Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations

Abstract

Background: Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis.

Results: Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf.

Conclusions: Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.

Keywords: 3D structure; ATAC-seq; Gene expression; Gene regulation; Hi-C; Peanut.

Fig. 1

Hi-C analyses of chromatin interactions in wild and dwarf mutant peanuts. A Genome-wide chromatin interaction map represented by the wild type (H2014) at 500-kb resolution. The chromosomes are stacked from top left to bottom right in order (chr01, chr02…chr20). Color bars beside heat maps indicate strong interactions in red and weak interactions in white. B Chromatin interactions represented by a single chromosome of the wild type (H2014) at 500-kb resolution. The upper track shows the partitioning of A-compartments (blue histogram) and B-compartments (red histogram). The middle track shows global patterns of chromatin interaction represented by chr04 and chr07, respectively. The lower track shows chromatin interactions in an enlarged region of chr04 and chr07 at 40-kb resolution, respectively. Each triangle distributed diagonally is represented as a topologically associated domain (TAD). C 3D model of whole chromosomes in the wild type (H2014) and the dwarf mutant (H1314). Each color represents one chromosome

Fig. 2

Genomic features of A/B compartments in peanut. A Illustration of gene density, GC content, and gene expression (FPKM value) of A compartments, A to B switching compartments, different compartments, B to A switching compartments, and B compartments, in the wild type H2014 and the mutant type H1314, respectively. B Distribution of A and B compartments represented by chr04, chr07, and chr08 of H2014, with the upper line showing the partition of A (blue histogram) and B (red histogram) compartments. The lower track indicates the first principal component values showing A/B compartment status at 500-kb resolution. C The representative genomic region 18.6–24.9Mb on chr08 of H2014 displayed A/B compartments. The top two lanes indicated the first principal component values corresponding to A compartments (blue histogram) and B compartments (red histogram) in H2014 and H1314, respectively. The third lane indicated the DEGs between H2014 and H1314. Blue bars represented the upregulation, and the red bars represented the downregulation. The fourth and fifth lanes indicated the FPKM values of genes in H2014 and H1314, respectively. The remaining two lanes indicated the compartment switching between H2014 and H1314. The yellow shaded region showed uneven distribution of A and B compartments

Fig. 3

Chromatin loops in peanut. A Circos of genomic cis-interactions represented by the wild type (H2014). B Circos of genomic trans-interactions represented by the wild type (H2014). C Distribution of genomic distance of cis-interactions in the wild type and the dwarf mutant. D Circos of interactions between subgenome-homoeologous chromosomes represented by chr01 and chr11 in the wild type (H2014). E Circos of interactions between homologous blocks of subgenome-homoeologous chromosomes represented by the wild type (H2014). F The number of trans-interactions among A subgenome, B subgenome, and between A and B subgenomes in the wild type (H2014) and the dwarf mutant (H1314)

Fig. 4

Characterization of specific cis-interactions in the wild type and the mutant peanut. A Venn diagram for all cis-interactions identified in the two peanut lines. B Venn diagram for all trans-interactions identified in these two lines. C Distribution of specific cis-interactions of 20 chromosomes. D KEGG pathway of 96 differentially expressed genes between the dwarf mutant (H1314) and the wild type (H2014). E Heatmap showing the log ratio of normalized FPKM of the 96 differentially expressed genes involved with chromatin loops between the dwarf mutant (H1314) and the wild type (H2014). Each line on the heatmap represents a gene, and the values are given for each of two replicates

Fig. 5

Characterization of topologically associated domains (TADs) in peanut. A Changes for TAD between the wild type and the dwarf mutant peanuts. B Merge of TADs represented by 98480000–100200000 of chr03 and Split of TADs represented by 110840000–112680000 of chr13. The upper and lower heat maps represented H2014 and H1314, respectively. The values on the left indicated the insulation score profile of TADs. The dotted line indicated the TAD border. Comparison of the gene density (C), GC contents (D), and gene expression (FPKM) (E) between TAD borders and inner regions in the wild type (H2014) and the mutant type (H1314)

Fig. 6

Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis in peanut. A Normalized read signal of ATAC-seq peak sites in H2014, the wild type (left) and H1314, the dwarf mutant (right). Numbers in the bottom box show stronger (red) and weaker (green) ATAC-seq signals in H1314, respectively. B The motif sequences identified around the stronger ATAC-seq peaks in H1314, including MYB (top), ESE1 (AP2EREBP) (center left), AT5G23930 (mTERF) (center right), ERF4 (AP2EREBP) (bottom left), and ERF10 (AP2EREBP) (bottom right). C Genomic location distribution of increased accessible chromatin signals in H1314. The ratio shows the ascending arrangement as distal intergenic (89.56%), promoter-TSS (4.01%), exon (3.00%), TTS (2.58%), and intron (0.86%). D KEGG pathway of the nearest gene located in genomic regions with stronger ATAC-seq signals in H1314. E GO enrichment of the nearest gene located in genomic regions with stronger ATAC-seq signals in H1314. Genes in D and E were identified as the putatively regulated target genes based on that the ATAC-seq peaks were assigned to its nearest transcription start site

Fig. 7

The regulatory network of plant height in the wild type (A) and the dwarf mutant (B). A, B The snapshot of the Wash U browser view shows chromatin loops and ATAC-seq in the wild type (H2014) and the dwarf mutant (H1314), respectively. Top, Hi-C contact map of a genomic region (22950000–23360000) on chr19; Second lane, insulation scores for TAD; third lane, the TAD regions sorted; fourth lane, loops sorted with red line; fifth lane, ATAC-seq peaks; bottom, gene annotation in the genomic region. C The column shows the relative content of GA in different tissues. The histological sections shown on both sides revealed the regular and irregular arrangement of cells in wild type and the mutant, respectively. D Heat map of GA2ox gene in different tissues. The regulatory pattern of endogenous GA levels by the Gibberellin 2 beta-dioxygenase (encoded by 1SCL5Q) through interacting with AP2EREBP. The phenotype of two peanut types shows the obvious differences in plant height