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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...), whereas MAPLE utilizes an ensemble supervised learning strategy to infer gene activity scores from DNA methylation features (Uzun et al. 2021). However, these methods also have notable limitations: (1) Some existing methods are constrained by their unidirectional prediction capability, limiting...
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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
....DiscussionEnDeep4mC achieves state-of-the-art prediction performance and provides novel insights into the evolutionary dynamics of DNA 4mC modification. A key insight is its enhanced intraclass transferability for prokaryotes, as evidenced in cross-species predictions. These observations are consistent...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
.... 2010. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci 107: 21931–21936. doi:10.1073/pnas.1016071107 ↵The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human . Nature 489: 57–74. doi:10.1038/nature11247...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...of nucleosomes make DNA more accessible for key regulators of transcription, including transcription factors, enhancers, or repressors. However, the routine and efficient measurement of -wide protection through regulatory DNA-binding proteins (DBPs) is not yet established. Recently, a minor fraction of double...
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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
...genes (Khandekar et al. 2007; Levine 2010) or a pattern of biological significance. To delve into this question, we analyzed the genomic location of CREs across a panel of 70 adult and embryonic human cell types available from the Encyclopedia of DNA Elements (ENCODE) Project (The ENCODE Project...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...and is applied to the prediction of cytosine methylation status. The methylation probability for the CpG sites, ranging from zero to one, is computed using a sigmoid function at the output layer. (Right) Selected clinical applications of the HK model: (1) deducing the placenta-derived cfDNA by the methylation...
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Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
...a particular role in active enhancer activity (Liu et al. 2016). In concordance with the depletion of the CTCF DNA binding motif, AP-1 hotspots had the least CTCF binding signal of the three defined classes (Fig. 2D). Further, AP-1 hotspots located at CTCF-driven loop anchors show significantly less binding...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
.... Compared with WT mice, the frequencies of long cfDNA molecules >1 kb in Dffb−/− mice were consistently lower, whereas the corresponding frequencies in Dnase1−/− mice were higher, and such an increasing pattern was further enhanced in Dnase1l3−/− mice and mice with double deletion of Dnase1 and Dnase1l3...
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Research: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
- Elise A. Mahé,
- Thierry Madigou,
- Aurélien A. Sérandour,
- Maud Bizot,
- Stéphane Avner,
- Frédéric Chalmel,
- Gaëlle Palierne,
- Raphaël Métivier,
- and Gilles Salbert
Genome Res. June 2017 27: 947-958; Published in Advance April 10, 2017, doi:10.1101/gr.211466.116
.... Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-eleven translocation (TET) proteins correlates with enhancer activation. However, the functional...

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