Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America.
BGI-Shenzhen, Shenzhen, China.
PLoS Genet. 2013;9(12):e1003984. doi: 10.1371/journal.pgen.1003984. Epub 2013 Dec 12.
The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.
H3K4 三甲基化酶 PRDM9 的鉴定作为负责重组热点定位的基因，为理解哺乳动物中重组的起始机制提供了重要的线索。然而，犬类在哺乳动物中是独一无二的，它们似乎缺乏功能性的 PRDM9 版本，因此可以为理解没有 PRDM9 时发生的重组以及 PRDM9 如何塑造重组景观提供模型。我们使用来自 51 只自由放养的犬（Canis lupus familiaris）的高通量测序数据评估连锁不平衡模式，构建了精细的遗传图谱。虽然重组的广泛特征与其他哺乳动物物种相似，但我们的精细估计表明，犬类在富含 CpG 的区域附近观察到高度升高的重组率，包括基因启动子区域，但与在精母细胞中鉴定的 H3K4 三甲基化标记几乎没有关联。与安第斯狐（Lycalopex culpaeus）的基因组数据相比，我们表明偏向基因转换是犬基因组中高 CpG 含量发生的一种可能机制。
