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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
...) Expression of genes associated with placental-specific DMRs based on closest transcription start site (Supplemental Table 6) is shown in TE, and 2nd and 3rd trimester placental villi.To investigate the potential role for placental-specific imprinting, gene expression in placenta was assessed using publicly...
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Research: A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation
- Hala Al Adhami,
- Brendan Evano,
- Anne Le Digarcher,
- Charlotte Gueydan,
- Emeric Dubois,
- Hugues Parrinello,
- Christelle Dantec,
- Tristan Bouschet,
- Annie Varrault,
- and Laurent Journot
Genome Res. March 2015 25: 353-367; Published in Advance January 22, 2015, doi:10.1101/gr.175919.114
...among murine IGs. Node size is proportional to node degree. Edge width maps the number of data sets in which two given nodes are coexpressed. (D) The Gemma database was searched for coexpression among human IGs and orthologs of murine IGs whose imprinting status in humans is unknown or uncertain (open...
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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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Methods: Genome-wide prediction of imprinted murine genes
- Philippe P. Luedi,
- Alexander J. Hartemink,
- and Randy L. Jirtle
Genome Res. June 2005 15: 875-884; doi:10.1101/gr.3303505
...a machine learning approach across the entire mouse for both identifying imprinted gene candidates and predicting their parental expression preference. We collected a series of DNA sequence features within and flanking each locus, such as statistics on repetitive elements, transcription factor binding sites...
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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
...) with consequences for gene expression. At specific loci, cohesin is required for cell-type-specific long-range chromosomal interactions in cis during cellular differentiation (Hadjur et al. 2009). Genomic imprinting refers to the parental allele-specific transcription of a subset of genes inmammals and flowering...
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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
...was evaluated. A total of 2073 of 2101 transcripts were mapped on the mouse ; 39 transcripts, excluding known imprinted genes, were mapped to previously reported imprinted regions. Their transcripts mapped close to known imprinted genes such as Wt1/Nnat/Gnas on Chr 2 (3 transcripts), Sgce /C opg2 on Chr6 (3...
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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
...is located at the Gnasxl/Nespas promoter, and its deletion affects expression of all transcript of the locus, whereas a gDMR located at the 1A promoter is consider as subsidiary ICR and controls tissue-specific imprinted expression of the Gnas transcript only (Table 1; Fig. 1; Williamson et al. 2004, 2006...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
.... 1987; Li et al. 2018), genomic imprinting (Li et al. 1993; Suzuki et al. 2007; Court et al. 2014), X-Chromosome inactivation (Sharp et al. 2011), and transcription repression (Moore et al. 2013). As a result, variations in DNA methylation have been associated with human diseases such as aging...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...of Methyl-SNP-seq for target enrichment, we tested Methyl-SNP-seq combined with the Twist human comprehensive exome panel. The targeted Methyl-SNP-seq had a high mapping efficiency with 96% of the reads mapping to the human . The bisulfite conversion rate is 97% in CHG and CHH contexts. Targeted Methyl...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.During early mammalian embryo...
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