Genetic recombination is targeted towards gene promoter regions in dogs.
Genetic recombination is targeted towards gene promoter regions in dogs.
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DOI：
10.1371/journal.pgen.1003984
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发表时间：
2013
期刊：
影响因子：
4.5
通讯作者：
Boyko AR
中科院分区：
文献类型：
--
作者：
Auton A;Rui Li Y;Kidd J;Oliveira K;Nadel J;Holloway JK;Hayward JJ;Cohen PE;Greally JM;Wang J;Bustamante CD;Boyko AR
H3K4三甲基化酶PRDM9作为负责重组热点定位的基因的鉴定为哺乳动物中启动重组的机制提供了相当多的见解。然而，在哺乳动物中独特的是，犬科动物似乎缺乏PRDM9的功能版本，因此可以提供一个模型来理解在没有PRDM9的情况下发生的重组，以及PRDM9如何发挥作用来塑造重组景观。我们已经构建了一个精细的连锁不平衡模式的遗传图谱，使用高通量的序列数据从51个自由放养的狗，犬狼疮familiaris评估。虽然大规模的重组特性似乎与其他哺乳动物物种相似，但我们的细尺度估计表明，在富含CpG的区域（包括基因启动子区域）附近观察到犬的重组率高度升高，但与精母细胞中鉴定的H3K4三甲基化标记几乎没有关联。通过比较从安第斯狐狸，Lycalopex culpaeus的基因组数据，我们表明，有偏见的基因转换是一个合理的机制，高CpG含量的狗的基因组可能已经发生。哺乳动物基因组中的重组倾向于发生在被称为重组热点的高度局部化区域内。这些热点似乎是哺乳动物基因组中普遍存在的特征，但尽管DNA序列相似性很高，但在密切相关的物种之间往往不共享。这种差异在很大程度上可以通过PRDM9的发现来解释，PRDM9是通过识别和结合特定DNA基序来定位重组热点的基因。PRDM9内的变异可以导致识别的基序的变化，并因此改变基因组中重组热点的位置。多项研究表明，PRDM9处于强大的选择压力下，显然导致物种之间热点位置的快速更替。然而，在哺乳动物中，PRDM9似乎在狗和其他犬科动物中功能失调。在本文中，我们研究了PRDM9的丢失如何影响狗的精细重组景观，并将其与其他物种中的模式进行对比。
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. Recombination in mammalian genomes tends to occur within highly localized regions known as recombination hotspots. These hotspots appear to be a ubiquitous feature of mammalian genomes, but tend to not be shared between closely related species despite high levels of DNA sequence similarity. This disparity has been largely explained by the discovery of PRDM9 as the gene responsible for localizing recombination hotspots via recognition and binding to specific DNA motifs. Variation within PRDM9 can lead to changes to the recognized motif, and hence changes to the location of recombination hotspots thought the genome. Multiple studies have shown that PRDM9 is under strong selective pressure, apparently leading to a rapid turnover of hotspot locations between species. However, uniquely amongst mammals, PRDM9 appears to be dysfunctional in dogs and other canids. In this paper, we investigate how the loss of PRDM9 has affected the fine-scale recombination landscape in dogs and contrast this with patterns seen in other species.
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影响因子：
4.4
作者：
Han, Leng;Zhao, Zhongming
通讯作者：
Zhao, Zhongming
CpG岛密度及其与哺乳动物基因组中基因组特征的相关性。
影响因子：
12.3
作者：
Han L;Su B;Li WH;Zhao Z
通讯作者：
Zhao Z
PRDM9物种形成基因在多种后生分类单元中加速了进化。
影响因子：
4.5
作者：
Oliver PL;Goodstadt L;Bayes JJ;Birtle Z;Roach KC;Phadnis N;Beatson SA;Lunter G;Malik HS;Ponting CP
通讯作者：
Ponting CP
影响因子：
7
作者：
Jensen-Seaman, MI;Furey, TS;Jacob, HJ
通讯作者：
Jacob, HJ
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew