Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation.
Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation.
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DOI：
10.1101/gr.273672.120
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发表时间：
2021-09
期刊：
影响因子：
7
通讯作者：
Henderson IR
中科院分区：
文献类型：
--
作者：
Tock AJ;Holland DM;Jiang W;Osman K;Sanchez-Moran E;Higgins JD;Edwards KJ;Uauy C;Franklin FCH;Henderson IR
六倍体面包小麦基因组包含21条染色体上超过16千兆碱基的序列。减数分裂交换是高度极化的沿着染色体，与海拔在基因密集的远端地区和吉普赛逆转录转座子密集的着丝粒近端地区的抑制。我们分析了小麦减数分裂重组酶DMC 1和染色体轴蛋白ASY 1的基因组景观，并研究了它们与杂交、染色质状态和遗传多样性的关系。DMC 1和ASY 1染色质免疫沉淀，然后测序（ChIP-seq）显示在小麦染色体的远端，交叉活性区域有很强的共富集。远端ChIP-seq富集与减数分裂前期I期间DMC 1和ASY 1靠近端粒的时空偏倚细胞学免疫定位一致。DMC 1和ASY 1 ChIP-seq峰显示与Mariner和Mutator超家族中的基因和转座因子显著重叠。然而，沿着每条染色体的长度沿着检测到DMC 1和ASY 1 ChIP-seq峰，包括在低交叉区域中。在精细尺度上，DMC 1和ASY 1峰和基因的交叉升高与Polycomb组蛋白修饰H3 K27 me 3的富集相关。这表明兼性异染色质与高DMC 1和ASY 1在促进小麦中的交换中的作用，并反映在通过ChIP-seq和免疫细胞学观察到的远端H3 K27 me 3富集中。具有高交叉率和高DMC 1和ASY 1 ChIP-seq信号的基因在防御反应和免疫注释中被过度代表，具有较高的序列多态性，并表现出选择的特征。我们的研究结果与减数分裂重组促进遗传多样性，塑造宿主-病原体共同进化，并通过提高选择效率加速适应一致。
The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.
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影响因子：
3
作者：
Feng X;Grossman R;Stein L
通讯作者：
Stein L
DOI：
10.1093/bioinformatics/btv562
发表时间：
2016-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Díez-Villanueva A;Serra E;Buschbeck M;Peinado MA;Malinverni R
通讯作者：
Malinverni R
影响因子：
5.9
作者：
Brinton J;Ramirez-Gonzalez RH;Simmonds J;Wingen L;Orford S;Griffiths S;10 Wheat Genome Project;Haberer G;Spannagl M;Walkowiak S;Pozniak C;Uauy C
通讯作者：
Uauy C
影响因子：
7.2
作者：
Demirci, Sevgin;van Dijk, Aalt D. J.;Peters, Sander A.
通讯作者：
Peters, Sander A.
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.