Progress in the identification and functional validation of Arabidopsis superenhancers

Recently, Meng Fanli, a researcher in the Farmland Pest Control Discipline Group of the Northeast Institute of Geography and Agroecology of the Chinese Academy of Sciences, published an online report entitled Identification and functional validation of the Proceedings of the National Academy of Sciences (PNAS) with the team of Jiming Jiang of Michigan State University and the team of Anne Osbourn of the John Innes Center in the United Kingdom Super-enhancers in Arabidopsis Thalina’s research paper. This study is the first to locate and identify plant superenhancers in plants and introduces the concept of superenhancers into the field of plant research.

Enhancers are noncoding DNA sequences about 200 bp in length that act on the corresponding promoters by binding to transcription factors and mediaators to enhance the efficiency of gene expression. In contrast to promoters, enhancer regulatory gene expression is not directional and can be located upstream or downstream of the target gene or in the target intron. Most enhancers activate or enhance the transcriptional efficiency of target genes only when induced by specific stages of cell development or specific external environments. Therefore, enhancers determine when, where, and at what level genes are expressed, and play a decisive role in gene expression regulation. In 2013, Richard Young’s lab first proposed the concept of “super enhancer” based on the research basis of mammalian enhancers at the time. Super enhancers (SEs) are enhancer clusters formed by the tandem of successively arranged enhancers, spanning up to 8-20 Kb, with higher transcriptional activation related histone modifications, enrichment of high-density transcription factors and cofactors, and stronger ability to regulate gene transcription, which are considered to play important regulatory functions in important biological processes such as cell differentiation and immune response in mammals. Since its discovery, super enhancers have become a research hotspot at the forefront of science and technology in the world, but there is still a lack of research on plant super enhancers.

Meng Fanli’s team used the Arabidopsis DNase I hypersensitive site sequencing data to find chromatin-open regions containing large enhancer clusters in the whole genome of Arabidopsis thaliana, and identified 749 candidate super-enhancers, the smallest length of 1.5Kb. The genomic region where the super-enhancer is located is more sensitive to DNase I than other promoter chromosomal open regions. Super enhancers are closely associated with topology-associated domains (TADs) (Figure 1). SEs and their predictive target genes are closely related to Arabidopsis organ and tissue development. This demonstrates that Arabidopsis superenhancers share the same functional characteristics as mammalian superenhancers. The study localized a 3578 bp long super enhancer in the middle of the thalianol biosynthetic gene cluster (BGC) consisting of five genes, and used CRISPR/Cas technology to create a mutant of the super enhancer. The deletion of small fragments 131-157 bp in the super enhancer significantly inhibited transcription of five genes in the gene cluster, resulting in significantly longer Arabidopsis thaliana roots (Figure 2). In addition, T-DNA insertion in the SE region resulted in transcriptional changes in five genes in the gene cluster. This study shows that super-enhancers play an important role in the expression of genes associated with the developmental characteristics of Arabidopsis thaliana and the co-expression of operon-like gene clusters.

Figure 1.Plant superenhancers are closely associated with topological association domains (TADs).

Figure 2.Co-expression of genes in a cluster of super-enhancer-regulated operon genes

The research work was supported by the National Key Research and Development Program of China and the National Natural Science Foundation of China. (Source: Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences)

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