Genome-wide identification of hypoxia-induced enhancer regions
- Published
- Accepted
- Subject Areas
- Biotechnology, Genomics
- Keywords
- Transcriptional Enhancer, Hypoxia, Next-Generation Sequencing, Massively Parallel Reporter Assay, Method Development
- Copyright
- © 2015 Kamps-Hughes et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. Genome-wide identification of hypoxia-induced enhancer regions. PeerJ PrePrints 3:e1393v1 https://doi.org/10.7287/peerj.preprints.1393v1
Abstract
Here we present a genome-wide method for de novo identification of enhancer regions and apply it to find enhancers that have increased activity after hypoxia. The method links fragmented genomic DNA to the transcription of randomer molecule identifiers and measures the functional enhancer activity of the library by massively parallel sequencing. We transfected a Drosophila melanogaster library into S2 cells in normoxia and hypoxia, and assayed 4,599,881 genomic DNA fragments in parallel. The locations of the enhancer regions strongly correlate with genes up-regulated after hypoxia and previously described enhancers. Novel enhancer regions were identified and integrated with RNAseq data and transcription factor motifs to describe the hypoxic response on a genome-wide basis as a complex regulatory network involving multiple stress-response pathways. This work provides a novel method for high-throughput assay of enhancer activity and the genome-scale identification of hypoxia-activated enhancers in Drosophila.
Author Comment
This is a submission to PeerJ for review.