TY - JOUR
T1 - DNA crossover motifs associated with epigenetic modifications delineate open chromatin regions in arabidopsis
AU - Shilo, Shay
AU - Melamed-Bessudo, Cathy
AU - Dorone, Yanniv
AU - Barkai, Naama
AU - Levy, Avraham
N1 - We thank Assaf Zemach for the data on epigenetic modifications in Arabidopsis, Shai Lubliner, Ephraim Kenigsberg, and Amos Tanay for help with the motifs analysis and for advice, members of the Levy and Barkai laboratories for useful comments, Yehudit Posen for language editing of the article, and the European Research Council for partial funding of the genome data analysis (EU-FP7 TRACTAR grant to A.A.L.). S.S. performed the bioinformatics analysis and initiated some of the analyses. C.M.-B. performed most of the experimental work. Y.D. validated some of the recombination events. N.B. cosupervised the work. A.A.L. planned and cosupervised the work and wrote parts of the article.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84943778851&partnerID=8YFLogxK
U2 - https://doi.org/10.1105/tpc.15.00391
DO - https://doi.org/10.1105/tpc.15.00391
M3 - مقالة
SN - 1532-298X
VL - 27
SP - 2427
EP - 2436
JO - The Plant cell
JF - The Plant cell
IS - 9
ER -