An Epigenetic Signature for Putative OR Enhancers

(A) Sequencing tracks for DHS-seq and ChIP-seq. Each row displays the number of reads for each track. Triangle indicates H enhancer.

(B) DHS-seq and ChIP-seq tracks over potential OR enhancer Sfaktiria (coordinates are mm9).

(C) Aggregate plots of ChIP-seq and DHS-seq reads over all potential OR enhancers (left) and all potential MOE enhancers (right). y axis is RPKM, and error is bootstrapped 95% confidence intervals. x axis is centered at DHS peaks.

(D) Schematic depicting the E1b-tol2 expression construct.

(E) Zebrafish embryo injected with Sfaktiria-GFP at 24 hr postfertilization (hpf). Olfactory epithelium is indicated with dotted lines. Bottom, OSN cell bodies and axons expressing GFP.

(F) Results of zebrafish enhancer screen. Percent of injected zebrafish embryos with GFP-positive olfactory neurons at 48 hpf for each OR enhancer candidate.

See also Figure S1 and Tables S1 and S2.

An Epigenetic Signature for Putative OR Enhancers, Related to Figure 1

(A) DHS-seq and ChIP-seq tracks at protocadherin α enhancer HS4.

(B) Analysis pipeline for generating OR enhancer candidates (column 1) and MOE enhancer candidates (column 2). Analysis for OR enhancers is restricted to genomic coordinates of the 52 OR clusters. Intergenic peaks were selected to be at a distance of 5kB or more from a Refseq gene or OR promoter. First three rows list the number of intergenic peaks from DHS-seq and H3K27ac and H3K24me1 ChIP-seq data. Fourth row lists the number of DHS peaks that intersected either H3K27ac or H3K4me1 peaks. Fifth row subtracts DHS peaks that intersected either H3K27ac or H3K4me1 SICER peaks from cerebellum ChIP-seq data set. These are the sequences referred to as “OR enhancers” or “MOE enhancers,” respectively, in the text. Sixth row is number of OR enhancers or MOE enhancers that intersect an H3K79me3 peak.

(C) Representative zebrafish embryos from oocyte injections of 11 candidate OR enhancers and H enhancer. GFP expression in the olfactory epithelium is indicated. See Table S2 for enhancer coordinates.

(D) Representative images of zebrafish OSNs expressing GFP at 48hpf from 6 OR enhancer transgene injections.

(E and F) Heatmaps of H3K79me3 and H3K4me1, respectively, RPKM over OR enhancer candidates. y axis is OR enhancer candidates ordered by principal component 1 of each chromatin modification matrix. x axis is centered at DHS peak. Red ticks indicate H, P, and the 11 sequences that drove GFP expression in zebrafish OSNs.