CNEs identify previously characterized enhancer sequences and when located in introns are associated with alternative transcriptional start sites. Five wCNEs are contained within four elements that regulate ser-2, the C. elegans ortholog of human serotonin receptor 1A. The products of ser-2 were identified as components of the AIY interneuron gene battery in C. elegans . ser-2 has at least three alternative transcription start sites that produce a number of different gene products, considered to be expressed in different but overlapping regions . Remarkably, each of the alternative transcription start sites is marked by a wCNE in the proximal upstream region, with additional wCNEs lying further away, highlighting the underlying cis-regulatory elements. The upstream sequences of each of the alternative transcription start sites were defined by deletion analysis . One of the wCNEs lies within an approximately 280 bp element driving expression in the AIY and SIA neuronal cellular subtypes. A second wCNE lies within an approximately 520 bp element driving expression in the RME neurons and also, consistently, in other unidentified neurons. A third wCNE lies within an approximately 1,150 bp element driving expression in the head muscles. Two more wCNEs are contained within a region driving expression in PVD and lateral OLL neurons. Only the experimentally tested constructs that overlap wCNEs are shown in this diagram.
Vavouri et al. Genome Biology 2007 8:R15 doi:10.1186/gb-2007-8-2-r15