Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome.

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS
Maryam Jehangir, Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum, Thanyapat Thong, Pakpoom Aramsirirujiwet, Artem Lisachov, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Kornsorn Srikulnath
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Abstract

Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.

Abstract Image

Hi-C测序揭示了猕猴谱系中动态三维染色质相互作用:来自Fea猕猴基因组染色体融合的见解。
真核生物在不同谱系或物种中具有不同数量和结构的特征染色体。物种的进化轨迹可能受到自发的基因组重排的影响。染色体融合彻底改变了核型。然而,染色体融合的机制和后果,特别是在麂物种中,知之甚少。三维(3D)基因组学的最新研究进展,特别是高通量染色质构象捕获(Hi-C)测序,使染色体融合鉴定成为可能,并为三种麂物种(Muntiacus muntjak, M. reevesi和M. crinifrons)提供了机制见解。这项研究的目的是揭示濒危物种Fea's montjac (Muntiacus feae)潜在的基因组重排模式,这些特征之前没有被研究过。采用深度Hi-C测序(31.42 ×覆盖率)揭示了Fea的麂基因组的三维染色质结构。鉴定了高丰度转座因子可能介导的重复染色体融合模式。对比Hi-C图谱显示,Fea麂的性染色体与M. reevesi的常染色体之间存在连锁同源性,表明融合可能在谱系性染色体的进化中发挥了关键作用。拓扑相关结构域(TAD)的物种水平动态表明,由于重复的染色体融合,TAD的组织可能会因差异染色体相互作用而改变。然而,关于TADs对麂基因组进化影响的研究还不够。这项研究为Fea的麂提供了Hi-C数据,为今后在染色体水平上研究染色质构象的进化模式提供了基因组资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
ACS Applied Bio Materials
ACS Applied Bio Materials Chemistry-Chemistry (all)
CiteScore
9.40
自引率
2.10%
发文量
464
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