Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

Abstract

SUMMARY Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ~3000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. Unexpectedly, we find that enhancer transcription precedes local mono- and di-methylation of histone H3 lysine 4 (H3K4me1/2). H3K4 methylation at de novo enhancers is primarily dependent on the histone methyltransferases Mll1, Mll2/4 and Mll3, and is significantly reduced by inhibition of RNA polymerase II elongation. Collectively, these findings suggest an essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts.

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia

“…Transcription of eRNA is considered the most precise mark of functional looping between an activated enhancer and its regulated gene promoter, and the dynamic changes observed in eRNA levels allow elucidation of key TFs upon cell differentiation and environmental stimuli (Wang et al 2011;Kaikkonen et al 2013). We present here the first application of eRNA quantification to elucidate aberrant transcriptional activity downstream from a fusion TF.…”

“…The nuclei isolation (yielding ∼5 × 10 6 nuclei per condition), the nuclear run-on reaction, and library preparation were performed as previously described (Wang et al 2011, Kaikkonen et al 2013Supplemental Material). The ChIP-seq data from human HSC and SEM cells (GSE45144, Beck et al 2013;GSE42075, Wilkinson et al 2013; originally mapped to hg18) were reanalyzed starting from raw reads.…”

“…At these regions, RNA polymerase II (RNAP II) generates so-called enhancer RNAs (eRNAs) that show dynamic activation patterns reflecting regional regulatory activity (Core et al 2008;Kaikkonen et al 2013). Enhancers contain binding sites for multiple sequence-specific TFs that can be revealed through profiling dynamical eRNA expression and de novo motif discovery.…”

Chromatin remodelling and autocrine TNFα are required for optimal interleukin-6 expression in activated human neutrophils

“…Altogether, these results suggest that endogenously produced TNFa sustains histone acetylation at the IL-6 promoter and surprisingly, histone methylation at the distal IL-6 enhancers, but not PU.1 recruitment, which is supposed to be the main factor responsible for H3K4me1 deposition. However, since C/EBPs were shown to collaborate with PU.1 in regulating H3K4 monomethylation at de novo formed enhancers 41 , it is likely that the effect of endogenous TNFa on H3K4me1 deposition in R848-treated neutrophils may be mediated by C/EBPb, whose recruitment to the IL-6 promoter ( Fig. 8a), as well as IL-6 enhancers, is strongly decreased by adalimumab.…”

Isolation of the protein and RNA content of active sites of transcription from mammalian cells

“…Hence, cataloguing nascent mammalian transcriptomes is challenging (in contrast to the now-routine mapping of mRNAs) due to the short half-lives, low abundance, and variety of processing pathways. Nonetheless, such cataloguing can be highly informative, especially when analyzing short-term responses to stimuli, and the associated changes in messenger, non-coding, and enhancer RNAs (eRNAs 23,24 ). Analysis of factory-associated transcripts offers a simple, low-cost, way for assessing transcriptional changes at the level of nascent RNA.…”