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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...activated (Eggermann et al. 2015). The underlying molecular defects are diverse, including pathogenic variants in imprinted genes, CNVs, uniparental disomy (UPD), and aberrant methylation over imprinting control regions. Traditionally, diagnosing these disorders required a stepwise combination...
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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
...disomy (UPD) of specific chromosomes or chromosomal regions (i.e., mice that inherit two maternal copies and no paternal copies, or vice versa, of a chromosome or part of a chromosome) have helped further define the genomic regions involved in this phenomenon. These studies identified several genomic...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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Method: A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
- Sanaa Choufani,
- Jonathan S. Shapiro,
- Martha Susiarjo,
- Darci T. Butcher,
- Daria Grafodatskaya,
- Youliang Lou,
- Jose C. Ferreira,
- Dalila Pinto,
- Stephen W. Scherer,
- Lisa G. Shaffer,
- Philippe Coullin,
- Isabella Caniggia,
- Joseph Beyene,
- Rima Slim,
- Marisa S. Bartolomei,
- and Rosanna Weksberg
Genome Res. March 2011 21: 465-476; Published in Advance February 7, 2011, doi:10.1101/gr.111922.110
...by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were...
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Research: Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder
- Przemyslaw Szafranski,
- Avinash V. Dharmadhikari,
- Erwin Brosens,
- Priyatansh Gurha,
- Katarzyna E. Kołodziejska,
- Ou Zhishuo,
- Piotr Dittwald,
- Tadeusz Majewski,
- K. Naga Mohan,
- Bo Chen,
- Richard E. Person,
- Dick Tibboel,
- Annelies de Klein,
- Jason Pinner,
- Maya Chopra,
- Girvan Malcolm,
- Gregory Peters,
- Susan Arbuckle,
- Sixto F. Guiang III,
- Virginia A. Hustead,
- Jose Jessurun,
- Russel Hirsch,
- David P. Witte,
- Isabelle Maystadt,
- Neil Sebire,
- Richard Fisher,
- Claire Langston,
- Partha Sen,
- and Paweł Stankiewicz
Genome Res. January 2013 23: 23-33; Published in Advance October 3, 2012, doi:10.1101/gr.141887.112
...differentially methylated region at 16q24.1, including lncRNA genes, cause a lethal lung developmental disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), with parent-of-origin effects. We identify overlapping deletions 250 kb upstream of FOXF1 in nine patients with ACD...
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Research: DNA methylation profiles of human active and inactive X chromosomes
- Andrew J. Sharp,
- Elisavet Stathaki,
- Eugenia Migliavacca,
- Manisha Brahmachary,
- Stephen B. Montgomery,
- Yann Dupre,
- and Stylianos E. Antonarakis
Genome Res. October 2011 21: 1592-1600; Published in Advance August 23, 2011, doi:10.1101/gr.112680.110
...or more imprinted loci on the human X chromosome that influence cognitive function (Skuse et al. 1997). We reasoned that as most imprinted genes are accompanied by parent-of-originspecific epigenetic marks, a search for differentially methylated regions between patients with 45,XMAT (n = 4) versus those...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...disomies, and hydatidiform moles, using a combination of whole-genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent...
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LETTER: Identification of a Large Novel Imprinted Gene Cluster on Mouse Proximal Chromosome 6
- Ryuichi Ono,
- Hirosuke Shiura,
- Hiroyuki Aburatani,
- Takashi Kohda,
- Tomoko Kaneko-Ishino,
- and Fumitoshi Ishino
Genome Res. July 2003 13: 1696-1705; doi:10.1101/gr.906803
...to the viral Gag and Pol proteins. A differentially methylated region established in sperm and eggs is located just within the region containing the two first exons of Peg10 and Sgce , and may play an important role in regulating the two paternally expressed genes: Peg10 and Sgce . Maternal uniparental...
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LETTER: Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
- Itoshi Nikaido,
- Chika Saito,
- Yosuke Mizuno,
- Makiko Meguro,
- Hidemasa Bono,
- Moritoshi Kadomura,
- Tomohiro Kono,
- Gerard A. Morris,
- Paul A. Lyons,
- Mitsuo Oshimura,
- RIKEN GER Group,
- GSL Members,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1402-1409; doi:10.1101/gr.1055303
...in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays were used to detect differential expression dependent upon chromosomal parent of origin by comparing the mRNA levels in the total tissue of 9.5 dpc...
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LETTER: Novel Imprinted DLK1/GTL2 Domain on Human Chromosome 14 Contains Motifs that Mimic Those Implicated in IGF2/H19 Regulation
- Andrew A. Wylie,
- Susan K. Murphy,
- Terry C. Orton,
- and Randy L. Jirtle
Genome Res. November 1, 2000 10: 1711-1718; doi:10.1101/gr.161600
...11p15.5 with the DLK1 / GTL2 domain on chromosome 14q32. Physical distances are indicated at the top of the diagram. CTCF binding sites are indicated as shaded vertical rectangles, and black circles indicate the positions of enhancer elements. Differentially methylated regions (DMR) are indicated. G1...

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