The NF-kB/Rel family of sequence-specific transcription factors provides a number of interesting paradigms for combinatorial control of gene regulation. Accumulating evidence indicates that specificity in NF-kB-regulated gene expression is generated at multiple levels, both intrinsic and extrinsic to the NF-kB system. In virtue of these mechanisms, the set of NF-kB-dependent genes induced by alternative stimuli differs significantly. Moreover, mechanisms explaining how specific dimers are linked to the induction of subsets of NF-kB-dependent genes are being clarified. Here, we comment on some of the recent advances in this field and we show the existence of a high level of interconnectivity between extrinsic and intrinsic mechanisms of control.
NF-jB Intrinsic MechanismsTemporal control of the NF-jB response and selective gene induction Alternative NF-kB inducers can generate NF-kB activation profiles of different duration: a direct link between temporal control of NF-kB activity and selective gene induction has been recently demonstrated. Hoffmann et al. 1 found that induction of some NF-kB-dependent genes in TNF-stimulated fibroblasts required the presence of NF-kB in the nucleus for a relatively long time (more than 2 h), while many other genes were induced even in response to a single and short cycle of NF-kB activity. In mouse fibroblasts, a short pulse of TNF treatment generates a transient NF-kB response that is terminated in about 1 h by re-synthesis of IkBa. 2 Pulsed TNF treatment was unable to induce a subset of NF-kB targets in wild-type cells, while it was able to induce these genes in cells lacking IkBa in which NF-kB activation in response to the same treatment is sustained. These data provide genetic evidence that alternative kinetics of NF-kB activation directly impact on the transcriptional response. However, the reason why some genes require a long-lasting presence of NF-kB in the nucleus to be activated may be extrinsic to the NF-kB system and related to differences in promoter accessibility to NF-kB (see below). In this light, a short NF-kB pulse will not induce those genes whose remodeling requires a relatively long time to be completed (see below).Following up this work, two recent papers by Covert et al. 3 and Werner et al. 4 showed that stimulus-specific differences in the temporal control of NF-kB activity generate distinct biological responses. While NF-kB activity induced by a pulse of TNFa is rapidly attenuated by negative feedback mechanisms (and in particular IkBa resynthesis), NF-kB activity induced by a pulse of LPS in fibroblasts is sustained due to an autocrine loop dependent on TNFa induction and secretion. TNFa induction in response to LPS requires IRF3, 3 which is activated via the Myd88-independent, Trif-dependent pathway emanating from TLR4. 5 TNFa and possibly additional cytokines are responsible for the late phase of NF-kB activation and NF-kB-dependent gene induction. Therefore, a source of difference between TNF and LPS-induced gene expression programs in mouse fibrobla...