ChIP-seq datasets (GSE79033) [32 (link)] for H3K4ac (Millipore, 07–539), H3K9ac (Millipore, 07–352), H3K27ac (Abcam,ab4729), H3K27me3 (Millipore, 07–449), H3K9me1 (Millipore, 07–395) and H3K9me3 (Millipore, 07–442), were generated from seeding using a previously described method [44 (link)]. Six of previously characterized ChIP-seq and MNase-seq (SRP045236)46 datasets obtained from seedlings for H3K4me3, H3K4me2, H3K36me3 and K4K12ac (GSE26734) [44 (link)] and H4K16ac and H3K23ac (GSE69426) [45 (link)] were downloaded from NCBI for further analysis. All ChIP-seq datasets were analyzed using the same pipeline as previously described [44 (link)].
To confirm the ChIP-seq results, we conducted a ChIP-qPCR assay following ChIP experiments using two histone marks (H3K27ac and H4K12ac). Five of the BDPs were randomly selected to design primers (Additional file15 : Table S11) for ChIP-qPCR analysis. One primer set was triplicated in the qPCR assay.
To profile the chromatin features of histone marks and nucleosome positioning associated with bidirectional gene pairs, we plotted the normalized ChIP-seq and MNase-seq reads across all bidirectional gene pairs and randomly selected unidirectional genes as controls.
To confirm the ChIP-seq results, we conducted a ChIP-qPCR assay following ChIP experiments using two histone marks (H3K27ac and H4K12ac). Five of the BDPs were randomly selected to design primers (Additional file
To profile the chromatin features of histone marks and nucleosome positioning associated with bidirectional gene pairs, we plotted the normalized ChIP-seq and MNase-seq reads across all bidirectional gene pairs and randomly selected unidirectional genes as controls.
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