Poster abstracts

Poster number 63 submitted by Jhumku Kohtz

The Evf2 enhancer lncRNA regulates hundreds of enhancer-chromosomal interactions across the extent of chr6 (~150Mb) in mouse developing brain

Ivelisse Cajigas (Department of Pediatrics, Northwestern University), Abhijit Chakraborty (Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology), Monique Bastidas (Department of Pediatrics, Northwestern University), Kelsey R. Swyter, Sara J. Kohtz (Department of Pediatrics, Northwestern University), Ferhat Ay (Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology), Jhumku D. Kohtz (Department of Pediatrics, Northwestern University)

Abstract:
Enhancers are defined as DNA sequences capable of regulating genes at a distance, independent of orientation. While validated enhancer regulatory landscapes in vertebrates typically span ~1 megabase (Mb) and facilitate tissue-specific and/or developmentally programmed gene expression, chromosome conformation capture studies (HiCseq and 4Cseq) predict that enhancer interactions can span multi-megabase distances (Dekker, 2016). A major question in genome biology is how DNA regulatory enhancers are selectively targeted to specific genes across megabase (Mb) distances. Here, we show that Evf2, a Dlx5/6 ultraconserved enhancer (Dlx5/6UCE) lncRNA (Feng et al., 2006), regulates genes that are asymmetrically-positioned across 27Mb. The Evf2 RNA cloud localizes to both activated (~1.6Mb distant) and repressed (~27Mb distant) target genes in mouse developing forebrain, controlling distances between Dlx5/6UCE and transcriptional targets. Through both short-range (Dlx6 anti-sense) and long-range (Akr1b8) repression, the Evf2-5’UCE region regulates multiple interneuron subtype genes, identifying a novel signaling pathway in interneuron specification. Surprisingly, Evf2 regulates the number, density, and position of hundreds of Dlx5/6UCE-chr6 interaction sites across chr6 (~150Mb), without affecting transcription. Active histone lysine modifications distinguish Evf2 positively- and negatively-regulated Dlx5/6UCE-chr6 sites, revealing that many sites are marked before Evf2 regulates enhancer chromosomal interactions. These studies reveal that an autosomal cloud-forming enhancer lncRNA regulates genes through antisense and chromosome topological mechanisms, controlling the 3-D architecture of an entire chromosome.

References:
Dekker, J. (2016). Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol 17, 741-742.

Feng, J., Bi, C., Clark, B.S., Mady, R., Shah, P., and Kohtz, J.D. (2006). The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20, 1470-1484.

Keywords: Long non-coding RNA, chromosome topology, enhancers