One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.
The authors declare no competing or financial interests.
J.C.P. and D.J.M. designed and performed the experiments. J.C.P., D.J.M. and S.T.C. analyzed the data and wrote the manuscript. J.D.L. supported the initiation of this study.
The project was supported by a National Institutes of Health/National Institute of Neurological Disorders and Stroke grant [R01 NS64264] to S.T.C., and D.L.M. was supported by University of North Carolina institutional start-up funds. Deposited in PMC for release after 12 months.
FAIRE-seq data have been deposited at Gene Expression Omnibus (GEO) under accession number GSE83463.
Supplementary information available online at http://dev.biologists.org/lookup/doi/10.1242/dev.136895.supplemental
- Received March 2, 2016.
- Accepted August 30, 2016.