Nuclear architecture as an epigenetic regulator of neural development and function.

The nervous system of higher organisms is characterized by an enormous diversity of cell types that function in concert to carry out a myriad of neuronal functions. Differences in connectivity, and subsequent physiology of the connected neurons, are a result of differences in transcriptional programs. The extraordinary complexity of the nervous system requires an equally complex regulatory system. It is well established that transcription factor combinations and the organization of cis-regulatory sequences control commitment to differentiation programs and preserve a nuclear plasticity required for neuronal functions. However, an additional level of regulation is provided by epigenetic controls. Among various epigenetic processes, nuclear organization and the control of genome architecture emerge as an efficient and powerful form of gene regulation that meets the unique needs of the post-mitotic neuron. Here, we present an outline of how nuclear architecture affects transcription and provide examples from the recent literature where these principles are used by the nervous system.

Nucleosome sliding via TBP DNA binding in vivo.

Here, we show that a nucleosome obstructing transcription from the IFN-beta promoter slides in vivo in response to virus infection, thus exposing the previously masked TATA box and the initiation site, a requirement for transcriptional activation. Our experiments also revealed that this mode of chromatin remodeling is a two-step reaction. First, the enhanceosome recruits the SWI/SNF chromatin-remodeling complex that modifies the nucleosome to allow binding of TBP. Second, DNA bending is induced by TBP binding, and the nucleosome slides to a new position. Experiments with other DNA binding proteins demonstrated a strong correlation between the ability to bend DNA and nucleosome sliding, suggesting that the sliding is induced by the bend.

Coordination of a transcriptional switch by HMGI(Y) acetylation.

Dynamic control of interferon-beta (IFN-beta) gene expression requires the regulated assembly and disassembly of the enhanceosome, a higher-order nucleoprotein complex formed in response to virus infection. The enhanceosome activates transcription by recruiting the histone acetyltransferase proteins CREB binding protein (CBP) and p300/CBP-associated factors (PCAF)/GCN5, which, in addition to modifying histones, acetylate HMGI(Y), the architectural component required for enhanceosome assembly. We show that the accurate execution of the IFN-beta transcriptional switch depends on the ordered acetylation of the high-mobility group I protein HMGI(Y) by PCAF/GCN5 and CBP, which acetylate HMGI(Y) at distinct lysine residues on endogenous promoters. Whereas acetylation of HMGI(Y) by CBP at lysine-65 destabilizes the enhanceosome, acetylation of HMGI(Y) by PCAF/GCN5 at lysine-71 potentiates transcription by stabilizing the enhanceosome and preventing acetylation by CBP.

Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter.

Here, we show that the IFN-beta enhanceosome activates transcription by directing the ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. The enhanceosome is assembled in the nucleosome-free enhancer region of the IFN-beta gene, leading to the modification and remodeling of a strategically positioned nucleosome that masks the TATA box and the start site of transcription. Initially, the GCN5 complex is recruited, which acetylates the nucleosome, and this is followed by recruitment of the CBP-PolII holoenzyme complex. Nucleosome acetylation in turn facilitates SWI/SNF recruitment by CBP, resulting in chromatin remodeling. This program of recruitment culminates in the binding of TFIID to the promoter and the activation of transcription.

A GSK3beta phosphorylation site in axin modulates interaction with beta-catenin and Tcf-mediated gene expression.

Upon binding of a Wnt to its receptor, GSK3beta is inhibited through an unknown mechanism involving Dishevelled (Dsh), resulting in the dephosphorylation and stabilization of beta-catenin, which translocates to the nucleus and interacts with Lef/Tcf transcription factors to activate target gene expression. Axin is a scaffold protein which binds beta-catenin and GSK3beta (as well as several other proteins) and thus promotes the phosphorylation of beta-catenin. Here we report that Axin is phosphorylated on Ser and Thr residues in several regions in vivo, while only one region (amino acids 600-672) is efficiently phosphorylated by GSK3beta in vitro. Site-directed mutagenesis, together with in vitro and in vivo phosphorylation assays, demonstrates that Axin residues T609 and S614 are physiological GSK3beta targets. Substitutions for one or more of these residues, which lie within a beta-catenin binding site, reduce the ability of Axin to modulate Wnt-induced signaling in a Lef/Tcf reporter assay. These amino acid substitutions also reduce the binding between Axin and beta-catenin. We propose a model in which inhibition of GSK3beta activity upon Wnt signaling leads to the dephosphorylation of GSK3beta sites in Axin, resulting in the release of beta-catenin from the phosphorylation complex.