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在人类3号染色体的T2T-CHM13组装中对级联α卫星高阶重复序列进行精确鉴定。

Precise identification of cascading alpha satellite higher order repeats in T2T-CHM13 assembly of human chromosome 3.

作者信息

Glunčić Matko, Vlahović Ines, Rosandić Marija, Paar Vladimir

机构信息

Matko Glunčić, Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, 10000 Zagreb, Croatia,

出版信息

Croat Med J. 2024 Jun 13;65(3):209-219. doi: 10.3325/cmj.2024.65.209.

DOI:10.3325/cmj.2024.65.209
PMID:38868967
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11157248/
Abstract

AIM: To precisely identify and analyze alpha-satellite higher-order repeats (HORs) in T2T-CHM13 assembly of human chromosome 3. METHODS: From the recently sequenced complete T2T-CHM13 assembly of human chromosome 3, the precise alpha satellite HOR structure was computed by using the novel high-precision GRM2023 algorithm with global repeat map (GRM) and monomer distance (MD) diagrams. RESULTS: The major alpha satellite HOR array in chromosome 3 revealed a novel cascading HOR, housing 17mer HOR copies with subfragments of periods 15 and 2. Within each row in the cascading HOR, the monomers were of different types, but different rows within the same cascading 17mer HOR contained more than one monomer of the same type. Each canonical 17mer HOR copy comprised 17 monomers belonging to 16 different monomer types. Another pronounced 10mer HOR array was of the regular Willard's type. CONCLUSION: Our findings emphasize the complexity within the chromosome 3 centromere as well as deviations from expected highly regular patterns.

摘要

目的：精确识别和分析人类3号染色体T2T-CHM13组装体中的α卫星高阶重复序列（HORs）。 方法：从最近测序的人类3号染色体完整T2T-CHM13组装体中，使用具有全局重复图谱（GRM）和单体距离（MD）图的新型高精度GRM2023算法计算精确的α卫星HOR结构。 结果：3号染色体中的主要α卫星HOR阵列显示出一种新型级联HOR，包含17聚体HOR拷贝以及周期为15和2的亚片段。在级联HOR的每一行中，单体类型不同，但同一级联17聚体HOR内的不同行包含不止一个相同类型的单体。每个典型的17聚体HOR拷贝由属于16种不同单体类型的17个单体组成。另一个明显的10聚体HOR阵列是规则的威拉德类型。 结论：我们的研究结果强调了3号染色体着丝粒内的复杂性以及与预期高度规则模式的偏差。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/1487e2efdebf/CroatMedJ_65_0209-F6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/06d6ffb5803a/CroatMedJ_65_0209-F1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/d46a0306d182/CroatMedJ_65_0209-F2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/22c65ada305c/CroatMedJ_65_0209-F3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/a1ff4f2d3d98/CroatMedJ_65_0209-F4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/2387057747aa/CroatMedJ_65_0209-F5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/1487e2efdebf/CroatMedJ_65_0209-F6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/06d6ffb5803a/CroatMedJ_65_0209-F1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/d46a0306d182/CroatMedJ_65_0209-F2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/22c65ada305c/CroatMedJ_65_0209-F3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/a1ff4f2d3d98/CroatMedJ_65_0209-F4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/2387057747aa/CroatMedJ_65_0209-F5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8267/11157248/1487e2efdebf/CroatMedJ_65_0209-F6.jpg

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Precise identification of cascading alpha satellite higher order repeats in T2T-CHM13 assembly of human chromosome 3.

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[2]
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[3]
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引用本文的文献

[1]
Efficient genome monomer higher-order structure annotation and identification using the GRMhor algorithm.

Bioinform Adv. 2024-11-28

本文引用的文献

[1]
Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly.

Sci Rep. 2023-9-2

[2]
TRASH: Tandem Repeat Annotation and Structural Hierarchy.

Bioinformatics. 2023-5-4

[3]
HiCAT: a tool for automatic annotation of centromere structure.

Genome Biol. 2023-3-28

[4]
Comprehensive variant discovery in the era of complete human reference genomes.

Nat Methods. 2023-1

[5]
Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution.

Life Sci Alliance. 2023-1

[6]
Automated annotation of human centromeres with HORmon.

Genome Res. 2022-6

[7]
A classical revival: Human satellite DNAs enter the genomics era.

Semin Cell Dev Biol. 2022-8

[8]
The complete sequence of a human genome.

Science. 2022-4

[9]
Epigenetic patterns in a complete human genome.

Science. 2022-4

[10]
Complete genomic and epigenetic maps of human centromeres.

Science. 2022-4

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