Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.

IF 2.5 3区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Briefings in Functional Genomics Pub Date : 2024-04-22 DOI:10.1093/bfgp/elae014

Anupam Banerjee, She Zhang, Ivet Bahar

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引用次数: 0

Abstract

Characterization of the spatiotemporal properties of the chromatin is essential to gaining insights into the physical bases of gene co-expression, transcriptional regulation and epigenetic modifications. The Gaussian network model (GNM) has proven in recent work to serve as a useful tool for modeling chromatin structural dynamics, using as input high-throughput chromosome conformation capture data. We focus here on the exploration of the collective dynamics of chromosomal structures at hierarchical levels of resolution, from single gene loci to topologically associating domains or entire chromosomes. The GNM permits us to identify long-range interactions between gene loci, shedding light on the role of cross-correlations between distal regions of the chromosomes in regulating gene expression. Notably, GNM analysis performed across diverse cell lines highlights the conservation of the global/cooperative movements of the chromatin across different types of cells. Variations driven by localized couplings between genomic loci, on the other hand, underlie cell differentiation, underscoring the significance of the four-dimensional properties of the genome in defining cellular identity. Finally, we demonstrate the close relation between the cell type-dependent mobility profiles of gene loci and their gene expression patterns, providing a clear demonstration of the role of chromosomal 4D features in defining cell-specific differential expression of genes.

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基因组结构动力学：从对 Hi-C 数据的高斯网络分析中获得的启示。

要深入了解基因共表达、转录调控和表观遗传修饰的物理基础，染色质时空特性的表征至关重要。最近的研究证明，高斯网络模型（GNM）是利用高通量染色体构象捕获数据建立染色质结构动态模型的有用工具。在此，我们将重点放在探索染色体结构的分层动态，从单基因位点到拓扑关联域或整个染色体。GNM 使我们能够识别基因位点之间的长程相互作用，从而揭示染色体远端区域之间的交叉关联在调控基因表达中的作用。值得注意的是，在不同细胞系中进行的 GNM 分析凸显了不同类型细胞中染色质全局/合作运动的一致性。另一方面，基因组位点间局部耦合驱动的变异是细胞分化的基础，凸显了基因组的四维特性在确定细胞身份方面的重要性。最后，我们证明了基因位点随细胞类型而变化的流动性特征与其基因表达模式之间的密切关系，清楚地表明了染色体四维特征在确定细胞特异性基因差异表达中的作用。

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

Briefings in Functional Genomics BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

6.30

自引率

2.50%

发文量

审稿时长

6-12 weeks

期刊介绍： Briefings in Functional Genomics publishes high quality peer reviewed articles that focus on the use, development or exploitation of genomic approaches, and their application to all areas of biological research. As well as exploring thematic areas where these techniques and protocols are being used, articles review the impact that these approaches have had, or are likely to have, on their field. Subjects covered by the Journal include but are not restricted to: the identification and functional characterisation of coding and non-coding features in genomes, microarray technologies, gene expression profiling, next generation sequencing, pharmacogenomics, phenomics, SNP technologies, transgenic systems, mutation screens and genotyping. Articles range in scope and depth from the introductory level to specific details of protocols and analyses, encompassing bacterial, fungal, plant, animal and human data. The editorial board welcome the submission of review articles for publication. Essential criteria for the publication of papers is that they do not contain primary data, and that they are high quality, clearly written review articles which provide a balanced, highly informative and up to date perspective to researchers in the field of functional genomics.