Identifications of a novel group of intra-genic interactive putative enhancers reveals a distinctive enhancer architectures in plants

ABSTRACT: ABSTRACT: Enhancers are important regulators of gene expression in eukaryotes; however, only a few enhancers have been identified in plants, and the genome-wide identifications are lacking. To investigate enhancers in Arabidopsis thaliana, we analyzed the chromatin landscape, RNA Pol II occupancy, and the polyadenylated and non-polyadenylated Arabidopsis transcriptomes, using exosome-deficient lines to capture stable and unstable transcripts. Here we identified the set of unique >1900 regions, termed Putative Enhancers (PEs), carrying canonical chromatin signatures of metazoan transcriptional enhancers. Almost of PEs are intra-genic and transcriptionally active. Unexpectedly, most of the PE carrying these signatures are associated with the 3′ ends of protein-coding genes, enriched in transcription factor binding, with binding motifs resembling polyadenylation signals, thus linking links two hubs of very different, functionally and mechanistically distinct processes – cleavage/polyadenylation and transcription termination of protein-coding genes with transcriptional activation/regulation of different genes. And may present a novel DNA elements with regulatory potential. Additionally, according to high resolution Arabidopsis Hi-C data 24% of identified PEs interact with other protein-coding genes intrachromosomally, through binding by the same set of transcription factors, supporting the notion of co-regulation of expression between PEs and their targets. We also confirmed that PEs are highly conserved in the recently sequenced 1035 different Arabidopsis accessions.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE99406 | GEO | 2019/08/20

REPOSITORIES: GEO