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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...tissues. These regions are therefore also referred to a germline differentially methylated region (gDMR) (Arnaud 2010; Kelsey and Feil 2013). Following this definition, 20 “ubiquitous” gDMR/ICRs have been identified in mice (Proudhon et al. 2012; Xie et al. 2012), most of which are conserved in humans...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...Gs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 8: 203–209. ↵Choufani S, Shapiro JS, Susiarjo M, Butcher DT, Grafodatskaya D, Lou Y, Ferreira JC, Pinto D, Scherer SW, Shaffer LG, et al. 2011. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
.... 1997). In all cases, their parental allele-specific expression is ultimately due to an imprinting control region (ICR), a region of DNA that is differentially methylated between the parental alleles. The parental allele-specific methylation of a differentially methylated region (DMR) is in most cases...
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Method: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
...between paternal and maternal alleles (Table 1). Of note, we identify a novel DMR within intron 2 of the IGF1R gene at 15q26.3, a region not previously thought to be imprinted (Fig. 1). The 11 other confirmed regions of differential methylation all occurred within 15q11-q13, a region that is known...
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Methods: DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression
- Shintaro Yagi,
- Keiji Hirabayashi,
- Shinya Sato,
- Wei Li,
- Yoko Takahashi,
- Tsutomu Hirakawa,
- Guoying Wu,
- Naoko Hattori,
- Naka Hattori,
- Jun Ohgane,
- Satoshi Tanaka,
- X. Shirley Liu,
- and Kunio Shiota
Genome Res. December 2008 18: 1969-1978; Published in Advance October 29, 2008, doi:10.1101/gr.074070.107
...DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression Shintaro Yagi 1 , Keiji Hirabayashi 1 , Shinya Sato 1 , Wei Li 2 , Yoko Takahashi 1...
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Letter: Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions
- Scott V. Dindot,
- Richard Person,
- Mark Strivens,
- Rejinaldo Garcia,
- and Arthur L. Beaudet
Genome Res. August 2009 19: 1374-1383; Published in Advance June 19, 2009, doi:10.1101/gr.089185.108
...methylation differs between sperm and somatic tissue. Differential DNA methylation between samples corresponds to CpG rich imprinted DMRs and to nonrepetitive regions Next we identified sperm-specific DMRs (sDMRs) and tissue-specific DMRs (tDMRs) that exhibited significant (P < 0.00001) differences...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...(Supplemental Fig. S1B,C), confirming previous observations in additional ICF1-derived iPSC lines (Huang et al. 2014). Although the global mCG levels in patient iPSCs were not extensively compromised, when we searched for differentially methylated regions (DMRs) between the two ICF1 iPSCs and our internal...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
...organs. Genome-wide analysis of H2A.B in mouse ES cells shows that H2A.B is associated with methylated DNA in gene body regions. Moreover, H2A.B-enriched gene loci are actively transcribed. One typical example is that H2A.B is enriched in a set of differentially methylated regions at imprinted loci...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
...-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss...
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Research: A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells
- Kei Fukuda,
- Akihiko Okuda,
- Kosuke Yusa,
- and Yoichi Shinkai
Genome Res. June 2018 28: 846-858; Published in Advance May 4, 2018, doi:10.1101/gr.227280.117
..., Peg13, Nap1l5, Nnat, Grb10, and Plagl1). RESF1 was also located in differentially methylated regions (DMRs) of imprinted genes in nonpromoter regions, including Rasgrf1 and Meg3 DMRs. Enrichment of FLAG- and V5-RESF1 in imprinted genes was validated by ChIP-qPCR (Supplemental Fig. S6e,f). Furthermore...

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