Extended Data Fig. 1: Conservation of gene expression and 3D chromatin structure in contrast to cis-regulatory element sequences. | Nature Genetics

Extended Data Fig. 1: Conservation of gene expression and 3D chromatin structure in contrast to cis-regulatory element sequences.

From: Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Extended Data Fig. 1

(a) Gene Ontology (GO) annotations of differentially expressed genes (Heart vs. FL) in mouse and chicken. Dark pink = upregulated, both species. Dark green = downregulated, both species. Light pink = upregulated, mouse-only. Light green = upregulated, chicken-only. Grey = no differential expression. (b) Estimation of sequence alignability (LiftOver minMatch=0.1) of ATAC-seq peaks from mouse embryonic heart at different annotated genomic locations. (c) Distribution of binarized directionality indices across centred and size-ordered genomic regulatory blocks in mouse and chicken (d) Synteny breakpoints between mouse and human, chicken, zebrafish and Ciona intestinalis genomes relative to the normalized TAD position (e) Number of predicted promoters and enhancers from stage-specific and shared/union sets in both species. (f) Estimation of sequence alignability from stage-specific predicted promoters and enhancers from heart and forelimb (FL) in both species.

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