Genome-wide identification of silencers and their regulatory mechanism in gene transcription in Arabidopsis

Gene transcription regulation is essential for eukaryotic development. Despite the considerable advances has been made in cis-regulatory elements, the roles of silencers in gene transcription, particularly in plants, remain largely elusive. Here, we employed a method called repressive self-transcribing active regulatory region sequencing (REST-seq) to systematically identify silencers across the Arabidopsis genome, modified from the STARR-seq for enhancer identification. In all, 13,032 silencers were identified from two distinct developmental stages of leaves, of which approximately 69.3% (74.6%) are located in the promoter and 3′–untranslated region (3’–UTR) regions. Genes overlapping with silencers exhibited higher expression levels than those without silencers, and the occurrence of silencers in the TES regions was positively correlated with the expression levels of proximal genes. Almost all acetylation modifications, H3K4me3, chromatin accessibility sites, as well as numerous transcription factor binding sites (TFBSs), were significantly enriched in the flanking regions of silencers, whereas they were deleted in the body regions. Numerous histone modifications and TFBSs have opposite distributional characteristics around silencers and enhancers, suggesting that they play opposing roles in controlling gene transcription. In static cases, silencers and enhancers might directly participate in proximal gene transcription rather than through distal chromatin contact loops. In dynamic cases, however, the enrichment patterns of silencers and enhancers in differentially expressed genes (DEGs) are reversed, and they govern DEG transcription through both proximal involvement and distal chromatin contact loops. Silencers and enhancers cooperatively regulate gene transcription to maintain an optimal transcript abundance of targeted genes during the development of Arabidopsis leaves. In addition, silencer activity was validated using the transgenic Arabidopsis, and several silencers displayed evident enhancer activity and strong tissue-specificity, implying that these elements may exhibit bifunctional activity in different tissues and spatiotemporal conditions. This study provided a reliable method for genome-wide silencer identification and demonstrated the roles of silencers and enhancers in the regulation of gene transcription, which will facilitate the elucidation of the regulatory mechanisms governing gene transcription in Arabidopsis.