Repetitive DNA Sequence Detection and Its Role in the Human Genome

Overview

Journal Commun Biol

Specialty Biology

Date 2023 Sep 19

PMID 37726397

Authors

Xingyu Liao

Wufei Zhu

Juexiao Zhou

Haoyang Li

Xiaopeng Xu

Bin Zhang

Xin Gao

Affiliations

Soon will be listed here.

Abstract

Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

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References

Alexander R, Fang G, Rozowsky J, Snyder M, Gerstein M . Annotating non-coding regions of the genome. Nat Rev Genet. 2010; 11(8):559-71. DOI: 10.1038/nrg2814. View

van Bree E, Guimaraes R, Lundberg M, Blujdea E, Rosenkrantz J, White F . A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res. 2022; 32(4):656-670. PMC: 8997352. DOI: 10.1101/gr.275515.121. View

Kamath G, Shomorony I, Xia F, Courtade T, Tse D . HINGE: long-read assembly achieves optimal repeat resolution. Genome Res. 2017; 27(5):747-756. PMC: 5411769. DOI: 10.1101/gr.216465.116. View

Haubold B, Wiehe T . How repetitive are genomes?. BMC Bioinformatics. 2006; 7:541. PMC: 1769404. DOI: 10.1186/1471-2105-7-541. View

Lim C, Cech T . Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization. Nat Rev Mol Cell Biol. 2021; 22(4):283-298. PMC: 8221230. DOI: 10.1038/s41580-021-00328-y. View

Guo R, Li Y, He S, Ou-Yang L, Sun Y, Zhu Z . RepLong: de novo repeat identification using long read sequencing data. Bioinformatics. 2017; 34(7):1099-1107. DOI: 10.1093/bioinformatics/btx717. View

Buzdin A, Ustyugova S, Khodosevich K, Mamedov I, Lebedev Y, Hunsmann G . Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages. Genomics. 2003; 81(2):149-56. DOI: 10.1016/s0888-7543(02)00027-7. View

Riehl K, Riccio C, Miska E, Hemberg M . TransposonUltimate: software for transposon classification, annotation and detection. Nucleic Acids Res. 2022; 50(11):e64. PMC: 9226531. DOI: 10.1093/nar/gkac136. View

Bao W, Kojima K, Kohany O . Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6:11. PMC: 4455052. DOI: 10.1186/s13100-015-0041-9. View

10.

Ardeljan D, Taylor M, Ting D, Burns K . The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clin Chem. 2017; 63(4):816-822. PMC: 6177209. DOI: 10.1373/clinchem.2016.257444. View

11.

Li Y, Jiang N, Sun Y . AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. Plant Physiol. 2021; 188(2):955-970. PMC: 8825457. DOI: 10.1093/plphys/kiab524. View

12.

Albertin C, Simakov O, Mitros T, Wang Z, Pungor J, Edsinger-Gonzales E . The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 2015; 524(7564):220-4. PMC: 4795812. DOI: 10.1038/nature14668. View

13.

Ziaei Jam H, Li Y, DeVito R, Mousavi N, Ma N, Lujumba I . A deep population reference panel of tandem repeat variation. Nat Commun. 2023; 14(1):6711. PMC: 10593948. DOI: 10.1038/s41467-023-42278-3. View

14.

Chu C, Nielsen R, Wu Y . REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads. PLoS One. 2016; 11(3):e0150719. PMC: 4792456. DOI: 10.1371/journal.pone.0150719. View

15.

Liao X, Hu K, Salhi A, Zou Y, Wang J, Gao X . msRepDB: a comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Res. 2021; 50(D1):D236-D245. PMC: 8728181. DOI: 10.1093/nar/gkab1089. View

16.

Youssef N, Budd A, Bielawski J . Introduction to Genome Biology and Diversity. Methods Mol Biol. 2019; 1910:3-31. DOI: 10.1007/978-1-4939-9074-0_1. View

17.

Qian Z, Li Y, Yang J, Shi T, Li Z, Chen J . The chromosome-level genome of a free-floating aquatic weed Pistia stratiotes provides insights into its rapid invasion. Mol Ecol Resour. 2022; 22(7):2732-2743. DOI: 10.1111/1755-0998.13653. View

18.

Ponomaryova A, Rykova E, Gervas P, Cherdyntseva N, Mamedov I, Azhikina T . Aberrant Methylation of LINE-1 Transposable Elements: A Search for Cancer Biomarkers. Cells. 2020; 9(9). PMC: 7563416. DOI: 10.3390/cells9092017. View

19.

Touati R, Tajouri A, Mesaoudi I, Elloumi Oueslati A, Lachiri Z, Kharrat M . New methodology for repetitive sequences identification in X and Y chromosomes. Biomed Signal Process Control. 2020; 64:102207. PMC: 7572123. DOI: 10.1016/j.bspc.2020.102207. View

20.

Gonzalez J, Lenkov K, Lipatov M, Macpherson J, Petrov D . High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol. 2008; 6(10):e251. PMC: 2570423. DOI: 10.1371/journal.pbio.0060251. View