Abstract
Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers.
Highlights
Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes
We investigated the distribution of epigenetic marks at topologically associated domains (TADs) boundaries and found prominent H3K4me[3], H3K9ac and H4K12ac peaks centred on TAD boundaries (Fig. 2, Supplementary Fig. 1), which is consistent with previous findings of enrichment of those epigenetic marks at rice TAD boundaries[7,8,13]
Our observations mirror that made in Drosophila melanogaster, where a proposed model suggests that chromatin is divided in TADs and inter-TAD regions[31]
Summary
Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. The genomes of animals and plants are partitioned into chromatin domains, referred to as topologically associated domains (TADs)[1,2] These are structural units of chromosome compartmentalization, which emerged as a key feature of higherorder genome organization. Compared to inter-TADs, TADs have increased sequence variant density, meiotic recombination rate, are overrepresented in transposable elements (TEs) and silencing epigenetic marks. Genes found in TADs are shorter, have lower expression levels and are overrepresented in functions related to signalling and response to environmental stimuli
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