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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...Methods 7: 461–472. doi:10.1038/nmeth.1459 ↵Galeone V, Dabernig-Heinz J, Lohde M, Brandt C, Kohler C, Wagner GE, Hölzer M. 2025. Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications. BMC Genomics 26: 394. doi...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...to the transcription machinery. As a result, transcription levels can undergo repression leading to a silencing effect of the associated gene. The dominant form of DNA methylation in terminally differentiated human cells occurs proximal to a guanosine residue, and the resulting loci are often referred to as CpG sites...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
....oakey@kcl.ac.ukAbstractHydroxycarbamide (HC, hydroxyurea) is a cytoreductive drug inducing cell cycle blockade. However, emerging evidence suggests that HC plays a role in the modulation of transcription through the activity of transcription factors and DNA methylation. Examining the global mechanism of action of HC in the context...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species, such as the roundworm (Caenorhabditis elegans, “worm” hereafter) or fruit...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...significantly enriched in genes with sequence-specific DNA-binding transcription factor activity (GO:3700; P < 10#2;12), particularly those with a homeobox domain (Pfam, P < 10#2;6). They were also enriched in genes with promoter regions, which comprise motives for binding of POU2F1 (P = 1.1 3 10#2;4), growth...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...) contributing 3.9 Mb of the size difference. Conversely, Young Ty1 LTRs that were preferentially removed in temperate s contributed 4.9 Mb or 14.1% to TE-content difference (Fig. 4F), with the ji_AC215728_13156 family contributing 2.9 Mb of this size difference. Notably, the xilon_diguus family is found in DNA...
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Method: Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
- Shijia Zhu,
- John Beaulaurier,
- Gintaras Deikus,
- Tao P. Wu,
- Maya Strahl,
- Ziyang Hao,
- Guanzheng Luo,
- James A. Gregory,
- Andrew Chess,
- Chuan He,
- Andrew Xiao,
- Robert Sebra,
- Eric E. Schadt,
- and Gang Fang
Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
...coexist with other forms of DNA modifications. These differences between bacterial and eukaryotic methylomes call for critical attention in the interpretation of putative m6dA calls based on SMRT sequencing to avoid misinterpretation of false-positive events. The methods and the overall framework we...
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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...of DNA Elements Project) annotations for this domain as viewed in the UCSC Genome Browser reveal CTCF transcription factor binding, Figure 2. Lymphoid cell fraction in TGCT samples. (A) Genome-wide methylation β-density distribution in TGCT subtypes, without and after correction for lymphoid infiltrates...
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Research: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
- Robert J. Schmitz,
- Yupeng He,
- Oswaldo Valdés-López,
- Saad M. Khan,
- Trupti Joshi,
- Mark A. Urich,
- Joseph R. Nery,
- Brian Diers,
- Dong Xu,
- Gary Stacey,
- and Joseph R. Ecker
Genome Res. October 2013 23: 1663-1674; Published in Advance June 5, 2013, doi:10.1101/gr.152538.112
...methylomes, and transcriptomes in the parents and RILs. This also enabled us to understand how DNA methylation patterns are established, inherited, andmaintained as they segregate through a complex genetic population. The vast majority of identified DMRs cosegregated with the genetic background from which...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...adaptations to exercise, are controlled through the interaction of proximal and distal regulatory domains on DNA that interact in 3D space (Schoenfelder and Fraser 2019). Gene regulatory circuits, comprising chromatin regulatory domains, transcription factors (TFs), and their target genes, represent...

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