Xiusheng Zhu, Lei Huang, Qing Li, Yubo Zhang
Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome. It is the paradox comparing with the motif analysis, which usually contains only a few or tens nucleotides, achieved by bioinformatics analysis. To address this issue, we develop an experimental method, termed as massive active enhancer sequencing (MAE-Seq), to designate active enhancer sequences from arbitrary sources of 25bp random DNA libraries. These sequences are constructed in a mini-promoter vector with fluorescent reporter. After transfection, positive cells are sorted out and for sequencing. With the results, we successfully identify hundreds known accurate active enhancer sequences as expected. Besides that, large amounts of unmarked regulatory elements (UREs) without epigenetic features are also been spotted. In conclusion, MAE-Seq would be useful to refine enhancer sequences and precisely annotate the genome in eukaryotes.
Xiusheng Zhu, Lei Huang, Qing Li, Yubo Zhang. Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing. 2019-04-10. https://doi.org/10.1101/604686
A random 25-bp human genomic fragment library was cloned into a mini-promoter mCherry reporter plasmid and transfected into HEK293T cells. Fluorescence-selected cells were amplified and sequenced to identify active core enhancer loci; the released table is the 9,771-site positive enhancer catalog.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 3 files (ZIP)GSE129453_family.soft.gzGSM3713164_N25-annotation.txt.gzsource_notes.txt