ArticleGenome research2017
The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 62 citations in OpenAlex.
- Widespread distribution of Alu/Alu-mediated genomic rearrangement predisposing to a broad range of Mendelian disease and cancer in human populations.Genome medicine · 2026Article
- Genome-scale DNA methylome and transcriptome profiling of midgut of Bombyx mori infected with BmCPV.Scientific data · 2026Article
- Methylation of LINE-1 and Alu repetitive sequence in keloid.Scientific reports · 2025Article
- Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer.NAR cancer · 2025Article
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- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo.EMBO reports · 2024Review
- Important role of DNA methylation hints at significant potential in tuberculosis.Archives of microbiology · 2024Review
- Alu RNA fold links splicing with signal recognition particle proteins.Nucleic acids research · 2023Article
- Exposure to smoky coal combustion emissions and leukocyte Alu retroelement copy number.Carcinogenesis · 2023Article
- Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci.Cancer research · 2023Article
- Reshaping the tumour immune microenvironment in solid tumours via tumour cell and immune cell DNA methylation: from mechanisms to therapeutics.British journal of cancer · 2023Review
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- Article
- Anchor-based bisulfite sequencing determines genome-wide DNA methylation.Communications biology · 2022Article
- Article
- Localization Matters: Epigenetic Regulation of Natural Killer Cells in Different Tissue Microenvironments.Frontiers in immunology · 2022Review
- Transposable elements that have recently been mobile in the human genome.BMC genomics · 2021Article
- Elevated Alu retroelement copy number among workers exposed to diesel engine exhaust.Occupational and environmental medicine · 2021Article
- Circular RNA in colorectal cancer.Journal of cellular and molecular medicine · 2021Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome. DNA methylation profiles of Alu repeats have been analyzed in colon cancers and normal tissues using NSUMA and whole-genome bisulfite sequencing. Normal cells show a low proportion of unmethylated Alu (1%-4%) that may increase up to 10-fold in cancer cells. In normal cells, unmethylated Alu elements tend to locate in the vicinity of functionally rich regions and display epigenetic features consistent with a direct impact on genome regulation. In cancer cells, Alu repeats are more resistant to hypomethylation than other retroelements. Genome segmentation based on high/low rates of Alu hypomethylation allows the identification of genomic compartments with differential genetic, epigenetic, and transcriptomic features. Alu hypomethylated regions show low transcriptional activity, late DNA replication, and its extent is associated with higher chromosomal instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate genome.
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