Evf2 ultraconserved enhancer long non-coding RNA (UCE lncRNA)-dependent UCE interactions (4Cseq), and cohesin binding, histone methylation and acetylation (ChIPseq) in mouse E13.5 ganglionic eminences

In this study we used mice lacking Evf2 (Evf2TS/TS) and mice expressing a truncated form of Evf2 (Evf1TS/TS) to determine UCE lncRNA epigenetic and chromosome toplogical control. We used 4Cseq to investigate how Evf2 regulates UCE interactions along chromosome 6 (where Evf2 is expressed). We used ChIpseq to compare histone methylation profiles from Evf2TS/TS and Evf1TS/TS. In addition, we used ChIPseq to determine Evf2-depedent regulation of cohesin subunit binding (SMC1 and SMC3) and histone H3K27acetylation. Together, these data support that Evf2 UCE lncRNA controls chromosome topology over multi-megabse distances, through cohesin binding and effects on histone methylation and acetylation. Also included is the ChIPseq profile of Dlx binding sites in SW (outbred strain of mice) from E13.5 GE. We use ChiPseq and 4Cseq and bioinformatic analytics to determine significant differences between mice expressing the Evf2 UCE lncRNA and mice lacking the Evf2 UCE lncRNA, and mice expressing a truncated form of Evf2.