Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition.
Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition.
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DOI：
10.1093/molbev/msab148
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发表时间：
2021-08-23
影响因子：
10.7
通讯作者：
Carbone L
中科院分区：
文献类型：
--
作者：
Hartley GA;Okhovat M;O'Neill RJ;Carbone L
着丝粒是细胞分裂过程中染色体分离所必需的功能保守的染色体位点，但它们在物种间显示出高度的序列多样性。尽管存在变异，但着丝粒的一个几乎普遍的特征是存在重复序列，如DNA卫星和转座因子（TE）。由于其快速演变的核型，长臂猿代表了一个引人注目的模型，以调查分歧的功能着丝粒序列在短的进化时间尺度。在这项研究中，我们使用ChIP-seq，RNA-seq，和荧光原位杂交，全面调查的着丝粒重复内容的四个现存的gibliotoms属（Hoolock，Hylobates，Nomelae，Siamang）。在所有的gigatrium属，我们发现，CENP-A核小体和DNA-蛋白质的接口与内部动粒优先结合逆转录元件的广泛的类，而不是卫星DNA。一个先前确定的gibbon特异性复合反转录转座子，LAVA，已知在一个gibbon属（Hoolock）的着丝粒区域内扩展，显示着丝粒和物种特异性序列差异，可能是由于其共同选择的着丝粒功能。当解剖的着丝粒卫星组成，我们发现的反式元件衍生的大卫星SST 1的存在下，在多个着丝粒的Hoolock，而α-卫星代表占主导地位的卫星在其他属，进一步表明一个独立的进化轨迹Hoolock着丝粒。最后，使用从头组装的着丝粒序列，我们确定，转录本源自gillocyte着丝粒重演的物种特异性TE组成。结合起来，我们的数据揭示了动态变化的重复内容，定义giglycerium着丝粒，并符合广泛的核型多样性在这个谱系。
Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq, and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus, and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.
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影响因子：
4.9
作者：
Fernandes, Jason D.;Zamudio-Hurtado, Armando;Haeussler, Maximilian
通讯作者：
Haeussler, Maximilian
影响因子：
4.5
作者：
Chueh, Anderly C.;Northrop, Emma L.;Brettingham-Moore, Kate H.;Choo, K. H. Andy;Wong, Lee H.
通讯作者：
Wong, Lee H.
影响因子：
4.5
作者：
Du Y;Topp CN;Dawe RK
通讯作者：
Dawe RK
影响因子：
7
作者：
Capozzi O;Carbone L;Stanyon RR;Marra A;Yang F;Whelan CW;de Jong PJ;Rocchi M;Archidiacono N
通讯作者：
Archidiacono N
影响因子：
3.3
作者：
Carbone L;Harris RA;Mootnick AR;Milosavljevic A;Martin DI;Rocchi M;Capozzi O;Archidiacono N;Konkel MK;Walker JA;Batzer MA;de Jong PJ
通讯作者：
de Jong PJ