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Link to original content: http://pubmed.ncbi.nlm.nih.gov/33171098/
Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis - PubMed Skip to main page content
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. 2020 Dec 7;55(5):648-664.e9.
doi: 10.1016/j.devcel.2020.10.009. Epub 2020 Nov 9.

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

James P Reddington  1 , David A Garfield  1 , Olga M Sigalova  1 , Aslihan Karabacak Calviello  2 , Raquel Marco-Ferreres  1 , Charles Girardot  1 , Rebecca R Viales  1 , Jacob F Degner  1 , Uwe Ohler  2 , Eileen E M Furlong  3
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Free article

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

James P Reddington et al. Dev Cell. .
Free article

Abstract

Enhancers are essential drivers of cell states, yet the relationship between accessibility, regulatory activity, and in vivo lineage commitment during embryogenesis remains poorly understood. Here, we measure chromatin accessibility in isolated neural and mesodermal lineages across a time course of Drosophila embryogenesis. Promoters, including tissue-specific genes, are often constitutively open, even in contexts where the gene is not expressed. In contrast, the majority of distal elements have dynamic, tissue-specific accessibility. Enhancer priming appears rarely within a lineage, perhaps reflecting the speed of Drosophila embryogenesis. However, many tissue-specific enhancers are accessible in other lineages early on and become progressively closed as embryogenesis proceeds. We demonstrate the usefulness of this tissue- and time-resolved resource to definitively identify single-cell clusters, to uncover predictive motifs, and to identify many regulators of tissue development. For one such predicted neural regulator, l(3)neo38, we generate a loss-of-function mutant and uncover an essential role for neuromuscular junction and brain development.

Keywords: DNase-seq; chromatin accessibility; developmental enhancers; embryogenesis; priming; transcription-factor occupancy.

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Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

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