Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states

Abstract

Cellular differentiation is orchestrated by lineage-specific transcription factors and associated with cell type-specific epigenetic signatures. In the present study, we used stage-specific, epigenetic "fingerprints" to deduce key transcriptional regulators of the human monocytic differentiation process. We globally mapped the distribution of epigenetic enhancer marks (histone H3 lysine 4 monomethylation, histone H3 lysine 27 acetylation, and the histone variant H2AZ), describe general properties of marked regions, and show that cell type-specific epigenetic "fingerprints" are correlated with specific, de novo-derived motif signatures at all of the differentiation stages studied (ie, hematopoietic stem cells, monocytes, and macrophages). We validated the novel, de novo-derived, macrophage-specific enhancer signature, which included ETS, CEBP, bZIP, EGR, E-Box and NF-B motifs, by ChIP sequencing for a subset of motif corresponding transcription factors (PU.1, C/EBP␤, and EGR2), confirming their association with differentiationassociated epigenetic changes. We describe herein the dynamic enhancer landscape of human macrophage differentiation, highlight the power of genome-wide epigenetic profiling studies to reveal novel functional insights, and provide a unique resource for macrophage biologists. IntroductionHuman monocyte-to-macrophage differentiation is a process involving marked morphologic, functional, and transcriptional changes that proceed in the absence of proliferation. The mechanisms controlling this transition are not well understood on the molecular level, in part because both human monocytes and macrophages are hard to manipulate without triggering defense programs that interfere with normal differentiation.Recent global epigenetic and transcription factor profiling studies in various cell types have provided ample evidence for a tight relationship between transcription factor binding and the local deposition/removal of some epigenetic marks, including histone methylation or acetylation, the appearance of histone variants, or DNA demethylation. 1 Cell type-specific epigenetic signatures are particularly evident at promoter-distal sites, where histone H3K4 monomethylation/dimethylation, 2,3 histone H3K27 acetylation, 3,4 the histone variant H2AZ, 2 or DNA demethylation 5,6 indicate the presence of poised or activated lineage-specific enhancer elements. These distal regulatory elements are often cell type-specific, are correlated with gene expression, and are bound by combinations of common and cell type-specific key regulators. 1,7 For example, in the murine hematopoietic system, macrophage-specific putative enhancer elements are characterized by PU.1, C/EBP␣/␤, and AP-1 binding, whereas putative enhancer elements in a related blood-cell type (murine B cells) that are also characterized by PU.1 binding associate with a distinct set of B cell-specific factors, including E2A, EBF, and OCT2. 8 Observations of correlating transcription factor binding and epigenetic patterns were also made in other cellul...

Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages

“…It is involved in both transcriptional activation and suppression, and recent evidence has implicated C/EBPb in the transcriptional silencing of miRNAs such as let-7i, miR-145, and miR-155 (53,63). Accessibility of promoters to C/EBPb depends on H3 methylation status at the C/EBPb binding region, as demonstrated previously (64,65). Indeed, H3 methylation was detected in the proximal region of the miR-155 and miR-146a promoters (Fig.…”

Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients

“…An additional sample, which was not analyzed by exome sequencing and lacked acquired mutations in EGR2, clustered together with the EGR2-mutated samples, suggesting that other alterations mimic the effect of EGR2 mutations. To investigate whether the differentially expressed genes might be direct EGR2 targets, we used ChIPseq data obtained from primary human monocyte extracts via chromatin immunoprecipitation with anti-EGR2 antibodies (27). Peaks were observed close to 168 of the 224 upregulated genes, indicating that these genes were likely directly regulated by EGR2 (P < 0.001; see Supplementary Table S5 and Methods).…”

Signatures of DNA target selectivity by ETS transcription factors

“…Detailed information on the localization, sequence characteristics of DNA targets, and associated binding partners is now available for ETS transcription factors in a range of cell types and developmental contexts. 27,[50][51][52][53][54][55] Although various levels of redundancy and specificity are observed that correlate with the ontology of the genes involved, one recurring feature is the close correspondence between in vivo and in vitro DNA sequence preferences. Moreover, in the case of PU.1 and Ets-1, the information contents (a direct informatic measure of target specificity) of the in vivo sequences preferences shown by both proteins are over 15% higher (> 3 bits over a 10-bp sequence space) than their in vitro counterparts.…”

“…While the importance of epigenetic regulation of ETSdependent transcription is well established in hematopoiesis and cancer, 55,[66][67][68] the mechanisms by which ETS activity are modulated at epigenetically modified DNA, with or without nucleosome, are not well understood. Genomic surveys have found that hematopoietic ETS transcription factors are over-represented in hypermethylated regions.…”