The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation

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.

Integrative nascent RNA methods to reveal cell-type specific transcription programs in peripheral blood and its derivative cells

“…But the degree of distance dependence was variable between the cell lines, polyploid HeLa cells 30 appear to have more rapid decay than the haploid HAP1 cells within 1 Mb regions, and HAP1 cells appear to have more long-range interactions. Although we will need to rule out potential biases, but this observation on potential association between ploidy and distance is somewhat consistent with a study reporting fewer short range interactions (< 1 Mb) in Arabidopsis tetraploid cells compared to diploid cells 31 .…”

Autopolyploidy: an epigenetic macromutation

“…New insights into the epigenetics of genome doubling have been provided by a high‐throughput chromosome conformation capture (Hi‐C) study comparing chromatin organization of a synthetic A. thaliana autopolyploid with its Col‐0 diploid progenitor (Zhang et al, 2019; Fig. 1B–F).…”

“…Zhang et al (2019) reported that nearly 750 genes were differentially expressed between the diploid and autotetraploid, many of them involved in stress responses as in other autopolyploids (Coate and Doyle, 2019). Differential expression did not correlate with changed methylation pattern, but over 70% of genes with altered expression were located in regions of the genome that showed changes in their levels of cis ‐ and trans ‐interactions; in particular, promoter–promoter interaction frequency was higher in the autotetraploid.…”

“…Additional studies that integrate epigenomics, nucleome architecture, gene expression, and phenomics will ultimately be necessary to understand fully the effects and consequences of genome multiplication and whether there are “rules” that dictate responses to polyploidization. For one thing, the Zhang et al (2019) study used tissue from aerial parts of whole seedlings, and as interesting as their results are, they represent the average effect of genome doubling on many different cell types. But not all cell types respond to genome duplication the same way—or at all.…”

“…1) it is clear that, in an autopolyploid, genome duplication has a direct effect on chromatin state. In the Zhang et al (2019) study, each gene whose transcription level or chromatin compartment is altered in the autopolyploid thus represents an opportunity to explore the interrelations between chromatin changes and gene expression in a genetic background unaltered by conventional genetic mutations.…”