Genome-wide Enhancer Identification And Method Comparison In Arabidopsis

Enhancers are important regulatory element which are widely distributed in genome.They can enhance the transcription of target genes without directional and distance preferences.The identification of enhancers in model organisms such as human,mouse,and Drosophila has been extensively studied.But Arabidopsis as a model plant still lacks a genome-wide functional identification for enhancers.Most existing enhancer identification methods are failed to measure enhancer activity.And the differences and relationships between these methods are also lack of systematic research.Therefore,we used STARR-seq to measure the genome-wide enhancers activities in Arabidopsis.And we developed an improved STARR-seq to detect more complete enhancer transcriptional information.Then we analyzed the genomic distribution,epigenetic signals,gene expression,transcription factor enrichment and chromatin interactions for STARR-seq identified enhancers.Simultaneously,we made comparative analysis between STARR-seq identified enhancers and the results of chromatin accessibility measurement DNase-seq and histone modification H3K4me1.We found that the STARR-seq enhancers are enriched in the start and terminal regions of genes,such as TSS,5'UTR,CDS and 3'UTR.And the presence,density and distribution of enhancers are positively correlated with the expression level of proximal genes.And we clustered enhancers into 4 categories by epigenetic signals,including active enhancer,primed enhancer,poised enhancer and repeat region enhancer.The epigenetic signals,genomic distribution and proximal gene expression between 4 types enhancers show significant differences.We found that a totally different genomic distribution by compared STARR-seq enhancers with DHS and H3K4me1 lead to very low overlap percentages.Proximal gene expression between STARR-seq,DHS and H3K4me1 enhancers shows STARR-seq enhancers own a higher transcriptional regulatory activity than the other two methods.According to the comparative analysis for genome-wide enhancer identification in Arabidopsis,we found enormous distinction between different methods.Therefore,we proposed that the optimal method for identifying enhancer is integrated enhancer activity,chromatin accessibility and histone modification together to evaluate every enhancer.In summary,we have provided a genome-wide enhancers map identified by different methods in Arabidopsis.This map established a basis knowledge for further study of enhancer's transcriptional regulation mechanism and applications.And the comparison results between different enhancer identification methods can also provide a methodological reference for enhancer research in other species.