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Genes & Dev. 20 (11): 1470-1484

Copyright © 2006 by Cold Spring Harbor Laboratory Press.

The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator

Jianchi Feng, Chunming Bi, Brian S. Clark, Rina Mady, Palak Shah, and Jhumku D. Kohtz1

Program in Neurobiology and Department of Pediatrics, Children’s Memorial Hospital and Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60614, USA

Abstract: 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.

Key Words: Noncoding RNA • homeodomain transcription factors • forebrain development • Dlx gene regulation • ultraconserved region

Received for publication January 31, 2006. Accepted for publication March 22, 2006.

1 Corresponding author.

E-MAIL j-kohtz{at}; FAX (773) 755-6344.

Article published online ahead of print. Article and publication date are online at

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