The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

B-ZIP transcription factors (98) are exclusively eukaryotic proteins that bind to sequence-specific double-stranded DNA as homodimers or heterodimers to either activate or repress gene transcription (34). We have examined both of the recently published DNA sequences of the human genome (51, 95) and identified 56 genes that contain the B-ZIP motif. Three sequences were identical, giving a total of 53 unique B-ZIP domains with the potential to form 2,809 dimers. This creates the possibility for a tremendous range of transcriptional control (23, 50, 52). While significant effort has been directed at identifying dimerization partners of B-ZIP proteins, the full complement of dimerization partners remains to be elucidated. This review highlights two topics: (i) the known structural rules that regulate leucine zipper dimerization specificity and (ii) experimental data addressing mammalian B-ZIP dimerization partners.We have annotated the leucine zippers of all human B-ZIP domains, highlighting amino acids in the a, d, e, and g positions that appear critical for leucine zipper dimerization specificity. These data were used to group B-ZIP proteins into 12 families with similar dimerization properties: (i) those that strongly favor homodimerization within the family (PAR, CREB, Oasis, and ATF6), (ii) those that have the ability to both homodimerize and heterodimerize with similar affinities (C/EBP, ATF4, ATF2, JUN, and the small MAFs), and (iii) those that favor heterodimerization with other families (FOS, CNC, and large MAFs). BACKGROUND

Summary Ligand-dependent transcription by the nuclear receptor glucocorticoid receptor (GR) is mediated by interactions with co-regulators. The role of these interactions in determining selective binding of GR to regulatory elements remains unclear. Recent findings indicate a large fraction of genomic GR binding coincides with chromatin that is accessible prior to hormone treatment, suggesting that receptor binding is dictated by proteins that maintain chromatin in an open state. Combining DNaseI accessibility and chromatin immunoprecipitation with high-throughput sequencing, we identify the activator protein 1 (AP1) as a major partner for productive GR-chromatin interactions. AP1 is critical for GR-regulated transcription and recruitment to co-occupied regulatory elements, illustrating an extensive AP1-GR interaction network. Importantly, the maintenance of baseline chromatin accessibility facilitates GR recruitment and is dependent on AP1 binding. We propose a model where the basal occupancy of transcription factors act to prime chromatin and direct inducible transcription factors to select regions in the genome.