H2A.B.3 is located at the intron—exon boundary of active genes in the testis (original) (raw)

2017

Abstract

<p>Input nucleosomes, nucleosomes immunoprecipitated with H2A.B.3 or H3K36me3 affinity purified antibodies, and poly (A)-transcripts obtained from 28–30 day old mice testes were sequenced yielding 100 base pair paired-end reads (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006633#sec011" target="_blank">Material and methods</a>). (a) The individual lines represent the normalised H2A.B.3 and total input reads aligned between -1 and +10 kb from the TSS in the testis. (b) The individual line represents the normalized input nucleosome reads (mean reads per base pair per million reads mapped (RPM)) aligned between -1 and +1 kb from the intron—exon boundary for all exons in the testis ranked according their expression level (repressed, low, medium and high). The colour-map panel shows the relationship between colour and the gene expression rank. (c) Normalized testis H2A.B.3 ChIP-Seq reads ranked according to their expression level aligned with the intron—exon boundary. (d) At each base position relative to the intron exon-boundary, a linear model was fitted to the mean H2A.B.3/input ratio versus gene log expression across all intron—exon boundaries, and the slope of the fitted model plotted for the testis. (e) Normalized testis H3K36me3 ChIP-Seq reads ranked according to their expression level aligned with the intron—exon boundary. (f) Pearson correlation of the log coverage, across 50 base pair windows, was calculated between testes H2A.B.3 ChIP-Seq reads and H3K36me3 ChIP-Seq reads for each base pair relative to the intron—exon boundary. (g) Normalized testis H3K36me3 ChIP-Seq reads ranked according to the incorporation of H2A.B.3 (very low, low, medium and high) aligned with the intron—exon boundary. 95% confidence bands are shown in grey.</p

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