Regulation of protocadherin gene expression by multiple neuron-restrictive silencer elements scattered in the gene cluster

Abstract

The clustered protocadherins are a subfamily of neuronal cell adhesion molecules that play an important role in development of the nervous systems in vertebrates. The clustered protocadherin genes exhibit complex expression patterns in the central nervous system. In this study, we have investigated the molecular mechanism underlying neuronal expression of protocadherin genes using the protocadherin gene cluster in fugu as a model. By in silico prediction, we identified multiple neuron-restrictive silencer elements (NRSEs) scattered in the fugu protocadherin cluster and demonstrated that these elements bind specifically to NRSF/REST in vitro and in vivo. By using a transgenic Xenopus approach, we show that these NRSEs regulate neuronal specificity of protocadherin promoters by suppressing their activity in non-neuronal tissues. We provide evidence that protocadherin genes that do not contain an NRSE in their 5′ intergenic region are regulated by NRSEs in the regulatory region of their neighboring genes. We also show that protocadherin clusters in other vertebrates such as elephant shark, zebrafish, coelacanth, lizard, mouse and human, contain different sets of multiple NRSEs. Taken together, our data suggest that the neuronal specificity of protocadherin cluster genes in vertebrates is regulated by the NRSE-NRSF/REST system.

REST and CoREST are transcriptional and epigenetic regulators of seminal neural fate decisions

“…Our observations are consistent with a recent functional analysis showing that REST regulates protocadherin genes, including genes that are not associated with an RE1 motif. 101 Our distinct REST and CoREST target gene profiles in neuronal subtypes also included factors not previously associated with the establishment of neuronal subtype identity, such as particular epigenetic factors (e.g., Mbd6, Smcx, Jarid1d, Lsd1 and Smarce1), but not those with roles in neural lineage specification (i.e., Mash1 and Math1), implying preferential REST regulation of neuronal terminal differentiation as compared with earlier stages of lineage specification.…”

Regulation of the Protocadherin Celsr3 Gene and Its Role in Globus Pallidus Development and Connectivity

“…In particular, the clustered Pcdh genes are organized into variable and constant regions and generate enormous neural diversity by stochastic promoter choice combined with alternative pre-mRNA splicing (51)(52)(53). Recently, the neural expression of the clustered Pcdh genes was found to be controlled by both CTCF and NRSF (30,38,54,55). In particular, the CTCF/ cohesin complex plays a pivotal role in the promoter choice of the clustered Pcdh genes by mediating specific DNA looping interactions between enhancers and selective variable promoters (30).…”

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

“…NRSF is a DNA binding protein that recognizes a 21-bp consensus motif NRSE and recruits corepressor complexes that inhibit transcription of neuron-specific genes in nonneuronal tissues (22-24). Tan et al identified numerous NRSE motifs in the fugu Pcdh cluster, and demonstrated that these motifs could repress expression of reporter genes (25). They also identified sequences matching NRSE motifs in the mammalian Pcdh cluster variable exons and the HS5-1 enhancer.…”