Extended Data Fig. 2: Comparative analysis of zebrafish cis-regulatory elements.
From: A map of cis-regulatory elements and 3D genome structures in zebrafish
a, Comparison of the predicted regulatory elements identified with previous data. Enhancers were based on H3K27ac signals in the same four tissues (brain, heart, intestine, testis) from Perez-Rico et al. 2017. The data we generated are from Tübingen zebrafish strain and the published results were from the AB strain. b, Number of predicted cis-regulatory elements in each tissue. E-brain stands for 1 dpf embryonic neuron cells. E-trunk stands for 1 dpf zebrafish whole trunk region. c, An example showing genes with active promoters have higher expression level. Blue hollow bar indicates the known mrpl39 promoter. Orange hollow bar indicates the potential novel promoter. The mrpl39 promoter has H3K4me3 peaks in both muscle and brain, but only has strong H3K27ac signals in muscle and its expression is higher (4.43-fold). d, Gene Ontology results for the muscle-specific enhancers and skin-specific enhancers. We used the GREAT tool for this analysis (the numbers of tissue-specific enhancers used in this figure are muscle = 813, skin = 512).
