Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Abstract

The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

“…To examine the relationship between three-423 dimensional proximity and replication timing patterns, we compared the RT classes to the 424 chromosome conformation capture datasets described by Liu et al (2016). We chose this dataset 425 because of its reproducibility was established by an earlier study (Wang et al, 2015). 426…”

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…14,17 To understand the relationship between H4K16ac and H3K23ac with other histone methylation marks, we examined the correlation of these 2 marks with previously reported histone modifications in Arabidopsis. Consistent with the expression difference among the 4 clusters, we found that active marks (H3K4me2/3 and H3K36me2/3) are significantly enriched at genes in the "Both" cluster (P < 2.2 £ 10 ¡16 ) and are depleted in the "None" cluster ( Fig.…”

“…[8][9][10][11][12][13] In plants, recent advances in high throughput sequencing technology have enabled the large-scale profiling of histone acetylation marks and have greatly improved our understanding of the function of histone acetylation and its relationship with transcription. [14][15][16][17][18] Besides its role in gene expression, plant histone acetylation plays crucial roles in the crosstalk between genomes and the environment during plant responses to diverse stresses at the cellular and organismal levels. [19][20][21][22][23][24] Acetylation occurs at many histone lysine residues and regulates chromatin activity by at least 2 different mechanisms.…”

Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 – 15, 2016 - Strasbourg, France

“…In addition, syntenic blocks enriched in conserved (ancestrallyderived) H3K27me3 domains showed their preferential association with genomic regions involved in many long-range intrachromosomal interactions that have been reported elsewhere. 42,43 These outcomes point out the influence of multiple evolutionary constraints on PRC2-mediated gene repression and the existence of distinct sets of H3K27me3-marked regions, thus explaining the difficulty to identify cis-regulatory elements common to all PRC2 targets.…”