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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...). Therefore, it is surmised that DNA interaction frequently appears in the regulatory elements. To confirm this hypothesis, Hi-C analysis was conducted to investigate the 3D chromatin structures of BmN cells (Fig. 1C). The chromatin interaction profiles were highly correlated between the two replicate samples...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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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
...lipid metabolites. We analyzed data from 3037 individuals in the NSPT cohort, for whom both metabolomic and methylation profiles were available. The metabolomic data set included 351 NMR-detected lipoprotein subfractions, comprising 176 direct measurements and 175 derived values.After adjusting for age...
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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
...Uncovering methylation-dependent genetic effects on regulatory element function in diverse s Rachel M. Petersen1,2, Christopher M. Vockley3 and Amanda J. Lea1,2,4 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA; 2Evolutionary Studies Initiative, Vanderbilt...
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Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
...not differentially expressed. Such results suggest that a large fraction of the DMRs observed in our samples may be merely passenger events that accompany cancer evolution with weak or no effect on gene expression (Kalari and Pfeifer 2010).The methylation state of a genomic region (a group of adjacent CpG sites...
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Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
- Ruben Boers,
- Joachim Boers,
- Bas de Hoon,
- Christel Kockx,
- Zeliha Ozgur,
- Anco Molijn,
- Wilfred van IJcken,
- Joop Laven,
- and Joost Gribnau
Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
.... 2C). Genome-wide examination of the distribution of mapped reads revealed CpG methylation patterns specific for fibroblasts, different from profiles obtained with 100% methylated DNA, indicating regions, such as the HOXA cluster, showing reduced methylation in fibroblasts (Fig. 2E; Supplemental Fig...
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Method: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
- Shelsa S. Marcel,
- Austin L. Quimby,
- Melodie P. Noel,
- Oscar C. Jaimes,
- Marjan Mehrab-Mohseni,
- Suud A. Ashur,
- Brian Velasco,
- James K. Tsuruta,
- Sandeep K. Kasoji,
- Charlene M. Santos,
- Paul A. Dayton,
- Joel S. Parker,
- Ian J. Davis,
- and Samantha G. Pattenden
Genome Res. December 2021 31: 2327-2339; Published in Advance November 23, 2021, doi:10.1101/gr.275219.121
...fate than gene expression profiles alone (Stergachis et al. 2013; Domcke et al. 2020; Ma et al. 2020). Further, we and others have shown that specific changes in chromatin accessibility can result from treatment with small molecule inhibitors (Hurtado et al. 2011; Patel et al. 2012; Pattenden et al...
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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
...before (DAP-seq) and after PCR amplification (ampDAP-seq), where the amplification depletes the library of DNA methylation. MBD5 and MBD6 showed sequence enrichment, but only for DAP-seq, where DNA methylation was present, and with binding site profiles that closely match those identified by Ch...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...characteristics of the R-loop pattern in the maize . We studied the relationships between R-loops and repetitive sequences in maize, such as tandem repeats and TEs. We also provide the first R-loop observation by atomic force microscopy (AFM) in plants.ResultsGenome-wide identification of R-loops in maize...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...). By looking at the mutations through -wide “breadth”, the limited number of equivalents becomes less restrictive, enabling the identification of tumor fractions (TFs) ∼100 times lower compared to targeted “depth” in SNV analysis (Zviran et al. 2020). Genome-wide cfDNA can also reveal tumor-specific copy...
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