A lncRNA identifiesIRF8enhancer element in negative feedback control of dendritic cell differentiation

Abstract

Transcription factors play a determining role in lineage commitment and cell differentiation. Interferon regulatory factor 8 (IRF8), a hematopoietic transcription factor, is prominently upregulated in dendritic cells (DC) by autoactivation and controls DC differentiation and function. However, it is unclear how IRF8 autoactivation is controlled and eventually limited. Here we identified a novel long non-coding RNA transcribed from the +32 kb enhancer downstream of IRF8 transcription start site and expressed specifically in plasmacytoid DC (pDC), referred to as lncIRF8. A sequence element of the lncIRF8 promoter, but not lncIRF8 itself, is crucial for pDC and classical DC type 1 (cDC1) differentiation. In DC development IRF8 autoactivation is first initiated by flanking enhancers and then second controlled by feedback inhibition through the lncIRF8 promoter element in the +32 kb enhancer. Our work reveals a previously unrecognized negative feedback loop of IRF8 that orchestrates its own expression and thereby controls DC differentiation.

Fully functional monocytic MDSC generation from the murine HoxB8 cell line

“…In our recent study, we discovered that the long noncoding RNA lncIRF8 plays a critical role in DC differentiation. This finding was made possible by utilizing DC generated from HoxB8 cells that were genetically modified employing CRISPR/Cas9 technology to knock out specific IRF8 enhancer elements or silence the lnIRF8 promoter by CRISPR/dCas9 [43,44]. In addition to differentiation, also DC migratory mechanisms were studied employing CRISPR editing in HoxB8 cells, where HoxB8-DC CCR7 −/− showed a failure in CCL19-dependent migration [26].…”

RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data

“…3b). We collected ChIP-seq data of the transcription factors PU.1 and IRF8, and five histone modifications (i.e., H3K4me1, H3K4me3, H3K9me3, H3K27me3, and H3K27ac) for each of the cell types [4, 16, 23, 24] (Supplementary Table 1). PU.1 is one of the master regulators of hematopoiesis and is expressed by all hematopoietic cells [25] and IRF8 is believed to co-bind with PU.1 to control the differentiation of DC progenitors (DCP) towards specific DC sub-types [4, 26].…”