TY - JOUR T1 - Discovery of genes required for body axis and limb formation by global identification of retinoic acid regulated enhancers and silencers JF - bioRxiv DO - 10.1101/778191 SP - 778191 AU - Marie Berenguer AU - Karolin F. Meyer AU - Jun Yin AU - Gregg Duester Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/09/21/778191.abstract N2 - 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. Such RAREs were identified in genes known to be required for body axis and limb formation, plus many new direct RA target genes were found. In addition to RARE enhancers, we identified numerous RARE silencers located near genes down-regulated by RA. Nr2f1, Nr2f2, Meis1, and Meis2 gene family members all have RARE enhancers, and double knockouts of each family demonstrated requirements for body axis and/or limb formation, thus validating our method for identifying RA target genes important for development. ER -