In plants and animals, long non-coding RNAs (lncRNAs) are known to impact genome architecture and guide significant epigenetic and structural changes in the nuclear organisation of DNA, resulting in changes in gene expression. These changes may be necessary for the establishment and maintenance of differentiated tissues. In Arabidopsis thaliana, lncRNAs such as AUXIN REGULATED PROMOTER LOOP (APOLO) bind to multiple loci to modify three-dimensional genome conformation and alter gene expression. However, the extent to which lncRNA-DNA interactions occur in plants and how they affect gene expression remains underexplored.
To analyse the impact of lncRNAs on genome architecture in Arabidopsis thaliana, we used high-throughput sequencing to identify DNA-DNA and DNA-RNA interactions in roots and cotyledons of seedlings. We found both tissues display similar chromosomal architecture patterns, although pericentromeric interactions were more prevalent in root samples. Most interactions occur within the same chromosome arm, with fewer events between different chromosomes. We also identified two previously undescribed regions participating in the A. thaliana KNOT superstructure. We found several known and novel lncRNAs that interact with regions showing differential chromosome architectures between roots and cotyledons. We are currently exploring how these lncRNAs may control the expression of genes crucial to organ identity. Our study will expand the current knowledge of genome architecture and its relation to organ differentiation in plants.