Genomic architecture constrained placental mammal X Chromosome evolution.
Genomic architecture constrained placental mammal X Chromosome evolution.
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DOI：
10.1101/gr.275274.121
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发表时间：
2021-08
期刊：
影响因子：
7
通讯作者：
Murphy WJ
中科院分区：
文献类型：
--
作者：
Brashear WA;Bredemeyer KR;Murphy WJ
Susumu Ohno 提出，由于剂量补偿，哺乳动物 X 染色体的基因内容应保持高度保守。 X染色体连锁（基因顺序）保守性在胎盘哺乳动物中广泛存在，但不属于Ohno的预测范围，可能是基因内容选择或可能破坏X染色体失活（XCI）的重排选择的间接结果。之前人类和小鼠 X 染色体序列之间的比较表明，尽管单拷贝 X 染色体基因在物种之间是保守的，但大多数扩增基因是独立获得的。为了更好地了解胎盘哺乳动物中 X 连锁基因内容和连锁保守性的进化和功能限制，我们将来自家猫的新的、高质量、长读长的 X 染色体参考装配体（包含 19.3 Mb 的目标 BAC 克隆序列）与猪、人类和小鼠装配体进行了比对。对公共数据库中带注释的 X 连锁直向同源物的综合分析表明，大多数扩增基因家族存在于祖先胎盘 X 染色体上。我们从 F1 家猫/亚洲豹猫杂交中生成了家猫 Hi-C 接触图，并证明了灵长类和啮齿类灭活 X 染色体中发现的二分结构的形成。基因顺序和重组模式的保守可归因于对超级环形成所需的三维基因组结构的强烈选择性限制。具有重新排列的 X 染色体的物种保留了 XCI 过程中对超级环形成至关重要的祖先顺序和基因座的相对间距，并通过补偿性倒位进化来维持这些远程物理相互作用。
Susumu Ohno proposed that the gene content of the mammalian X Chromosome should remain highly conserved due to dosage compensation. X Chromosome linkage (gene order) conservation is widespread in placental mammals but does not fall within the scope of Ohno's prediction and may be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most ampliconic genes were independently acquired. To better understand the evolutionary and functional constraints on X-linked gene content and linkage conservation in placental mammals, we aligned a new, high-quality, long-read X Chromosome reference assembly from the domestic cat (incorporating 19.3 Mb of targeted BAC clone sequence) to the pig, human, and mouse assemblies. A comprehensive analysis of annotated X-linked orthologs in public databases demonstrated that the majority of ampliconic gene families were present on the ancestral placental X Chromosome. We generated a domestic cat Hi-C contact map from an F1 domestic cat/Asian leopard cat hybrid and demonstrated the formation of the bipartite structure found in primate and rodent inactivated X Chromosomes. Conservation of gene order and recombination patterns is attributable to strong selective constraints on three-dimensional genomic architecture necessary for superloop formation. Species with rearranged X Chromosomes retain the ancestral order and relative spacing of loci critical for superloop formation during XCI, with compensatory inversions evolving to maintain these long-range physical interactions.
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DOI：
10.1093/bioinformatics/btx346
发表时间：
2017-10-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Serra E
通讯作者：
Serra E
在小鼠X染色体上具有独特的基因组和表观基因组特征的大型男性生殖细胞特异性DNA结构域。
DOI：
10.1093/dnares/dst030
发表时间：
2013-12
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Ikeda R;Shiura H;Numata K;Sugimoto M;Kondo M;Mise N;Suzuki M;Greally JM;Abe K
通讯作者：
Abe K
影响因子：
3.5
作者：
Horakova, Andrea H.;Moseley, Shawn C.;Chadwick, Brian P.
通讯作者：
Chadwick, Brian P.
影响因子：
2.6
作者：
Darrow, Emily M.;Seberg, Andrew P.;Chadwick, Brian P.
通讯作者：
Chadwick, Brian P.
DOI：
10.1073/pnas.0408021101
发表时间：
2004-12-14
影响因子：
11.1
作者：
Chadwick, BP;Willard, HF
通讯作者：
Willard, HF