![]() ![]() Another characteristic of these regulatory regions is their higher DNA accessibility. Įpigenome maps have contributed to the identification of regulatory regions, which are characterized by specific chromatin marks or signatures. The relevance of these regulatory elements is highlighted by their significant enrichment at intergenic QTL in the maize ( Zea mays L.) genome. Currently, it is easier to identify and annotate the gene repertory present in a genome than their cis-regulatory elements and modules, which represents an important gap in our understanding of genome functionality ]. Today we have good reference genomes and pangenomes for the principal crop species, and that information has been critical to understand the genetic basis of biological processes, to identify natural variation responsible for phenotypic diversity, and for other applications.Ī critical aspect of this information is the annotation of genes and regulatory sequences that control their expression. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome.ĭuring the last 20 years, the significant progress in DNA sequencing technologies has allowed the rapid sequencing of complete genomes from multiple species, including a large number of varieties within each species. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. We have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Importantly, we observed overlap between ATAC-seq peaks and cis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing to identify open chromatin regions in wheat root tip samples. In this work we developed a transgenic INTACT system in tetraploid wheat for nuclei purifications. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however, cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression.
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