PT  - JOURNAL ARTICLE
AU  - Xiusheng Zhu
AU  - Lei Huang
AU  - Qing Li
AU  - Yubo Zhang
TI  - Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing
AID  - 10.1101/604686
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 604686
4099  - http://biorxiv.org/content/early/2019/04/10/604686.short
4100  - http://biorxiv.org/content/early/2019/04/10/604686.full
AB  - 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.ATAC-seq(Assay for Transposase-Accessible Chromatin using sequencing),(bp)base pairs,ChIP(chromatin immunoprecipitation),(CEnh)conventional enhancer,(DEnh)distal enhancer,DHS(DNase Hypersensitive Site),DNase-seq(DNase I hypersensitive sites sequencing),ENCODE(Encyclopedia of DNA elements),FAIRE-seq(formaldehyde-assisted isolation of regulatory elements sequencing),FI(fluorescence intensity),GEO(Gene Expression Omnibus),HTS(high-throughput sequencing),MAE-Seq(massive active enhancer sequencing),STARR-seq(self-transcribing active regulatory region sequencing).