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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
..., Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, Lara-Astiaso D, Amit I. 2013. High-throughput chromatin immunoprecipitation for -wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 8: 539–554. doi:10.1038/nprot.2013.023 ↵Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...DNA was cleaned using a Axygen AxyPrep MAG PCR clean-up kit (Corning MAG-PCR-CL-50). DNA was incubated with 2× volume of magnetic bead solution on a shaker for 5 min, washed twice with 70% EtOH, and eluted with 100 μL of elution buffer. The yield was 10 μg per reaction. The highly methylated control...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...-Rad 500-0006). One to two milligrams of protein extract was used per ChIP, and 5% was taken out to use as input DNA. The remaining protein extract was incubated with 3 to 10 μg of antibody rotating overnight at 4°C in a volume of 440 μL. Forty microliters of (1:1 V) Protein A and/or G-Sepharose beads...
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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
...in a murine MPN model. This study was replicated in MPN patients by profiling -wide gene expression and DNA methylation using patient blood samples collected longitudinally, before and following HC exposure. The effects of HC on the transcriptome were not only associated with cell cycle interruption but also...
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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
...) array clusters, and unique peaks were seen for the Chr 1 LM-tRNA cluster, the Chr 1 5S rDNA cluster, and the Chr 19 SST1 cluster. Methylation plots from the HG002 cell line showed evidence of methylation gradients in the rDNA arrays, the Chr 1 tRNA cluster, and the Chr 1 5S rDNA cluster (Supplemental...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...devised new methods to map DNA supercoiling and single-stranded DNA in Caenorhabditis elegans embryos and diapause larvae. To map supercoiling, we quantified the incorporation of biotinylated psoralen into DNA using high-throughput sequencing. To map single-stranded DNA, we combined permanganate treatment...
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Methods: Comprehensive high-throughput arrays for relative methylation (CHARM)
- Rafael A. Irizarry,
- Christine Ladd-Acosta,
- Benilton Carvalho,
- Hao Wu,
- Sheri A. Brandenburg,
- Jeffrey A. Jeddeloh,
- Bo Wen,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 780-790; Published in Advance March 3, 2008, doi:10.1101/gr.7301508
...; 3 Orion Genomics, LLC, St. Louis, Missouri 63108, USA Abstract This study was originally conceived to test in a rigorous way the specificity of three major approaches to high-throughput array-based DNA methylation analysis: (1) MeDIP, or methylated DNA immunoprecipitation, an example...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...).Genome-wide analysis of DNA methylation at CGIs, using the Infinium HumanMethylation450 (HM450K) BeadChip Arrays, showed that DNA methylation defects were more widespread in IDHmut samples, constituting a Glioma CIMP (G-CIMP) subclass (Supplemental Fig. S1B). In agreement with the literature (Noushmehr et al. 2010...
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Methods: High-throughput methylation profiling by MCA coupled to CpG island microarray
- Marcos R.H. Estécio,
- Pearlly S. Yan,
- Ashraf E.K. Ibrahim,
- Carmen S. Tellez,
- Lanlan Shen,
- Tim H.-M. Huang,
- and Jean-Pierre J. Issa
Genome Res. October 2007 17: 1529-1536; Published in Advance September 4, 2007, doi:10.1101/gr.6417007
..., Cambridge CB2 1TN, United Kingdom Abstract An abnormal pattern of DNA methylation occurs at specific genes in almost all neoplasms. The lack of high-throughput methods with high specificity and sensitivity to detect changes in DNA methylation has limited its application for clinical profiling...
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Research: EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos
- Ghislain Auclair,
- Julie Borgel,
- Lionel A. Sanz,
- Judith Vallet,
- Sylvain Guibert,
- Michael Dumas,
- Patricia Cavelier,
- Michael Girardot,
- Thierry Forné,
- Robert Feil,
- and Michael Weber
Genome Res. February 2016 26: 192-202; Published in Advance November 17, 2015, doi:10.1101/gr.198291.115
.... References Anders S, Pyl PT, Huber W. 2015. HTSeq: a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166–169. Athanasiadou R, de Sousa D, Myant K, Merusi C, Stancheva I, Bird A. 2010. Targeting of de novo DNA methylation...

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