Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis

• Published in: Cell reports (Cambridge) Vol. 27; no. 4; pp. 1027 - 1038.e3
• Main Authors: van der Burg, Karin R.L., Lewis, James J., Martin, Arnaud, Nijhout, H. Frederik, Danko, Charles G., Reed, Robert D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 23.04.2019
• Subjects: ATAC-seq; chromatin accessibility; ecdysone receptor; metamorphosis; spineless; spineless; ecdysone receptor; metamorphosis; ATAC-seq; chromatin accessibility
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.03.092

Development requires highly coordinated changes in chromatin accessibility in order for proper gene regulation to occur. Here, we identify factors associated with major, discrete changes in chromatin accessibility during butterfly wing metamorphosis. By combining mRNA sequencing (mRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and machine learning analysis of motifs, we show that distinct sets of transcription factors are predictive of chromatin opening at different developmental stages. Our data suggest an important role for nuclear hormone receptors early in metamorphosis, whereas PAS-domain transcription factors are strongly associated with later chromatin opening. Chromatin immunoprecipitation sequencing (ChIP-seq) validation of select candidate factors showed spineless binding to be a major predictor of opening chromatin. Surprisingly, binding of ecdysone receptor (EcR), a candidate accessibility factor in Drosophila, was not predictive of opening but instead marked persistent sites. This work characterizes the chromatin dynamics of insect wing metamorphosis, identifies candidate chromatin remodeling factors in insects, and presents a genome assembly of the model butterfly Junonia coenia. [Display omitted] •Chromatin accessibility during butterfly wing development is highly dynamic•Different sets of transcription factors associate with accessibility at different stages•ChIP-seq indicates spineless binding predicts changes in accessibility•Assembly and annotation of the Junonia coenia genome are provided Using ATAC-seq, van der Burg et al. show that chromatin organization during butterfly wing development is highly dynamic. Motif enrichment analysis followed by ChIP-seq shows that DNA binding of transcription factor spineless, but not EcR, is strongly associated with opening chromatin.