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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...detection of repeat counts combined with methylation over AR or RP2 CpG islands (Johansson et al. 2023) or even using chromatin accessibility (Lee et al. 2020; Vollger et al. 2025).Long cell-free DNACell-free DNA (cfDNA) fragments circulating in bodily fluids like plasma and urine carry unique methylation...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...cost.The ability of nanopore sequencing to provide the methylation status of CpG sites on individual molecules allowed us to observe in detail asymmetric methylation gradients that form at the proximal end of D4Z4 repeat arrays and reach a saturation point at approximately the tenth repeat...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...(Li and Tollefsbol 2016; López-Otín et al. 2023). Among these, DNA methylation drift has emerged as the most extensively characterized component of epigenetic aging. It is typified by increased variance in methylation levels at specific CpG sites—termed drift-CpGs—over chronological age...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...in neurons but not B or T cellsIt is known that the chromatin accessibility of CpG islands is related to the absence of DNA methylation and the presence of specific histone modifications (Thomson et al. 2010; Bian et al. 2011; Wachter et al. 2014; Li et al. 2016b; Kurup et al. 2019; Hughes et al. 2020). We...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...) and then tested each SNV for association with DNA methylation levels of the target CpG (median of 1168 SNVs tested per locus). After selecting the lead SNV for each CpG associated with a candidate mSTR, we repeated the STR:CpG association analysis using only those samples that were homozygous for the major allele...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...al. 1992; Knight et al. 1993) or the gene promoter in progressive myoclonus epilepsy type 1 (Lafrenière et al. 1997; Virtaneva et al. 1997) causes hypermethylation of the repeat and adjacent CpG islands and pathogenically silences gene transcription. While this mechanism has been known for some time...
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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...(Supplemental Fig. S17A). We found that the number of significant differentially methylated CpGs in fibroblasts is higher than in iPSCs (Supplemental Fig. S18A,B). Next, we assessed the methylation status of the Y Chromosome in the two cell types. Primary fibroblasts displayed a heterogeneous pattern of CpG...
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Research: Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family
- Alex de Mendoza,
- Jahnvi Pflueger,
- and Ryan Lister
Genome Res. August 2019 29: 1277-1286; Published in Advance June 25, 2019, doi:10.1101/gr.243774.118
...methylome by whole- bisulfite sequencing (WGBS) of the matched Strigamia genomic DNA used for DAP-seq. This revealed that CopiaMBD DAP-seq peaks were strongly enriched in highly methylated regions, as well as showing a high density of CpGs (Fig. 2A). Additionally, CopiaMBD peaks showed motifs enriched in CpG...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...for this article.] In mammalian DNA, cytosines within CpG dinucleotides are heavily methylated throughout the , yet there are several discrete “islands” that contain a high frequency of unmethylated CpG sites. These are called CpG islands (CGI), and their identification has long been considered important...
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Research: CG dinucleotides enhance promoter activity independent of DNA methylation
- Dominik Hartl,
- Arnaud R. Krebs,
- Ralph S. Grand,
- Tuncay Baubec,
- Luke Isbel,
- Christiane Wirbelauer,
- Lukas Burger,
- and Dirk Schübeler
Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
...of several nucleotides, it is unclear whether lower complexity sequence features, such as dinucleotides, contribute independently to gene activity. CpG is the most studied dinucleotide in mammalian s and the site of cytosine methylation (Bird 1980; Lister and Ecker 2009; Stadler et al. 2011). In mammals...
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