Figure 5.

Allelome validated using ChIP-seq H3K4me3. (A) Categorization of RefSeq promoter regions (±2 kb windows over RefSeq gene transcription start sites) as produced by the Allelome.PRO for H3K4me3 ChIP sequencing data of MEFs. The CAST strain bias on chromosome X is seen as well as the categorization of Xist as showing a FVB strain bias. (B) The maternal/paternal ratio is shown as red/blue bars for the imprinted genes from (A). Promoter windows are named after their respective genes and sorted as in Figure 4C. (C) Allelic expression in the Igf2r cluster is validated by differential H3K4me3 enrichment in MEFs. UCSC genome browser screenshot showing the Igf2r imprinted gene cluster and adjacent genes together with the Allelome.PRO output for RNA-seq and ChIP-seq. The tracks depict (from top to bottom): gametic and somatic differentially DNA methylated regions (gDMRs and sDMRs), Allelome.PRO allelic expression categorization, strand-specific RNA-seq, Allelome.PRO H3K4me3 allelic enrichment categorization, H3K4me3 ChIP-seq, and total SNPs in black. (D) Sliding windows detect differential H3K4me3 peaks outside annotated transcription start sites. Allelome.PRO detected maternal expression of Asb4 from RNA-seq data using the RefSeq annotation, but a CAST strain bias was detected by Allelome.PRO analysis of H3K4me3 ChIP-seq data using the RefSeq promoter annotation. However, analysing the ChIP-seq data instead with a 2 kb sliding window annotation revealed maternal H3K4me3 enrichment over the promoter of a shorter isoform of Asb4 that was annotated by UCSC and appeared from RNA-seq data to be the predominant isoform in MEFs. UCSC genome browser screenshot showing (from top to bottom) the UCSC gene annotation, Allelome.PRO allelic expression categorization from RefSeq, strand specific RNA-seq, Allelome.PRO H3K4me3 allelic enrichment categorization using RefSeq annotation, H3K4me3 ChIP-seq, and Allelome,PRO H3K4me3 allelic enrichment categorization using a 2 kb sliding window annotation.