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微卫星密度图谱展示了完整参考人类基因组中短串联重复序列的聚集。

Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome.

机构信息

Bioinformatic Center, College of Biology, Hunan University, Lushan Road (S), Yuelu District, Changsha, 410082, China.

Faculty of Agriculture, Saga University, Saga, 840-8502, Japan.

出版信息

BMC Genomics. 2024 Oct 14;25(1):960. doi: 10.1186/s12864-024-10843-9.

DOI:10.1186/s12864-024-10843-9
PMID:39402450
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11477012/
Abstract

BACKGROUND

Microsatellites are increasingly realized to have biological significance in human genome and health in past decades, the assembled complete reference sequence of human genome T2T-CHM13 brought great help for a comprehensive study of short tandem repeats in the human genome.

RESULTS

Microsatellites density landscapes of all 24 chromosomes were built here for the first complete reference sequence of human genome T2T-CHM13. These landscapes showed that short tandem repeats (STRs) are prone to aggregate characteristically to form a large number of STRs density peaks. We classified 8,823 High Microsatellites Density Peaks (HMDPs), 35,257 Middle Microsatellites Density Peaks (MMDPs) and 199, 649 Low Microsatellites Density Peaks (LMDPs) on the 24 chromosomes; and also classified the motif types of every microsatellites density peak. These STRs density aggregation peaks are mainly composing of a single motif, and AT is the most dominant motif, followed by AATGG and CCATT motifs. And 514 genomic regions were characterized by microsatellite density feature in the full T2T-CHM13 genome.

CONCLUSIONS

These landscape maps exhibited that microsatellites aggregate in many genomic positions to form a large number of microsatellite density peaks with composing of mainly single motif type in the complete reference genome, indicating that the local microsatellites density varies enormously along the every chromosome of T2T-CHM13.

摘要

背景

在过去的几十年中，人们越来越意识到微卫星在人类基因组和健康中具有重要的生物学意义，人类基因组 T2T-CHM13 的完整参考序列的组装为全面研究人类基因组中的短串联重复序列提供了极大的帮助。

结果

我们首次为人类基因组 T2T-CHM13 的完整参考序列构建了所有 24 条染色体的微卫星密度图谱。这些图谱表明，短串联重复序列（STRs）倾向于聚集形成大量的 STRs 密度峰。我们在 24 条染色体上分类了 8823 个高微卫星密度峰（HMDPs）、35257 个中微卫星密度峰（MMDPs）和 199649 个低微卫星密度峰（LMDPs）；并对每个微卫星密度峰的基序类型进行了分类。这些 STRs 密度聚集峰主要由单个基序组成，其中 AT 是最主要的基序，其次是 AATGG 和 CCATT 基序。在完整的 T2T-CHM13 基因组中，有 514 个基因组区域具有微卫星密度特征。

结论

这些图谱表明，微卫星在许多基因组位置聚集，形成了大量的微卫星密度峰，这些密度峰主要由单一的基序类型组成，表明 T2T-CHM13 每条染色体上的局部微卫星密度差异巨大。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/df3e251b2654/12864_2024_10843_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/5e0f635f8624/12864_2024_10843_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/c59ce67b2468/12864_2024_10843_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/ba79bd5142c6/12864_2024_10843_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/df3e251b2654/12864_2024_10843_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/5e0f635f8624/12864_2024_10843_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/c59ce67b2468/12864_2024_10843_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/ba79bd5142c6/12864_2024_10843_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3163/11477012/df3e251b2654/12864_2024_10843_Fig4_HTML.jpg

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本文引用的文献

1
The complete sequence of a human Y chromosome.人类 Y 染色体的完整序列。
Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23.
2
Genome-wide identification and characterization of microsatellite markers within the Avipoxviruses.禽痘病毒微卫星标记的全基因组鉴定与特征分析
3 Biotech. 2022 May;12(5):113. doi: 10.1007/s13205-022-03169-4. Epub 2022 Apr 13.
3
A complete reference genome improves analysis of human genetic variation.完整的参考基因组提高了人类遗传变异分析的能力。
Science. 2022 Apr;376(6588):eabl3533. doi: 10.1126/science.abl3533. Epub 2022 Apr 1.
4
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.从端粒到端粒：人类重复元件的转录和表观遗传状态。
Science. 2022 Apr;376(6588):eabk3112. doi: 10.1126/science.abk3112. Epub 2022 Apr 1.
5
The complete sequence of a human genome.人类基因组的完整序列。
Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31.
6
Segmental duplications and their variation in a complete human genome.人类全基因组中的串联重复序列及其变异。
Science. 2022 Apr;376(6588):eabj6965. doi: 10.1126/science.abj6965. Epub 2022 Apr 1.
7
Epigenetic patterns in a complete human genome.人类全基因组中的表观遗传模式。
Science. 2022 Apr;376(6588):eabj5089. doi: 10.1126/science.abj5089. Epub 2022 Apr 1.
8
Complete genomic and epigenetic maps of human centromeres.人类着丝粒的完整基因组和表观基因组图谱。
Science. 2022 Apr;376(6588):eabl4178. doi: 10.1126/science.abl4178. Epub 2022 Apr 1.
9
An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?mtSSRs 的实证分析：微卫星分布模式能否解释植物线粒体基因组的进化？
Funct Integr Genomics. 2022 Feb;22(1):35-53. doi: 10.1007/s10142-021-00815-7. Epub 2021 Nov 9.
10
Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions.鱼类微卫星 DNA 的全基因组特征：在基因组特定区域中对其丰度和频率的调查和分析。
BMC Genomics. 2021 Jun 7;22(1):421. doi: 10.1186/s12864-021-07752-6.