Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

This first comprehensive view of the Arabidopsis epigenome reveals that it is organized into four main chromatin types based on the integrative mapping of a broad set of 11 histone marks and DNA methylation in seedlings

Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes

In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis

Distribution of CO rates across the 14a (A) and 130× (B) hotspots in different genetic backgrounds.

<p>(A). One hundred and four, 108 and 87 COs were analyzed in ColxL<i>er</i> (black), “<i>MSH4</i>” (orange) and ColxWs (purple), respectively. Thin dotted vertical lines: median position at 14a1 and 14a2 for each distribution. (B). One hundred and sixty seven and 245 COs were analyzed in ColxL<i>er</i> and “<i>MSH4</i>”, respectively. Thin dotted vertical lines: median position for each distribution. Using a Fisher exact test, the two distributions were found to be highly significantly different (<i>p-value</i> = 2.2×10⁻¹⁶).</p

Distribution of CO rates across the 14a (A) and 130× (B) hotspots.

<p>One hundred and four COs were analyzed at 14a (62 at 14a1 and 42 at 14a2) and 167 at 130×. Grey dotted vertical lines: median positions of the hotspots. On the x axis: triangles are positions of insertions-deletions larger than 7 bp (from the left to the right of 130×: 20, 13, 12, 70, 10, 7 and, 11 bp); green triangles are positions of indels used to detect NCOs; green dots are SNPs used to detect NCOs; the black dot on the x axis in (A) is the position of the microsatellite. Gene structures along the hotspot regions are displayed on top of graphical areas (light hashed grey: exons, dark grey: UTR, broken lines: introns). (C)(D) Low nucleosome density (LND) at 14a and 130×. LND is from published nucleosomal DNA microarray hybridization experiments, where a high signal represents an absence of nucleosomal DNA <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003922#pgen.1003922-Zhang1" target="_blank">[28]</a>.</p

NCO events at 130×.

<p>(A) SNP #44, (B) SNP #21, (C) SNP #52. The positions of the SNPs genotyped are indicated by green filled circles (SNPs) or triangles (indels). The polymorphisms are indicated by filled black circles along the chromosome coordinate axes. Triangles: insertion or deletion greater than 7 bp. Thick red or blue horizontal lines: converted SNPs, Thick grey dotted horizontal lines: interval in which NCO tract ends are located. Blue: Col; Red: L<i>er</i>.</p

Specific detection of CO and NCO molecules in genomic DNA extracted from pollen.

<p>The F1 hybrid contains one allele from each parent at each locus. Filled circles represent polymorphisms on the C (Col, blue) or L (Ler, red) chromosomes. After meiosis, in DNA extracted from pollen, there are either non-recombinant molecules (C, L) or CO (‘LtoC’ or ‘CtoL’) or NCOs (‘LtoCtoL’ or ‘CtoLtoC’) in various proportions depending on the locus studied. To detect CO molecules, two rounds of allele-specific PCR were carried out with allele-specific oligonucleotides (ASOs, blue and red triangles) on pools of genomic DNA. To detect NCO molecules, alleles containing polymorphisms from one specific parent on each side were first amplified by one or two rounds of allele-specific PCR. Then the region of interest was cloned in <i>E.coli</i> and interesting SNPs were genotyped using fluorescent mapping as described <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003922#pgen.1003922-Ng1" target="_blank">[31]</a>. Alternatively, two rounds of complementary allele-specific PCR were performed to analyze the status of interesting SNPs. A NCO event was scored when both PCRs were positive.</p

CO distribution and cumulative CO rates for reciprocal orientations at 14a (A) and 130× (B).

<p>Twenty nine ‘CtoL’ and 33 ‘LtoC’ COs were analyzed at 14a1, 23 and 19 at 14a2, and 75 and 92 at 130×. The ‘LtoC’ distribution is presented in red and the ‘CtoL’ in blue. For all three hotspots and both reciprocal orientations, cumulated (from left to right) relative CO rates were scored at successive polymorphic sites along the region. Blue curves: cumulated relative ‘CtoL’ CO rates. Red curves: cumulated relative ‘LtoC’ CO rates. Blue histogram: distribution of ‘CtoL’ CO rates. Red histogram: distribution of ‘LtoC’ CO rates. Grey dotted vertical lines: median positions of the hotspots.</p

NCO rates in <i>“MSH4” and Atmsh4^−/−</i> at 130× and 14a1.

<p>Confidence intervals are shown in brackets. R is the ratio of NCO rates obtained in “<i>MSH4</i>” on <i>Atmsh4</i>^−/−.</p>*<p><i>p-value</i> = 0.0035.</p

Specific detection of CO molecules in genomic DNA extracted from pollen.

<p>PCR was performed with allele-specific oligonucleotides (ASOs) designed for the amplification of CO molecules (see Material and Methods, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003922#pgen-1003922-g001" target="_blank">Figure 1</a>), using decreasing amounts of genomic DNA (the number of template molecules is indicated on the photograph) extracted from F1 Col x L<i>er</i> hybrid plants, either from leaf (two top rows) or pollen (two bottom rows). Eight aliquot reactions were carried out for each dilution. No PCR products were amplified from leaf. However, using equivalent low concentrations of DNA extracted from pollen (4096 molecules and less), CO molecules were strongly and specifically amplified .</p