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Fig. 4 | BMC Biology

Fig. 4

From: Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination

Fig. 4

Association of 5hmC and NCO recombination rates. a Association in epigenetically defined regions. NCO rate, chromatin state and DNA marks are shown for 15 epigenetic sub-regions comprising active transcription start sites (TssA), TssA flanking regions (TssAFlnk), transcribed regions (Tx), weak transcribed regions (TxWk), Tx flanking regions (TxFlnk), gene-associated enhancer (EnhG), enhancer (Enh), zinc finger nuclear factor regions (ZNF), repeats (Rpts), heterochromatin (Het), bivalent transcriptional start site (TssBiv), bivalent flanking regions (BivFlnk), bivalent enhancer (EnhBiv), polycomb repressed region (ReprPC), weak polycomb repressed region (ReprPCWk) and quiescent regions (Quies) [1]. Histone marks are shown in Additional file 1: Fig. S4. The calculations were carried out separately for each of 111 reference genomes using the entire data set of 1.9 million archaic SNPs. The boxplots indicate for each region the average NCO rate (1 − D’2a,hap), as well as the average track overlap of these SNPs with 5hmC marks, DNase I-defined, and 5mC-defined open chromatin. The NCO rate was calculated using the data from the LWK cohort, while 5mC, DNase I, and 5mC tracks were defined for the H1 stem cell line [1, 21]. The r- and p-values refer to a Spearman rank correlation carried out between these relative frequencies of the marks and the respective NCO rate data. b Correlation of NCO recombination rate with the 5hmC frequency. The plot shows the average NCO rate and corresponding track overlap of the SNP with 5hmC marks for each of the 15 epigenetically defined subregions. The line was derived by Pearson correlation, the p and r2 values are indicated

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