Abstract
Autopolyploidy is widespread in higher plants and important for agricultural yield and quality. However, the effects of genome duplication on the chromatin organization and transcriptional regulation are largely unknown in plants. Using High-throughput Chromosome Conformation Capture (Hi-C), we showed that autotetraploid Arabidopsis presented more inter-chromosomal interactions and fewer short-range chromatin interactions compared with its diploid progenitor. In addition, genome duplication contributed to the switching of some loose and compact structure domains with altered H3K4me3 and H3K27me3 histone modification status. 539 genes were identified with altered transcriptions and chromatin interactions in autotetraploid Arabidopsis. Especially, we found that genome duplication changed chromatin looping and H3K27me3 histone modification in Flowering Locus C. We propose that genome doubling modulates the transcription genome-wide by changed chromatin interactions and at the specific locus by altered chromatin loops and histone modifications.
Highlights
Polyploidy plays a significant role in plant evolution and formation of the important agriculture traits such as high yield and stress resistances in crops [1,2,3]
The results showed that the compacted structural domain (CSD) compartments in both Col-0 and 4 × Col-0 had a higher level of H3K27me3 and lower level of H3K4me3 compared to loose structure domains (LSD) (Figure 4C and D), and LSD compartments in both Col-0 and 4 × Col-0 had a lower level of H3K27me3 and higher level of H3K4me3 compared to CSD (Figure 4C and D)
Our results showed that genome-doubled Arabidopsis acquires morphologic traits like, more and larger rosette leaves and elevated biomass which are similar to other polyploidy plants [31,60]
Summary
Polyploidy plays a significant role in plant evolution and formation of the important agriculture traits such as high yield and stress resistances in crops [1,2,3]. Polyploidy crops own higher plasticity and environmental adaptability [4] with specific gene expression patterns for the organ development and resistances to abiotic and biotic stresses [1,5]. Each chromosome has a preferred but not fixed position named chromosome territory (CT) [14], which consist of several megabase-scale genomic compartments [15,16]. These compartments are categorized into A-type compartment rich for euchromatic and highly transcribed regions and B-type compartment rich for heterochromatic and gene-poor regions [17]. Chromatin looping could bring cis-regulatory elements and promoters together to affect gene transcription [23]
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