用模拟数据辅助实验数据,推断酵母染色体着丝粒位置。
Simulation-based inference of yeast centromeres
- 结合实验Hi-C图谱与模拟接触图,随机推断着丝粒位置。
- 在无先验定位情况下准确识别全部着丝粒。
- 适合研究染色质构象与基因组结构的学者参考。
染色质折叠与染色体空间排列对DNA复制和基因表达至关重要,异常折叠可能导致功能失调甚至疾病。在真核生物中,着丝粒对染色体正确分离与折叠起关键作用。尽管已有大量基于基因组从头测序和注释分析的研究,大多数酵母物种的着丝粒位置仍难以确定。近年来,基于高通量测序的全基因组染色体构象捕获(Hi-C)已成为研究染色体结构的重要方法。部分研究利用Hi-C数据对每个着丝粒给出点估计,但这些方法严重依赖良好预定位。本文提出一种新方法,基于实验Hi-C图谱与模拟接触图,以随机方式推断出裂殖酵母中所有着丝粒的位置。
原文摘要 · Abstract (English)
The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes, centromeres are essential for proper chromosome segregation and folding. Despite extensive research using de novo sequencing of genomes and annotation analysis, centromere locations in yeasts remain difficult to infer and are still unknown in most species. Recently, genome-wide chromosome conformation capture coupled with next-generation sequencing (Hi-C) has become one of the leading methods to investigate chromosome structures. Some recent studies have used Hi-C data to give a point estimate of each centromere, but those approaches highly rely on a good pre-localization. Here, we present a novel approach that infers in a stochastic manner the locations of all centromeres in budding yeast based on both the experimental Hi-C map and simulated contact maps.
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