High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

Abstract

Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of -regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised, macrophage-specific enhancers and promoters. The role of ELFs in promoting high-level constitutive transcription was suggested by multiple evidence: ELF sites enabled robust transcriptional activation by endogenous and minimal synthetic promoters, ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data suggest that the co-optation of a limited number of highly active transcription factors represents a broadly adopted strategy to equip both cell type-specific and housekeeping -regulatory elements with the ability to efficiently promote transcription.

Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells

“…Cell cultures. Macrophages were derived from bone marrows of C57/BL6 mice (Harlan) as described (Curina et al 2017).…”

“…Table 4). This analysis revealed that: i) constitutive binding of PU.1 (SPI1) was associated with all types of remodeling events; ii) constitutive binding of ELF4 was associated with nucleosome shifts, likely reflecting the high transcriptional activity of ELF4-associated promoters (Curina et al 2017); iii) basal and inducible IRF1 (Interferon Regulatory Factor 1) binding along with inducible IRF3 and STAT2 binding were selectively associated with remodeling events (especially evictions) at the TSS of secondary response genes, which include genes activated in a paracrine/autocrine manner by early released IFNb; iv) inducible NF-kB binding was associated with shifts but not evictions, and this association was stronger for primary than for secondary response gene promoters. The correlation between basal, inducible and reduced TF binding events and nucleosome remodeling at different classes of genes is highlighted in Suppl.…”

“…5). In addition to typical stimulus activated transcription factors (NF-kB, AP-1, CREB, IRF, STAT, SRF) we included two myeloid lineage transcription factors (PU.1 and C/EBPb) (Feng et al 2008;Goode et al 2016) and the ETS family member ELF4, which is selectively associated with active cis-regulatory elements, contributing to their basal activity (Curina et al 2017). We also included total RNA Pol II and BRG1, the active subunit of the Swi/Snf chromatin remodeling complex.…”

FOXA 2 controls the cis ‐regulatory networks of pancreatic cancer cells in a differentiation grade‐specific manner

“…ChIP-seq was carried out using previously described protocols (Curina et al, 2017;Balestrieri et al, 2018) on an Illumina HiSeq 2000 platform. 10 6 (H3K27ac) or 50-150 × 10 6 (TFs) were either fixed with formaldehyde as described before (for H3K27ac, FOXA2, HOXB8, and JUNB ChIP-seq) or fixed with a double cross-linking protocol (for FOS ChIP-seq).…”

Transcription factor enrichment analysis (TFEA): Quantifying the activity of hundreds of transcription factors from a single experiment

“…Concurrent with the immediate innate immune response, TFEA identified a set of TFs that exhibit a rapid decrease in E-Scores including ELF1/2 [17], TYY1 [30][63], USF1/2 [31], and GABPA [62]. The decreased E-Score set includes TYY1, a transcriptional inhibitor known to be activated directly by NFκB [54].…”