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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
..., the maintenance of this fine-scale pattern with increasing methylation is evident, and the phasic methylation pattern beginning near the start of DUX4 exon 1 was seen with repeats from both chromosomes and with increasing overall methylation levels.The 180-nt periodicity of CpG methylation suggested...
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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
...of the fifth carbon atom of cytosine, typically in mammals in a CG dinucleotide context. This dinucleotide is depleted largely across the and found predominantly in clusters known as “CpG islands” (Bird 1986). Cytosine methylation is catalyzed by methyltransferases (e.g., DNMT1, DNMT3A) that transfer a methyl...
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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
...-related increase (D) or decrease (E) in methylation variance. (F,G) Genomic enrichment of positive and negative drift-CpGs (F: CpG island-related; G: gene-related features). (H,I) Genomic enrichment of drift- and clock-CpGs (H: CpG island-related; I: gene-related features). (J) Scatter plot of initial (young...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...not directly abolishing a CpG site have enhanced reference allele expression in one condition and enhanced alternate allele expression in the other (Fig. 4B), suggesting mechanisms that reverse the direction of ASE depending on methylation status.View larger version: In this window In a new window Figure 4...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...expresses Xist, is unmethylated (haplotype 1), whereas the active X (Xist silenced) is the methylated allele (haplotype 2). For all other CpG islands on the X Chromosome, methylation-based clustering of reads assigns Xa to the group of low-methylation reads and Xi to the group of high-methylation reads (Fig...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
...with four imprinting disorders. Methylated (>75%) or unmethylated (<25%) fraction at IC1 in H19 and IC2 in KCNQ1OT1. Haplotype-resolved methylation fraction is also shown for the CpG island within SNURF-SNRPN that is evaluated when testing for PWS or AS. Two samples have either gain (GM19473) or loss (HG...
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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...increase was observed for both CpGs in the filled allele: Methylation at +740 CpG increased to 75.7% ± 6.1% (P = 0.013), whereas the more distant +1198 CpG increased to 63.6% ± 5.3% (P = 0.167). An opposite change in methylation was observed in the adult testis (Fig. 2C; Supplemental Fig. 4C). Both CpGs...
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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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Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
- Yuelin Liu,
- Xuan Cindy Li,
- Farid Rashidi Mehrabadi,
- Alejandro A. Schäffer,
- Drew Pratt,
- David R. Crawford,
- Salem Malikić,
- Erin K. Molloy,
- Vishaka Gopalan,
- Stephen M. Mount,
- Eytan Ruppin,
- Kenneth D. Aldape,
- and S. Cenk Sahinalp
Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
...-informative CpG sites identified by Sgootr are in inter-CpG island (CGI) regions, as opposed to intra-CGIs, which have been the main regions of interest in genomic methylation-related analyses.The problem of algorithmically inferring a phylogenetic tree that may be interpreted as a tumor progression history from...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...on the distribution of mean methylation levels. Advances in whole- bisulfite sequencing (WGBS) have enabled the characterization of DNA methylation haplotypes (MHAPs), representing CpG sites from the same read fragment on a single chromosome, and the subsequent identification of methylation haplotype blocks (MHBs...

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