Dendritic cells (DCs) are important immune cells. This study focused on transcriptional networks active in murine DCs, but DCs are difficult to study using conventional molecular techniques. Therefore, comparative promoter analysis was used to identify evolutionarily conserved features between the murine CD11c and DC-STAMP promoters. A promoter framework consisting of 4 transcription factor binding sites was identified that included signal transducer and activator of transcription, homeodomain transcription factors, and 2 members of the Brn POU domain factors family. This promoter module was functionally verified by in vivo promoter analysis and site-directed mutagenesis. Hematopoietic stem cells were engineered by lentiviral vectors and expression of green fluorescent protein reporter was monitored in primary hematopoietic cell types that develop without further manipulation in irradiated recipient mice. The verified promoter module was then modeled and used in a bioinformatics-based search for other potential coregulated genes in murine DCs. A promoter database search identified 2 additional genes, Ppef2 and Pftk1, which have a similar promoter organization and are preferentially expressed in murine DCs. The results define a regulatory network linked to development of murine DCs. (Blood. 2011;118(11):e40-e49)
IntroductionDendritic cells (DCs) play key roles in shaping the immune response. 1,2 They are highly specialized in uptake and presentation of antigen. In their steady state, DCs migrate from peripheral tissues to the draining lymph node and present self-antigen to naive T cells, inducing tolerance. On encounter of pathogen, DCs change their phenotype (undergo maturation), which leads to a more pronounced migratory behavior and an increase in stimulatory capacity. 3 Plasticity is a pervasive feature of DC biology. DC subsets from different tissues show differential morphology, phenotypes, and functions. An additional distinction can also be made between conventional DCs (cDCs) and plasmacytoid DCs (pDCs), which are mainly involved in viral immune responses. cDCs also include a subset (CD8 ϩ in mice) specialized in antigen cross-presentation. 4 Networks of genes linked by common control mechanisms may help orchestrate homeostasis, as well as the response of DCs to external stimuli. The prediction and analysis of these networks represent a major challenge in understanding immunology. Transcriptional mechanisms have been very difficult to study in DCs because of their propensity to quickly change phenotypes in response to physical manipulation and their limited numbers. Gene expression is controlled by a series of processes that include locus control regions, chromatin rearrangement, methylation, gene enhancers, etc. These regulatory events ultimately end at the promoter level to effect gene transcription. Promoters integrate this information to achieve the tissue and signal specific control of gene expression required for complex biologic processes, such as DC biology and function.Within promoters, transcri...