Fig. 1: Sequence evolution in putative human immune-cell enhancers since the human-macaque split. | Nature Communications

Fig. 1: Sequence evolution in putative human immune-cell enhancers since the human-macaque split.

From: Transposon invasion of primate genomes shaped human inflammatory enhancers and susceptibility to inflammatory diseases

Fig. 1: Sequence evolution in putative human immune-cell enhancers since the human-macaque split.The alt text for this image may have been generated using AI.

a Stratification of human enhancers by evolutionary age based on their LiftOver conversion to the macaque and chimpanzee genomes. Number of enhancers in each group is indicated. b PhastCons conservation scores across 17 primate genomes. c Percentage of single-nucleotide substitutions per enhancer in human relative to macaque based on BLASTn alignment. In panels (b, c), comparisons were performed using pairwise two-sided t test with P-values adjusted for multiple testing with the Benjamini–Hochberg method. **** P ~ 0. d Proportion of enhancers overlapping with pTEs, either present in the same genomic location in macaque (shared) or corresponding to genomic gaps (gained) in macaque (middle panel) or chimpanzee (right panel) compared to human. Pairwise two-sided χ² tests were applied with Benjamini–Hochberg correction ***P < 0.001. Exact values: P = 1.12e–37 (rapid vs inter), P = 8.13e–28 (rapid vs static), and P ~ 0 (inter vs static). e Fraction of enhancer length covered by pTE sequences, considering either all pTE (left) or only those absent from macaque (right). b, c, e boxplots show the median (centre line), 25th-75th percentiles (box), and minima and maxima within 1.5× IQR (whiskers). f TE subfamilies most significantly enriched in enhancers, but not enriched in 1,000 times permutations matched for enhancer group number, length distribution, and LiftOver-based classification. Scale shows hypergeometric enrichment with Benjamini–Hochberg-adjusted P-values. Represented are pTEs with P < 10e–10, fold change ≥ 2, n ≥ 10. Middle and bottom: proportion of the enhancer-linked pTE instances gained since the split from chimpanzee (middle panel) or macaque (lower panel). g Proportion of enhancers overlapping a pTE (≥10 bp), an ancient TE only (no pTE), or no TE. “Inter” represents intermediate enhancers throughout. The number of enhancers per group is given in panel a and applied throughout. Primate icons are created in BioRender. Zueva, E. (2025) https://BioRender.com/8d7b1bb. Source data are provided as a Source Data file.

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