DNA accessibility and histone modifications hold information about the activity of underlying genes in any given tissue and at any given time in an organism’s development. During the second phase of ENCODE, such data were generated for various mouse tissues from a single late embryonic time point and two adult stages. Now, for ENCODE3, the authors have profiled the chromatin landscapes in up to 12 different tissues over seven time points of embryonic development plus birth in the mouse, a total of 72 distinct tissue stages1. Assays of eight histone marks were used to build a 15-chromatin state model, classified into four broad categories — promoter, enhancer, transcriptional and heterochromatin states, with 33% of the genome showing one of these signatures. Looking at the spatial and temporal dynamics of chromatin states, about 1.2% of the genome differed in chromatin state between tissues at the same developmental stage, and about 1.3% differed across developmental stages in a given tissue. Based on DNA accessibility data, 523,159 regions were classified as open chromatin and candidate cis-regulatory elements (cCREs) in at least one tissue stage, and 139,894 of these were dynamic (their accessibility changed through development). Transgenic reporter gene assays revealed that regions with high levels of acetylation at lysine 27 of histone H3 (H3K27ac) were more likely to drive reporter gene expression in a specific tissue than regions with weak H3K27ac. While not all developmental tissues were surveyed and tissue heterogeneity in cell type composition is noted as a limitation, this work presents a valuable resource for annotating the mammalian genome through embryonic development.
- RESEARCH HIGHLIGHT
Accessibility of DNA during mouse embryonic development
doi: https://doi.org/10.1038/d42859-020-00051-2
References
Gorkin, D. U. et al. An atlas of dynamic chromatin landscapes in the developing mouse fetus. Nature https://doi.org/10.1038/s41586-020-2093-3 (2020)