Regulatory elements required for the activation and repression of the protocadherin-α gene cluster

Abstract

The mouse protocadherin (Pcdh) -α, -β, and -γ gene clusters encode more than 50 protein isoforms, the combinatorial expression of which generates vast single-cell diversity in the brain. At present, the mechanisms by which this diversity is expressed are not understood. Here we show that two transcriptional enhancer elements, HS5-1 and HS7, play a critical role in Pcdhα gene expression in mice. We show that the HS5-1 element functions as an enhancer in neurons and a silencer in nonneuronal cells. The enhancer activity correlates with the binding of zinc finger DNA binding protein CTCF to the target promoters, and the silencer activity requires the binding of the REST/NRSF repressor complex in nonneuronal cells. Thus, the HS5-1 element functions as a neuron-specific enhancer and nonneuronal cell repressor. In contrast, the HS7 element functions as a Pcdhα cluster-wide transcription enhancer element. These studies reveal a complex organization of regulatory elements required for generating single cell Pcdh diversity.chromatin | stochastic gene expression | transcription repression

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

“…Expression of the isoforms is reduced upon conditional CTCF knockout in postmitotic neurons. This suggests that long-range interactions are part of the regulatory process that controls transcription of these genes [70][71][72].…”

“…This cluster encodes neuronal-specific transmembrane proteins that are mono-allelically expressed and thought to be involved in the recognition and diversification of neurons. Expression of the cluster is under control of a downstream enhancer that influences the expression of the 12 isoforms, each of which is having its own alternative promoter [70]. Interestingly, the enhancer as well as each individual promoter has a binding site for CTCF.…”

CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice

“…Significant advances have been made in understanding the mechanisms by which individual neurons express distinct combinations of the clustered Pcdh genes (2,3,(8)(9)(10). Two long-range cis-regulatory elements in the α cluster, HS5-1 and HS7 (hypersensitive sites 5-1 and 7), function as developmental and tissuespecific transcriptional enhancers required for maximal levels of α gene expression (8).…”

“…HS5-1, which contains two CTCF-binding sites (referred as HS5-1a and HS5-1b), is required for maximal levels of the α6 to α12 and αc1 expression but displays only a moderate role in the regulation of the α1 to α5 genes and no role in αc2 expression (8,9,11). In contrast, HS7 regulates gene expression of almost all members of the α cluster, including the αc2 gene (8,9). Here, we make use of the diploid neuroblastoma cell line SK-N-SH to discover that the active Pcdh promoters and enhancers directly interact with each other through DNA looping, and that this interaction requires CTCF and cohesin.…”

“…Two long-range cis-regulatory elements in the α cluster, HS5-1 and HS7 (hypersensitive sites 5-1 and 7), function as developmental and tissuespecific transcriptional enhancers required for maximal levels of α gene expression (8). HS5-1, which contains two CTCF-binding sites (referred as HS5-1a and HS5-1b), is required for maximal levels of the α6 to α12 and αc1 expression but displays only a moderate role in the regulation of the α1 to α5 genes and no role in αc2 expression (8,9,11). In contrast, HS7 regulates gene expression of almost all members of the α cluster, including the αc2 gene (8,9).…”