PT - JOURNAL ARTICLE AU - Daria Gavriouchkina AU - Ruth M Williams AU - Martyna Lukoseviciute AU - Tatiana Hochgreb-Hägele AU - Upeka Senanayake AU - Vanessa Chong-Morrison AU - Supat Thongjuea AU - Emmanouela Repapi AU - Adam Mead AU - Tatjana Sauka-Spengler TI - From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape <em>in vivo</em> AID - 10.1101/213611 DP - 2017 Jan 01 TA - bioRxiv PG - 213611 4099 - http://biorxiv.org/content/early/2017/11/22/213611.short 4100 - http://biorxiv.org/content/early/2017/11/22/213611.full AB - The neural crest (NC) is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant versus wild type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffing nucleosomes. Strikingly, foxd3 then switches from an activator to its canonical role as a transcriptional repressor. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from permissive to repressive nucleosome/chromatin organisation to maintain stemness and define cell fates.