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利用DAFCA(染色质可及性的Dam辅助荧光标记)探索染色体组发生:整合染色质可及性与光学基因组图谱以增强结构变异检测

Exploring Chromoanagenesis with DAFCA (Dam Assisted Fluorescent Tagging of Chromatin Accessibility): Integrating Chromatin Accessibility and Optical Genome Mapping for Enhanced Structural Variant Detection.

作者信息

Nifker Gil, Ebenstein Yuval

机构信息

Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.

出版信息

Methods Mol Biol. 2025;2968:191-212. doi: 10.1007/978-1-0716-4750-9_11.


DOI:10.1007/978-1-0716-4750-9_11
PMID:40884645
Abstract

Chromatin, consisting of DNA, proteins, and RNA, is essential for eukaryotic genome organization and gene regulation, influencing gene expression through its accessibility. Not only that its the accessibility profile holds essential information on the cell type and state, but abnormal chromatin accessibility is also linked to genetic diseases like cancer and Alzheimer's. Traditional chromatin accessibility methods are next-generation sequencing (NGS) based and struggle with detecting repetitive and large-scale genomic variations. Optical Genome Mapping (OGM) provides high-resolution structural variation (SV) and copy number variation (CNV) detection. We introduce Dam Assisted Fluorescent tagging of Chromatin Accessibility (DAFCA) for OGM, validated in the GM12878 cell line. DAFCA combines chromatin accessibility profiling with SV and CNV detection, offering comprehensive insights into chromatin dynamics and genetic variation. This method has potential clinical applications by offering comprehensive insights into chromatin dynamics and genetic variation.

摘要

染色质由DNA、蛋白质和RNA组成,对真核生物基因组的组织和基因调控至关重要,通过其可及性影响基因表达。不仅其可及性图谱包含有关细胞类型和状态的重要信息,而且异常的染色质可及性还与癌症和阿尔茨海默病等遗传疾病有关。传统的染色质可及性方法基于下一代测序(NGS),在检测重复和大规模基因组变异方面存在困难。光学基因组图谱(OGM)可提供高分辨率的结构变异(SV)和拷贝数变异(CNV)检测。我们介绍了用于OGM的染色质可及性的Dam辅助荧光标记(DAFCA),并在GM12878细胞系中进行了验证。DAFCA将染色质可及性分析与SV和CNV检测相结合,为染色质动力学和遗传变异提供了全面的见解。该方法通过提供对染色质动力学和遗传变异的全面见解而具有潜在的临床应用价值。

相似文献

[1]
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Methods Mol Biol. 2025

[2]
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本文引用的文献

[1]
A comprehensive approach to evaluate genetic abnormalities in multiple myeloma using optical genome mapping.

Blood Cancer J. 2024-5-3

[2]
Optical Genome Mapping for Comprehensive Cytogenetic Analysis of Soft-Tissue and Bone Tumors for Diagnostic Purposes.

J Mol Diagn. 2024-5

[3]
Epigenetic regulation during cancer transitions across 11 tumour types.

Nature. 2023-11

[4]
Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays.

ACS Nano. 2023-5-23

[5]
Chromatin accessibility: methods, mechanisms, and biological insights.

Nucleus. 2022-12

[6]
Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets.

Science. 2022-5-27

[7]
Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors.

Genome Res. 2021-12

[8]
Chromatin accessibility regulates chemotherapy-induced dormancy and reactivation.

Mol Ther Nucleic Acids. 2021-8-8

[9]
GAGE mediates radio resistance in cervical cancers via the regulation of chromatin accessibility.

Cell Rep. 2021-8-31

[10]
Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of .

Life (Basel). 2021-8-23

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