Large palindromes on the primate X Chromosome are preserved by natural selection.
Large palindromes on the primate X Chromosome are preserved by natural selection.
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灵长类动物X染色体上的大回文通过自然选择得以保存。
DOI：
10.1101/gr.275188.120
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发表时间：
2021-08
期刊：
影响因子：
7
通讯作者：
Page DC
中科院分区：
文献类型：
--
作者：
Jackson EK;Bellott DW;Cho TJ;Skaletsky H;Hughes JF;Pyntikova T;Page DC
哺乳动物的性染色体携带大量的回文，其中包含有睾丸偏向性表达的蛋白质编码基因家族。然而，很少有已知的性染色体回文在物种之间保守的例子。我们在人类X染色体上发现了26个回文，占其序列的2%以上，并使用基于克隆的测序方法（包括全长纳米孔读取）对黑猩猩和恒河猴的同源回文进行了表征。在这些物种基因组的当前参考组合中，许多这些回文缺失或错误组装。我们发现12个人类X回文至少保存了2500万年，在黑猩猩和恒河猴中都有同源物。与非编码序列相比，物种间的插入和缺失在X回文的蛋白质编码基因中明显减少，表明自然选择保留了这些基因家族。分隔回文左右臂的间隔是一个局部结构不稳定的地方，12个保守的回文中有7个没有显示人类和恒河猴之间的间隔同源性。对1000个基因组计划数据集的分析显示，人类X-回文间隔段相对于臂和侧翼序列具有丰富的缺失，包括影响13%人类X染色体的常见间隔段缺失。这项工作揭示了灵长类动物X染色体上大量保守的回文，并表明回文中的蛋白质编码基因家族（其中大部分仍然缺乏特征）在面对持续的结构不稳定时促进了X回文的存活。
Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species’ genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes’ protein-coding genes compared to their noncoding sequence, demonstrating that natural selection has preserved these gene families. The spacers that separate the left and right arms of palindromes are a site of localized structural instability, with seven of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project data set revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.
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遗传对人体组织基因表达的影响。
影响因子：
64.8
作者：
GTEx Consortium;Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group;Statistical Methods groups—Analysis Working Group;Enhancing GTEx (eGTEx) groups;NIH Common Fund;NIH/NCI;NIH/NHGRI;NIH/NIMH;NIH/NIDA;Biospecimen Collection Source Site—NDRI;Biospecimen Collection Source Site—RPCI;Biospecimen Core Resource—VARI;Brain Bank Repository—University of Miami Brain Endowment Bank;Leidos Biomedical—Project Management;ELSI Study;Genome Browser Data Integration &Visualization—EBI;Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz;Lead analysts:;Laboratory, Data Analysis &Coordinating Center (LDACC):;NIH program management:;Biospecimen collection:;Pathology:;eQTL manuscript working group:;Battle A;Brown CD;Engelhardt BE;Montgomery SB
通讯作者：
Montgomery SB
影响因子：
4.5
作者：
Cocquet J;Ellis PJ;Mahadevaiah SK;Affara NA;Vaiman D;Burgoyne PS
通讯作者：
Burgoyne PS
影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
64.8
作者：
Hughes, Jennifer F.;Skaletsky, Helen;Brown, Laura G.;Pyntikova, Tatyana;Graves, Tina;Fulton, Robert S.;Dugan, Shannon;Ding, Yan;Buhay, Christian J.;Kremitzki, Colin;Wang, Qiaoyan;Shen, Hua;Holder, Michael;Villasana, Donna;Nazareth, Lynne V.;Cree, Andrew;Courtney, Laura;Veizer, Joelle;Kotkiewicz, Holland;Cho, Ting-Jan;Koutseva, Natalia;Rozen, Steve;Muzny, Donna M.;Warren, Wesley C.;Gibbs, Richard A.;Wilson, Richard K.;Page, David C.
通讯作者：
Page, David C.
DOI：
10.1126/science.aae0344
发表时间：
2016-04-01
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gordon D;Huddleston J;Chaisson MJ;Hill CM;Kronenberg ZN;Munson KM;Malig M;Raja A;Fiddes I;Hillier LW;Dunn C;Baker C;Armstrong J;Diekhans M;Paten B;Shendure J;Wilson RK;Haussler D;Chin CS;Eichler EE
通讯作者：
Eichler EE