The innate immune system is absolutely required for host defence, but, uncontrolled, it leads to inflammatory disease. This control is mediated, in part, by cytokines that are secreted by macrophages. Immune regulation is extraordinarily complex, and can be best investigated with systems approaches (that is, using computational tools to predict regulatory networks arising from global, high-throughput data sets). Here we use cluster analysis of a comprehensive set of transcriptomic data derived from Toll-like receptor (TLR)-activated macrophages to identify a prominent group of genes that appear to be regulated by activating transcription factor 3 (ATF3), a member of the CREB/ATF family of transcription factors. Network analysis predicted that ATF3 is part of a transcriptional complex that also contains members of the nuclear factor (NF)-kappaB family of transcription factors. Promoter analysis of the putative ATF3-regulated gene cluster demonstrated an over-representation of closely apposed ATF3 and NF-kappaB binding sites, which was verified by chromatin immunoprecipitation and hybridization to a DNA microarray. This cluster included important cytokines such as interleukin (IL)-6 and IL-12b. ATF3 and Rel (a component of NF-kappaB) were shown to bind to the regulatory regions of these genes upon macrophage activation. A kinetic model of Il6 and Il12b messenger RNA expression as a function of ATF3 and NF-kappaB promoter binding predicted that ATF3 is a negative regulator of Il6 and Il12b transcription, and this hypothesis was validated using Atf3-null mice. ATF3 seems to inhibit Il6 and Il12b transcription by altering chromatin structure, thereby restricting access to transcription factors. Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop.

No abstract

The Fos/Jun and ATF/CREB families of transcription factors function in coupling extracellular signals to alterations in expression of specific target genes. Like many eukaryotic transcription factors, these proteins bind to DNA as dimers. Dimerization is mediated by a structure known as the "leucine-zipper" motif. Although Fos/Jun and ATF/CREB were previously thought to interact preferentially with different DNA regulatory elements (the AP-1/TRE and ATF/CRE sites, respectively), we rind that members of these two families form selective cross-family heterodimers. The resulting heterodimers display distinguishable DNA binding speclfcities from each other and from their parental homodimers. These fidings indicate that the Fos/Jun and ATF/CREB families of transcription factors are not as distinct as was previously thought. We suggest that they can be grouped into a superfamily of transcription factors.

No abstract

The promoters of eukaryotic protein-coding genes are combinations of short, cis-acting elements, which provide 'binding sites for sequence-specific transcription factors (for review, see McKnight and Tjian 1986;Dynan 1989). In general, a given promoter contains several binding sites, and, conversely, a given binding site is present in different promoters.We have been studying the transcription factor ATF, -whose consensus binding site is 5'-GTGACGTAc^G-3 ' (Lin and Green 1988). This sequence is present in many viral and cellular promoters (Lin and Green 1988), and DNA-binding activities that interact with this element are found in a variety of eukaryotes (Jones and Jones 1989; Lin and Green 1989). The E1A-inducible adenovirus F.2, F.3, and E4 promoters contain one or more ATF sites . For the F4 promoter, the ATF sites have been shown to be required for E1A inducibility . In addition to viral promoters, many cellular promoters also contain ATF sites. The best studied among them are the cAMP-inducible promoters. In these promoters, the ATF site is referred to as a cAMP response element (CRE) and is required for inducibility by cAMP (for review, see Roesler et al, 1988). However, many cellular promoters contain ATF sites and are not known to be regulated by either E1A or cAMP (Table 1).Therefore, a common cis-acting DNA sequence, the ATF-binding site, is present in promoters regulated by a variety of different agents.These observations raise the question of whether a single ATF proteiri mediates all of these apparently diverse transcription responses. In a previous biochemical study (Hal et al. 1988), we provided evidence that ATF is not a single factor but, rather a family of related polypeptides. Moreover, we demonstrated that ATF polypeptides are immunologically related to the AP-1/c-jun family of transcription factors. In this paper, we describe the isolation and characterization of ATF cDNA clones. The results confirm and extend the conclusions of our previous study. We show that ATF represents an extensive gene and protein family, which has amino acid similarity to the AP-1/c-jun family of transcription factors. ATF proteins bind to DNA as dimers, and they selectively form heterodimers that can bind to DNA.