed and functional in erythroid cells. Sites of occupancy were correlated with levels of gene expression. Promoter sites within 2kb of annotated transcriptional start sites (TSS) were excluded. Consistent with their predicted function, there was significant enrichment of p300 peaks within 2–50kb of the TSS of genes highly expressed in erythroid cells c.f. peaks >100kb of a TSS. There was also significant enrichment of combinations of 2, 3, and 4 co-localizing erythroid transcription factor peaks within 2–50kb of the TSS of genes highly expressed in erythroid cells. In contrast, similar to other cell type-specific enhancers, there was no enrichment of p300 or erythroid transcription factor sites within 2–50kb of genes highly expressed in nonerythroid cells. When analyses were performed comparing a set of erythroid-specific genes vs. a random set of genes, there was significant enrichment of combinations of 2, 3, and 4 co-localizing erythroid transcription factor binding sites, but not p300, within 2–50kb of the TSS of erythroid-specific genes. Evolutionary analyses revealed high conservation between man and chimp for p300 and erythroid transcription factors. However, there was a very large falloff between human and mouse, with.
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Asterisk with author names denotes non-ASH members.