Activator Inhibition is Dependent on Heterodimeric Partners

Heterodimeric partners lacking functional DNA-binding domains can make DNA-binding defective dimers with activators (Fig. 9.2F). For example, a heterodimer of two bHLH proteins, MyoD and E12/E47, promotes myogenesis (Lassar et al., 1991), however, dimerization of Id with MyoD inhibits both DNA binding of MyoD and muscle differentiation (Benezraei al, 1990; Jen et al, 1992). The Id protein lacks the basic domain that binds to DNA and is usually adjacent to the HLH dimerization motif. Similarly, CHOP (also known as C/EBPzeta), a member of C/EBP family, contains the leucine zipper dimerization domain but a defective basic domain (Ramji and Foka, 2002; Ron and Habener, 1992). When heterodimerized with CHOP, other members of the C/EBP family that have the basic leucine zipper domain fail to activate transcription due to their inability to bind DNA.

Heterodimeric partners lacking activation domains can repress transcription. NF-E2 p45 hetrodimerizes with small Mafs (MafF, MafG, and MafK) through the bZip domain (Igarashi et al, 1994; Motohashi et al,

1997). This heterodimer is able to activate expression of erythroid-specific genes. The small Mafs lack a canonical activation domain and their homodimers bind the p45/small Mafs activator site. As a result, the small Maf homodimers act as repressors as they compete for the same binding site. Similarly, dimerization of bHLH-Zip proteins, Myc, Max and Mad, regulate transcription through their DNA binding site called E-box (Grandori et al., 2000; Laherty et al., 1997; Luscher, 2001). A Max/Myc heterodimer that recruits SWI/SNF complex works as an activator, however a Max/Max homodimer bound to the E-box keeps transcription off passively. Furthermore, Max can heterodimerize with Mad, which in turn interacts with the HDAC corepressor complex and hence the Max/Mad heterodimer bound to the E-box actively represses transcription.

E: Repression at the Chromatin Level

As discussed in other chapters, both histone and DNA modifications are involved in repression (Fig. 9.3A). In brief, deacetylation of histones by HDACs might establish repressive chromatin (Thiel et al., 2004; Yang and Seto, 2003). In addition, the lysine-specific methylation of histones by SU(VAR)3-9 is essential for the formation of heterochromatin (Jenuwein, 2001). DNA methylation is also correlated with transcriptional repression (Wade, 2001). DNA methylation changes the chromatin structure by affecting nucleosome position and stability. In particular, a STAT3 activator binding site containing the dinucleotide sequence CpG in the GFAP promoter (an astrocyte marker gene) is highly methylated in astrocyte precursor cells (Takizawa et al., 2001). In differentiated astrocytes, demethylation of the STAT3 binding site allows binding of STAT3 to the GFAP promoter, resulting in the activation of the GFAP gene.

In this section, we will describe epigenetic transcriptional repression involving the Polycomb group proteins (PcG). PcG proteins maintain Hox genes stably and heritably silenced during development of Drosophila and vertebrates (Gould, 1997; Orlando, 2003; Orlando and Paro, 1995; Otte and Kwaks, 2003; Pirrotta, 1999). Drosophila PcG complexes inhibit transcription upon binding to specialized DNA elements, known as Polycomb response elements (PREs), while PREs have not been identified in mammalian genomes (Orlando, 2003). Chromatin immunoprecipitation assays show that Drosophila PcG is not only associated to the PRE sequences near the Ubx gene, but also to adjacent DNA regions over several thousand base pairs (Orlando et al., 1998; Orlando and Paro, 1993). In contrast, PcG binding is not detected near active homeotic genes. Spreading of the PcG proteins along chromatin fibers perhaps prevents activators from binding to DNA (Fig.9.3C) (Fitzgerald and Bender, 2001; Zink and Paro, 1995). Drosophila PcG proteins consist of up to 15 genes and can be separated into two classes biochemically. The 2-6 MDa Polycomb repressive complex 1 (PRC1) contains Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), Zeste, dSbfl, and Ringl, while the 400-600 kDa Polycomb repressive complex 2 (PRC2) is composed of Extra sex combs (Esc), Enhancer of zeste (E(z)), Pleiohomeotic (Pho), Suppressor 12 of zeste (Su(z)12), and NURF-55 (Lund and van Lohuizen, 2004; Otte and Kwaks, 2003). Two evolutionarily conserved complexes are found also in mammals: PRC1 contains HPC1, HPC2, HPC3, HPH1, HPH2, HPH3, RNF110, and RING1, while PRC2 contains EZH1, EZH2, EED, YY1, and SUZ12 (Lund and van Lohuizen, 2004; Otte and Kwaks, 2003). Pho and YY1 are the only sequence-specific DNA binding factors in the PcG complexes. E(z) contains a SET domain and is a methyltransferase that preferentially facilitates the methylation of histone H3 at lysine 27 (Cao and Zhang, 2004). Both Drosophila E(z) and mammalian EZH2 interact with HDACs (Chang et al., 2001; Tie et al., 2001; van der Vlag and Otte, 1999). The E(z)/EZH2-HDAC interaction may function as a "silencing core" in which deacetylation and subsequent methylation of histones induce transcriptional repression. Thus, histone H3 is epigenetically marked by the methylation through the PRC2 complex. The methylated histone H3 then serves as a recognition site for the chromodomain of Pc in the PRC1 complex (Cao et al., 2002; Czermin et al., 2002). The PRC1 complex bound to DNA inhibits chromatin remodeling by the SWI/SNF complex in vitro (Shao etal, 1999).

Spreading of the PcG complex along DNA was thought to convert the chromatin to a repressed state, thus blocking the access of activators. In contrast, recent reports suggest an alternative "looping" model (Fig. 9.3D) (Orlando, 2003; Pirrotta et al., 2003; Wang et al., 2004). This model is supported by the evidence that the Drosophila PcG complex can be purified together with TBP and TAFs, and that the PcG complex is found in the core promoter regions together with components of preinitiation complex, TBP, TFIIB, and TFIIF (Breiling et al., 2001; Saurin et al., 2001). Perhaps, the methylation of histone H3 by the PRC2 complex defines the landing zone for the PRC1 complex to PREs. Subsequently, PRC1 bound to PRE can contact TFIID and other GTFs on the core promoter by looping, thereby inhibiting transcription. In fact, it has been recently reported that PcG-mediated repression blocks the formation of the preinitiation complex (Dellino et al., 2004).

It should be noted that expression of each component of human PcG is different between tissues, cell types, and developmental stages. These observations suggest that the PcG complexes containing different components may regulate distinct target genes (Gunster et al., 2001).


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