The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator.
The identification of ultraconserved noncoding sequences in vertebrates has been associated with developmental regulators and DNA-binding proteins. One of the first of these was identified in the intergenic region between the Dlx-5 and Dlx-6 genes, members of the Dlx/dll homeodomain-containing protein family. In previous experiments, we showed that Sonic hedgehog treatment of forebrain neural explants results in the activation of Dlx-2 and the novel noncoding RNA (ncRNA), Evf-1. In this report, we show that the Dlx-5/6 ultraconserved region is transcribed to generate an alternatively spliced form of Evf-1, the ncRNA Evf-2. Evf-2 specifically cooperates with Dlx-2 to increase the transcriptional activity of the Dlx-5/6 enhancer in a target and homeodomain-specific manner. A stable complex containing the Evf-2 ncRNA and the Dlx-2 protein forms in vivo, suggesting that the Evf-2 ncRNA activates transcriptional activity by directly influencing Dlx-2 activity. These experiments identify a novel mechanism whereby transcription is controlled by the cooperative actions of an ncRNA and a homeodomain protein. The possibility that a subset of vertebrate ultraconserved regions may function at both the DNA and RNA level to control key developmental regulators may explain why ultraconserved sequences exhibit 90% or more conservation even after 450 million years of vertebrate evolution.
Feng
Jianchi
J
Program in Neurobiology and Department of Pediatrics, Children's Memorial Hospital and Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60614, USA.
Bi
Chunming
C
Clark
Brian S
BS
Mady
Rina
R
Shah
Palak
P
Kohtz
Jhumku D
JD
D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D017931:DNA Primers; D018398:Homeodomain Proteins / Q000235:genetics*; D047468:Immunoprecipitation; D017403:In Situ Hybridization; D051379:Mice; D012313:RNA / Q000235:genetics*; D051381:Rats; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
D017931:DNA Primers; C088334:Distal-less homeobox proteins; D018398:Homeodomain Proteins; D014157:Transcription Factors; D012313:RNA