Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 27 (9), 2427-36

DNA Crossover Motifs Associated With Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

Affiliations

DNA Crossover Motifs Associated With Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis

Shay Shilo et al. Plant Cell.

Abstract

The rate of crossover, the reciprocal exchanges of homologous chromosomal segments, is not uniform along chromosomes differing between male and female meiocytes. To better understand the factors regulating this variable landscape, we performed a detailed genetic and epigenetic analysis of 737 crossover events in Arabidopsis thaliana. Crossovers were more frequent than expected in promoters. Three DNA motifs enriched in crossover regions and less abundant in crossover-poor pericentric regions were identified. One of these motifs, the CCN repeat, was previously unknown in plants. The A-rich motif was preferentially associated with promoters, while the CCN repeat and the CTT repeat motifs were preferentially associated with genes. Analysis of epigenetic modifications around the motifs showed, in most cases, a specific epigenetic architecture. For example, we show that there is a peak of nucleosome occupancy and of H3K4me3 around the CCN and CTT repeat motifs while nucleosome occupancy was lowest around the A-rich motif. Cytosine methylation levels showed a gradual decrease within ∼2 kb of the three motifs, being lowest at sites where crossover occurred. This landscape was conserved in the decreased DNA methylation1 mutant. In summary, the crossover motifs are associated with epigenetic landscapes corresponding to open chromatin and contributing to the nonuniformity of crossovers in Arabidopsis.

Figures

Figure 1.
Figure 1.
Identification of CO Events through Next-Generation Sequencing of F2 Plants. (A) Overall design of detection of CO events. DNA segments are colored according to the supporting parent-specific SNP: Ler (red) and Col (blue). Samples with SNPs from both parents were considered heterozygotes (purple). Reads supporting parent-specific SNPs are shown as the horizontal lines in the frame. Green arrows and vertical bars (in frame) show transition between zygosity states. (B) Recombination landscape in the five chromosomes (Chr) of one F2 plant. Centromeres are indicated as gray boxes. Plus signs indicate patches different from the surrounding zygotic level that have reverse transition to the surrounding zygotic level within a distance smaller than 50 kb.
Figure 2.
Figure 2.
Association of Motifs with Known Genomic Features. Percentage of genomic features, such as promoters (defined as 500 bp upstream of transcription start site), genes (5′ and 3′ untranslated regions, exons, and introns), transposons, and others (all the remaining sequences, such as non-annotated repeats and tRNAs), within the whole genome (left panel) and within the data set of the 737 CO events (right panel). Genes are represented in purple, promoters in brown, transposons in light blue, and “others” in yellow. COs that overlapped with more than one feature were counted once for each feature.
Figure 3.
Figure 3.
DNA CO Motifs. Logo plots of DNA sequence showing motifs enriched in CO regions. Three motifs were identified using two different algorithms: MEME (left) and HOMER (right). An A-rich motif (E-value = 1.67e-186; P value = 1e-10), a CTT repeat motif (E-value = 7.67e-65; P value = 1e-11), and a CCN repeat motif (E-value = 6.33e-22; P value = 1e-14). The significance was expressed as E-value when using MEME or P value when using HOMER.
Figure 4.
Figure 4.
Abundance and Distribution of the Three CO Motifs. (A) Distribution of the A-rich, CTT repeat, and CNN repeat motifs in chromosome 1 in the upper, middle, and lower panels, respectively. The pericentric region (∼2 Mb around the centromere) is shown as a gray box. (B) Motif abundance (normalized as the number of motifs per Mb) is shown for the high-resolution CO data set (red), hot regions (orange), genome-wide (green), and cold regions (blue). (C) Manhattan plot of the statistical significance (-log10 of P value) of the CO data set compared with each of the contrast groups: genome-wide (green circles), subtelomeric female-specific cold intervals (pink triangle), general cold intervals (blue squares), and hot regions (orange diamonds). (D) Distribution of motifs within various data sets. CO events: data set of 737 CO events; genome wide: whole genome; promoters: 500 bp upstream of the transcription start site; genes: 5′ and 3′ untranslated regions, exons, introns, and transposable elements (TE).
Figure 5.
Figure 5.
The CG Methylation Landscape around the CO Motifs. The ratio of methylated CG dinucleotides versus total CGs is shown in 50-bp bins around the CO motifs, namely, the CCN repeat (purple square), CTT repeat (red circle), and the A-rich motif (green triangle). As a control, CG methylation was analyzed around randomly picked sequences (continuous black line). Motifs are located at the center (0 bp) of the x axis. Each point is the average CG methylation for all the motifs in a given bin. The analysis was performed for all the motifs in the wild-type genome (A), for the data set of the actual CO events detected here (B), and for the whole genome in the ddm1 mutant (C).
Figure 6.
Figure 6.
Epigenetic Landscape around the CO Motifs. Epigenetic marks were analyzed around the CCN repeat (purple square), the CTT repeat (red circle), the A-rich CO motifs (green triangle), and the randomly picked control sequences (continuous black line). All the motifs are at the center of the x axis (0 bp). The average epigenetic mark value is shown on the y axis for 50-bp bins from the center of the x axis and up to 2000 bp upstream and downstream of the motifs. The epigenetic marks were analyzed in the whole wild-type genome ([A], [C], and [E]) and for the data set of CO events ([B], [D], and [F]). The epigenetic marks analyzed here are the nucleosome occupancy ([A] and [B]), H3K4me3 modifications ([C] and [D]), and variations in H2A.Z histone marks ([E] and [F]).

Similar articles

See all similar articles

Cited by 27 PubMed Central articles

See all "Cited by" articles

Publication types

Associated data

LinkOut - more resources

Feedback