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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
...at individual copies. Due to multimapping issues, WGBS remains limited in its ability to resolve the DNA methylation landscape of individual transposon copies. This limitation may be overcome by using direct DNA methylation detection through nanopore sequencing, which remains a future direction of our research...
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Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
- Weishi Yu,
- Carl McIntosh,
- Ryan Lister,
- Iris Zhu,
- Yixing Han,
- Jianke Ren,
- David Landsman,
- Eunice Lee,
- Victorino Briones,
- Minoru Terashima,
- Robert Leighty,
- Joseph R. Ecker,
- and Kathrin Muegge
Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
...methylation alters lamin B1 association with the nuclear envelope or changes nuclear compartmentalization, or whether lamin B1 in turn is functionally interactive with the DNA methylation pathway. It is possible that the location of some genes within LADs contributes to their silenced state despite CG...
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Research: LSH and G9a/GLP complex are required for developmentally programmed DNA methylation
- Kevin Myant,
- Ausma Termanis,
- Arvind Y.M. Sundaram,
- Tristin Boe,
- Chao Li,
- Cara Merusi,
- Joe Burrage,
- Jose I. de Las Heras,
- and Irina Stancheva
Genome Res. January 2011 21: 83-94; Published in Advance December 13, 2010, doi:10.1101/gr.108498.110
...methylation in Hells#2;/ mouse embryonic fibroblasts (MEFs) in comparison with wild-type MEFs and wild-type and EHMT2 (G9a) histonemethylase ES cells.We found that in LSH-deficient cells, DNA methylation is lost or reduced from a large subset of promoters, including genes that normally undergo de novo...
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Research: Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
- Hannah Demond,
- Courtney W. Hanna,
- Juan Castillo-Fernandez,
- Fátima Santos,
- Evangelia K. Papachristou,
- Anne Segonds-Pichon,
- Kamal Kishore,
- Simon Andrews,
- Clive S. D'Santos,
- and Gavin Kelsey
Genome Res. January 2023 33: 18-31; Published in Advance January 23, 2023, doi:10.1101/gr.277046.122
...on embryo development remain unclear. To investigate the importance of EHMT1 in oogenesis and compare its function to EHMT2, we used oocyte cKO mice for Ehmt2 and Ehmt1, as well as a Ehmt1/2 cDKO. We use a multi-omics approach to evaluate changes in H3K9 methylation, gene expression, DNA methylation...
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Research: H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
- Carol C.L. Chen,
- Preeti Goyal,
- Mohammad M. Karimi,
- Marie H. Abildgaard,
- Hiroshi Kimura,
- and Matthew C. Lorincz
Genome Res. January 2018 28: 37-51; Published in Advance December 11, 2017, doi:10.1101/gr.224717.117
...-regulated in the absence of EHMT2 or EHMT1, including the MageA and Rhox gene clusters (Tachibana et al. 2002), are within TTRs and are co-oriented with the gross direction of DNA replication (Fig. 4F), revealing that this phenomenon may be extended to endogenous genes. Regardless, as replication timing in EHMT2-deficient...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...affinities following from differences in RNA Polymerase II kinetics owing to local GC content.Alternative splicing occurs predominantly cotranscriptionally and thus takes place in close proximity to the DNA from which the transcript originated (Reimer et al. 2021). Beyond being impacted by transcription...
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Research: TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
- Helen M. Rowe,
- Adamandia Kapopoulou,
- Andrea Corsinotti,
- Liana Fasching,
- Todd S. Macfarlan,
- Yara Tarabay,
- Stéphane Viville,
- Johan Jakobsson,
- Samuel L. Pfaff,
- and Didier Trono
Genome Res. March 2013 23: 452-461; Published in Advance December 10, 2012, doi:10.1101/gr.147678.112
...deletion in MEFs, it significantly decreased in their ES cell counterparts, albeit not as dramatically as in ES cells deleted for Ehmt2 (G9a), a histone methyltransferase involved in the maintenance of DNA methylation (Fig. 3C, right; Dong et al. 2008; Tachibana et al. 2008). Perhaps explaining this latter...
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LETTER: Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells
- Vitalina M. Komashko,
- Luis G. Acevedo,
- Sharon L. Squazzo,
- Sushma S. Iyengar,
- Alina Rabinovich,
- Henriette O’Geen,
- Roland Green,
- and Peggy J. Farnham
Genome Res. April 2008 18: 521-532; Published in Advance March 17, 2008, doi:10.1101/gr.074609.107
...by distinct chromatin-modifying complexes. For example, EZH1 and EZH2 can cause methylation of H3 at lysine 27, EHMT1, EHMT2, SUV39H1/2, and SETDB1 can cause methylation of H3 at lysine 9, and DNMT1, TRDMT1, and DNMT3A/B can methylate DNA at CpG dinucleotides ( Kirmizis et al. 2004 ; Klose and Bird 2006...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...DBPs has established that sitespecific DNA methylation at promoters can repress endogenous gene expression (Li et al. 2007; Rivenbark et al. 2012; Siddique et al. 2013). Currently, direct and targeted DNAmethyltransferase activity to endogenous genes has only been applied using engineered ZF and TALE...
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Research: Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
- Tyrone Ryba,
- Ichiro Hiratani,
- Junjie Lu,
- Mari Itoh,
- Michael Kulik,
- Jinfeng Zhang,
- Thomas C. Schulz,
- Allan J. Robins,
- Stephen Dalton,
- and David M. Gilbert
Genome Res. June 2010 20: 761-770; Published in Advance April 29, 2010, doi:10.1101/gr.099655.109
...-dimensional chromosomal architecture. [Supplemental material is available online at http://www..org. The microarray data from this study have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE20027.] DNA replication in higher eukaryotes is regulated at the level...

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