We present evidence that both corepressors SMRT and N-CoR exist in large protein complexes with estimated sizes of 1.5±2 MDa in HeLa nuclear extracts. Using a combination of conventional and immunoaf®nity chromatography, we have successfully isolated a SMRT complex and identi®ed histone deacetylase 3 (HDAC3) and transducin (b)-like I (TBL1), a WD-40 repeat-containing protein, as the subunits of the puri®ed SMRT complex. We show that the HDAC3-containing SMRT and N-CoR complexes can bind to unliganded thyroid hormone receptors (TRs) in vitro. We demonstrate further that in Xenopus oocytes, both SMRT and N-CoR also associate with HDAC3 in large protein complexes and that injection of antibodies against HDAC3 or SMRT/N-CoR led to a partial relief of repression by unliganded TR/RXR. These ®ndings thus establish both SMRT and N-CoR complexes as bona ®de HDAC-containing complexes and shed new light on the molecular pathways by which N-CoR and SMRT function in transcriptional repression.

Corepressors N-CoR and SMRT participate in diverse repression pathways and exist in large protein complexes including HDAC3, TBL1 and TBLR1. However, the roles of these proteins in SMRT±N-CoR complex function are largely unknown. Here we report the puri®cation and functional characterization of the human N-CoR complex. The puri®ed N-CoR complex contains 10±12 associated proteins, including previously identi®ed components and a novel actinbinding protein IR10. We show that TBL1/TBLR1 associates with N-CoR through two independent interactions: the N-terminal region and the C-terminal WD-40 repeats interact with the N-CoR RD1 and RD4 region, respectively. In vitro, TBL1/TBLR1 bind histones H2B and H4, and, importantly, repression by TBL1/TBLR1 correlates with their interaction with histones. By using speci®c small interference RNAs (siRNAs), we demonstrate that HDAC3 is essential, whereas TBL1 and TBLR1 are functionally redundant but essential for repression by unliganded thyroid hormone receptor. Together, our data reveal the roles of HDAC3 and TBL/TBLR1 and provide evidence for the functional importance of histone interaction in repression mediated by SMRT±N-CoR complexes.

Cortical GABAergic inhibitory interneurons have crucial roles in the development and function of the cerebral cortex. In rodents, nearly all neocortical interneurons are generated from the subcortical ganglionic eminences. In humans and nonhuman primates, however, the developmental origin of neocortical GABAergic interneurons remains unclear. Here we show that the expression patterns of several key transcription factors in the developing primate telencephalon are very similar to those in rodents, delineating the three main subcortical progenitor domains (the medial, lateral and caudal ganglionic eminences) and the interneurons tangentially migrating from them. On the basis of the continuity of Sox6, COUP-TFII and Sp8 transcription factor expression and evidence from cell migration and cell fate analyses, we propose that the majority of primate neocortical GABAergic interneurons originate from ganglionic eminences of the ventral telencephalon. Our findings reveal that the mammalian neocortex shares basic rules for interneuron development, substantially reshaping our understanding of the origin and classification of primate neocortical interneurons.

Epigenetic inheritance of DNA methylation in mammals requires a multifunctional protein UHRF1, which is believed to recruit DNMT1 to DNA replication forks through a unique hemi-methylated CpG-binding activity. Here we demonstrate that the UHRF1 mutants deficient in binding either hemi-methylated CpG or H3K9me2/3, but not both, are able to associate with pericentric heterochromatin, recruit Dnmt1 and partially rescue DNA methylation defects in mouse Uhrf1 null ES cells. Furthermore, we present evidence that the flip out of the methylated cytosine induced by UHRF1 binding is unlikely essential for subsequent DNA methylation by DNMT1. Together, our study demonstrates that UHRF1 can target DNMT1 for DNA maintenance methylation through binding either H3K9me2/3 or hemi-methylated CpG, and that the presence of both binding activities ensures high fidelity DNA maintenance methylation. In addition, our study indicates that UHRF1 mediates cross-talk between H3K9 methylation and DNA methylation at the level of DNA methylation maintenance.

Histone H3 lysine 9 (H3-K9) methylation has been shown to correlate with transcriptional repression and serve as a specific binding site for heterochromatin protein 1 (HP1). In this study, we investigated the relationship between H3-K9 methylation, transcriptional repression, and HP1 recruitment by comparing the effects of tethering two H3-K9-specific histone methyltransferases, SUV39H1 and G9a, to chromatin on transcription and HP1 recruitment. Although both SUV39H1 and G9a induced H3-K9 methylation and repressed transcription, only SUV39H1 was able to recruit HP1 to chromatin. Targeting HP1 to chromatin required not only K9 methylation but also a direct protein-protein interaction between SUV39H1 and HP1. Targeting methyl-K9 or a HP1-interacting region of SUV39H1 alone to chromatin was not sufficient to recruit HP1. We also demonstrate that methyl-K9 can suppress transcription independently of HP1 through a mechanism involving histone deacetylation. In an effort to understand how H3-K9 methylation led to histone deacetylation in both H3 and H4, we found that H3-K9 methylation inhibited histone acetylation by p300 but not its association with chromatin. Collectively, these data indicate that H3-K9 methylation alone can suppress transcription but is insufficient for HP1 recruitment in the context of chromatin exemplifying the importance of chromatin-associated factors in reading the histone code.In eukaryotic cells, DNA is tightly associated with histones and other factors to form chromatin. The nucleosome is the basic building block of chromatin and consists of approximately 150 bp of DNA coiled around an octamer of histones. The histone octamer contains two copies of each of the core histones, H2A, H2B, H3, and H4. The N-terminal region of each core histone is unstructured when crystallized and therefore is likely to be a highly dynamic structure. These histone tails protrude out from the globular center of the nucleosome where they may interact with nuclear factors. The N-terminal tails are subject to a variety of posttranslational modifications, including phosphorylation, acetylation, methylation, and ubiquitylation. These modifications affect the binding of proteins to the histone tails and thus regulate the nature of the protein complexes that will associate with a region of chromatin. The ability of proteins to specifically associate with certain histone modifications is the basis of the histone code theory (15, 48). According to this theory, specific proteins will associate with histone tails containing certain modifications. These proteins may function to activate or inhibit transcription or serve to maintain a specific chromatin structure.The best-studied histone modifications are acetylation and methylation. Histone acetylation is generally associated with regions of active transcription. Many transcriptional coactivators contain histone acetyltransferase (HAT) activity, including CBP/p300 (3, 35), the p160 family (46), and P/CAF (63). While arginine methylation of H3 and H4 is associated with transcr...