Control of nuclear receptor function by local chromatin structure

Abstract

Steroid hormone receptors regulate gene transcription in a highly tissue-specific manner. The local chromatin structure underlying promoters and hormone response elements is a major component involved in controlling these highly restricted expression patterns. Chromatin remodeling complexes, as well as histone and DNA modifying enzymes, are directed to gene-specific regions and create permissive or repressive chromatin environments. These structures further enable proper communication between transcription factors, co-regulators and basic transcription machinery. The regulatory elements active at target genes can be either constitutively accessible to receptors or subject to rapid receptor-dependent modification. The chromatin states responsible for these processes are in turn determined during development and differentiation. Thus access of regulatory factors to elements in chromatin provides a major level of cell selective regulation.

Fig. 1.

Tissue-specific chromatin architecture revealed in localization of DHSs. A schematic representation of DHSs before and after hormone stimulation in two cell types. The majority of hormone-responsive genes have a TSS that is embedded within a localized region of DNase I hypersensitivity. These promoter regions are generally hypersensitive across multiple cell types, and usually correlate with CpG islands (A). Common and preprogrammed DHSs present at distal regulatory elements often overlap with insulators (B). Hormone receptors recognize short DNA motifs (HREs), but only a small percentage of them are occupied by a receptor in a given cell type. NR binding occurs usually at distal enhancers and is highly correlated with the presence of accessible chromatin regions (C, D, E). Only a small fraction of enhancer-related DHSs are universally utilized in multiple cell lines and they usually represent hormone-independent chromatin structures (pre-programmed DHSs) (C). Most distal DHSs are tissue-specific and can be either hormone-independent (D) or appear only after hormone stimulation (inducible DHSs) (E). Thus the presence of a DHS and subsequent receptor/transcription factor binding results in a hormone-dependent and tissue-specific transcriptional regulation of a particular gene (gene II). A gene can be activated by the same hormone receptor in different tissues, although through different regulatory elements (gene I; elements C and E).

Fig. 2.

Dynamics of chromatin structures at inducible genes. (A) Inducible genes are regulated by a ‘covered’ class of promoters characterized by the presence of a TATA box and nucleosomes competing efficiently with TFs for access to DNA. Both promoters and enhancers are marked as chromatin structures staged for remodeling by the H2A.Z histone variant. In addition, enhancers available for subsequent receptor binding have a decreased level of DNA methylation. (B) Induction (i.e. hormone stimulation) leads to localized incorporation of H3.3 and formation of very labile H2A.Z/H3.3 nucleosomes at both the promoter and enhancer. These nucleosomes are very dynamic and can be easily ejected thus enabling TF binding. At enhancers, the receptor binding leads to nucleosome reorganization where two stable nucleosomes flank the receptor binding sites. Additionally, the +1 nucleosome at the promoter has been reported to move 30 bp downstream leaving space for RNA Pol II and the basic transcriptional machinery to dock at the TSS. Mediator complexes hold the promoter and enhancer together and changes in DNA methylation (red dots) are observed in at least a subset of enhancers. (C) Full transcriptional response is achieved due to synchronized binding of hormone receptor and other TFs, as well as to additional receptor binding events at neighboring HREs.

Fig. 3.

Characteristics of local chromatin structures within promoters, enhancers and coding regions. The non-random positioning of a nucleosome is dictated by DNA sequence, activity of remodeling complexes (like SWI/SNF) and competition of the nucleosome with TFs for access to specific DNA sequences. The regulatory regions are characterized by high turnover of histone proteins (depicted by purple nucleosomes). The histone marks identified at the promoters and enhancers of active (red) and silent (blue) genes are indicated. The gradients reflect changes of histone marks across the coding region. Contradictory observations about the presence of H3-K9me3 and H3-K4me3 within enhancer regions have been reported. Both promoters and enhancers are marked by DHSs and H2A.Z histone variants. Most promoters are characterized by increased density of CpG dinucleotides (CpG islands) which are usually unmethylated (open circles). Enhancers also show highly localized CpG enrichment with DNA methylation status correlating with their activity. The CpG dinucleotides are under-represented within coding regions and contain high methylation levels (filled circles) in order to prevent spurious transcription.