Table 1. Studies using ATAC-seq in model organisms for development.

Species	Biological context	Reference
Drosophila	Domain-restricted analysis for anterior–posterior patterning of blastoderm to identify accessible regions	[30]
	Tissue-specific accessibility during three embryonic stages with germ-layer enhancer validation	[44]
Zebrafish	Chromatin accessibility atlas of embryonic and adult tissues	[43]
	Identification of key elements during zygotic genome activation	[45]
	Neural crest and melanoma development	[53,56]
	Heart regeneration	[64,67]
	Liver development and response to injury	[68]
	Fin regeneration	[69]
	Endothelial enhancers	[29]
Xenopus	Wnt signalling in dorsal–ventral patterning in comparison with mesoderm and neural crest development	[47]
	Mesendoderm specification	[48]
Chicken	Neural crest development, GRN reconstruction and identification of specific enhancers	[27,28]
	Anterior–posterior axis elongation and paraxial mesoderm development, differential TF occupancy and in vivo enhancer validation	[16]
Mouse	Chromatin accessibility atlas of adult tissues	[42]
	Sex-specific accessibility of in vivo and IVF inner cell mass	[50]
	Chromatin accessibility preconfigures region-specific neural fates along anterior–posterior axis	[52]
	Sinoatrial node development	[65]
	Heart development of key developmental stages	[66]
Mouse/Pig	Limb development and digit adaptation	[63]
Bovine	Chromatin accessibility in oocytes and early embryos, and comparison of in vivo and in vitro blastocysts	[49]
Human	Chromatin accessibility of inner cell mass and trophectoderm of blastocysts	[51]
	Human ESC differentiation into neural crest identifies disease enhancer	[5]