Chromatin interaction maps reveal genetic regulation for quantitative traits in maize

Abstract

Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation.

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize

“…Hi-C technology characterized chromatin loops (Delaneau et al 2019; Dong et al 2017;Szabo et al 2019), and their dynamic is associated with transcription activity (Dong et al 2020). DNA interaction junctions identified by HI-C and HICHIP (Ricci et al 2019;Peng et al 2019) comprise a substantial extra proportion (21.23%) of intergenic pan-And-CNS. TE-derived CNSs have been reported by several independent studies (Dupeyron et al 2019;Smith et al 2008;Xie et al 2006), although the contribution of TEs as regulatory elements is still controversial (de Souza et al 2013;Zeng et al 2018;Trizzino et al 2018).…”

ZEAMAP, a comprehensive database adapted to the maize multi-omics era

“…These regulatory factors are crucial for the ability of sessile plants to respond to diverse environmental challenges (57). In ZEAMAP, we have collected the chromatin interaction maps associated with RNA polymerase II occupancy and the histone mark H3K4me3 according to the B73 reference genome (6) . Open chromatin regions are based on micrococcal nuclease (MNase) digestion (7), histone acetylation and methylation regions, and populational DNA methylation information generated from the third leaves at V3 of the 263 AMP inbred lines (26).…”

“…The maize B73 reference genome has recently been updated (1), and four more maize genome assemblies have been released during the last two years (2)(3)(4)(5). The previous two-dimensional genome has recently been resolved in three dimensions with the mapping of open chromatin and the identification of chromatin interactions based on ChiA-PET and Hi-C technologies (6,7). Omics data, including deep DNA resequencing, transcriptome and metabolome, have been accumulated at the population scale (8)(9)(10)(11)(12)(13)(14)(15).…”

BioViz Connect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser

“…This problem is immediately apparent upon viewing the alignments in a genome browser and almost impossible to notice otherwise. Because researchers have lacked convenient ways to visualize their data, many studies have overlooked this not-well-known aspect of spliced alignment tools [6][7][8][9][10][11][12].…”