bioRxiv preprint doi: https://doi.org/10.1101/778191; this version posted September 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Discovery of genes required for body axis and limb formation by global identification of retinoic acid regulated enhancers and silencers Marie Berenguer1, Karolin F. Meyer1, Jun Yin2, and Gregg Duester1,* 1Development, Aging, and Regeneration Program 2Bioinformatics Core Facility Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA *Correspondence should be addressed to G.D. (
[email protected]) Keywords: Body axis formation; retinoic acid response elements; Aldh1a2 knockout; Nr2f1; Nr2f2; Meis1; Meis2 1 bioRxiv preprint doi: https://doi.org/10.1101/778191; this version posted September 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Identification of direct target genes for transcription factors is hampered by the large number of genes whose expression changes when the factor is removed and numerous binding sites in the genome. Retinoic acid (RA) receptors bound to RA directly regulate transcription through RA response elements (RAREs) of which there are thousands in the mouse genome. Here, we focused on identification of direct RA target genes in the embryonic trunk during body axis and limb formation. Using ChIP-seq and RNA-seq on trunk tissue from wild-type and Aldh1a2-/- embryos lacking RA synthesis, we identified a relatively small number of genes with altered expression when RA is missing that also have nearby RA-regulated deposition of H3K27ac (gene activation mark) or H3K27me3 (gene repression mark) associated with RAREs.