Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Abstract

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.

Figure 1. Conservation of mouse regulatory DNA in humans

(A) The accessible landscape of the mouse was derived from 45 tissues and cell types (B) Proportions of the mouse regulatory DNA landscape with sequence homology and functional conservation with human. (C) Example of the conservation of the cis-regulatory elements surrounding within the Vgf/VGF locus in mouse and human intestine. (D) Gene proximal DHSs are more likely to be conserved than distal DHSs. Dashed red line indicates the average conservation of DHSs. (E) The rate of intergenic DHS conservation vs. distance to nearest TSS indicates a rapidly evolving cis-regulatory domain.

Figure 2. Cell and tissue lineage encoding within shared regulatory elements

(A) k-means clustering of DHSs by accessibility at each of the 475,701 mouse DHSs shared with human. Columns correspond clusters of mouse DHSs that are also accessible in human and rows correspond to the 45 mouse cell/tissue types. Colors (axes and boxes) distinguish tissue groupings. Left, tissue-selective clusters. Right, clusters containing DHSs active in multiple tissues. (B) Proportion of shared DHSs that are tissue-selective or active in multiple tissues. (C) Enrichment of TF recognition sequences within tissue-selective DHSs computed using the cumulative hypergeometric distribution.

Figure 3. Conservation and repurposing of regulatory DNA accessibility

(A) Pairwise comparison (median Jaccard distance) of shared DHS landscape usage between all mouse (rows) and human (columns) tissues largely mirrors their conserved morphological and embryological origins. (B) The conservation of mouse cis-regulatory DNA accessibility in human for individual tissue types. Orange ticks indicate the expected overlap of randomly selected DHSs. (C) The activity patterns of individual shared DHSs during mouse and human evolution may have been conserved (activity in at least one similar tissue) or repurposed to another tissue. (D) Overall conservation of tissue-level accessibility patterns of mouse DHSs shared with human.

Figure 4. Evolutionary dynamics of transcription factor recognition sequences

(A) Conservation of TF recognition sequences within shared DHSs. (B) Positional and operational conservation of TF recognition sequences are enriched within DHSs that have conserved tissue activity patterns. (C) Recognition sequences for cell-selective transcription factors are preferentially lost at mouse DHSs that are repurposed in human, while maintained in or gained in human. Representative examples of individual TF regulators in retina, intestine and erythroid tissues. (D) Same as C for recognition sequences of all cell-selective TF regulators (identified in fig. 2C) within mouse DHSs repurposed in human.

Figure 5. Conservation of cis-regulatory content dominates over the conservation of individual regulatory elements

(A) Density of individual TF recognition sequences in both human (x-axis) and mouse (y-axis) regulatory T cells. Dotted black lines demarcate a 2-fold difference in density between mouse and human. (B) Same as A for human and mouse brain. (C–D) Proportion of mouse DHSs that are conserved in a matched human tissue. Top, mouse regulatory T cells DHSs that are conserved in human regulatory T cells. Bottom, mouse embryonic brain DHSs that are conserved in human fetal brain. (E) Radar plots showing the median similarity (Euclidean distance between the distributions of TF recognition sequence densities) of the cis-regulatory content between mouse and human tissues.