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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
...scale.The placental-specific imprinted genes reported to date in human and mouse are not well-conserved (Frost and Moore 2010); therefore, we evaluated the DNA methylation of orthologous regions to placental-specific DMRs in mouse development using publicly available data (Smith et al. 2012, 2014; Hon...
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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
...databases. We performed a similar analysis with the 86 human IGs (Supplemental Table S5) present in Gemma, including 15 genes whose imprinting status is unknown but whose murine orthologs are imprinted. Again, the vast majority of IGs (80 out of 86) were frequently coexpressed (Fig. 1D; Supplemental Table S...
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Chicken Special/Letters: Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region
- Takaaki Yokomine,
- Hisao Shirohzu,
- Wahyu Purbowasito,
- Atsushi Toyoda,
- Hisakazu Iwama,
- Kazuho Ikeo,
- Tetsuya Hori,
- Shigeki Mizuno,
- Masaoki Tsudzuki,
- Yoh-ichi Matsuda,
- Masahira Hattori,
- Yoshiyuki Sakaki,
- and Hiroyuki Sasaki
Genome Res. January 2005 15: 154-165; Published in Advance December 8, 2004, doi:10.1101/gr.2609605
...Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region Takaaki Yokomine 1 , 2 , Hisao Shirohzu 1 , Wahyu Purbowasito 1 , 3 , Atsushi Toyoda 4 , Hisakazu Iwama 5...
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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
...tissues during early development. However, we were not successful in finding differential DNAmethylation in mouse at the sequence orthologous to the human DMR (data not shown). Nevertheless, themaintenanceDNAmethyltransferaseDNMT1,which is known to ensure the faithful copying of germline imprinted...
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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
...contains the imprinted genes DLK1 and GTL2 ( Wylie et al. 2000 ), and a number of other imprinted genes have been identified in orthologous regions in sheep and mouse ( Miyoshi et al. 2000 ; Schmidt et al. 2000 ; Charlier et al. 2001 ); however, no imprinted genes have yet been found in the other two...
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LETTER: Computational and experimental identification of novel human imprinted genes
- Philippe P. Luedi,
- Fred S. Dietrich,
- Jennifer R. Weidman,
- Jason M. Bosko,
- Randy L. Jirtle,
- and Alexander J. Hartemink
Genome Res. December 2007 17: 1723-1730; Published in Advance November 30, 2007, doi:10.1101/gr.6584707
...imprinted gene TP73 along with the novel candidate PRDM16 , associated with leukemia ( Du et al. 2005 ). The ortholog of this gene was also predicted to be imprinted in mouse ( Luedi et al. 2005 ). The high-density 14q32.31 band contains the known imprinted gene MEG3 along with the novel candidate RTL1...
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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
..., is established post-implantation and/or is brain specific. The regulation of the imprinted domain comprising Ndn, Magel2, Mkrn3, and Peg12 deserves further study since the human orthologs of Ndn, Magel2, and Mkrn3 are in the region associated with Prader-Willi syndrome (Lee and Wevrick 2000), with patients...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...) lying between Tsix and Jpx in the regulation of Xist and XCI in mouse extra-embryonic endoderm stem cells (XEN), which represent the maintenance phase of imprinted XCI. Here, we show that the deletion of this Xist upstream sequence in the inactive X leads to the upregulation of Xist expression...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...% of benchmarking universal single-copy orthologs (BUSCO) genes (Supplemental Fig. S1). Furthermore, the gene annotation for these s covered 98.63% of all reference genes in the D. mojavensis subspecies and 95.98% in D. arizonae. The de novo gene annotation in D. buzzatii and D. koepferae revealed a total of 18...
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LETTER: A Large Imprinted microRNA Gene Cluster at the Mouse Dlk1-Gtl2 Domain
- Hervé Seitz,
- Hélène Royo,
- Marie-Line Bortolin,
- Shau-Ping Lin,
- Anne C. Ferguson-Smith,
- and Jérôme Cavaillé
Genome Res. September 2004 14: 1741-1748; Published in Advance August 12, 2004, doi:10.1101/gr.2743304
...://.ucsc.edu/ ) and 100-nt-long stem-loop structures with a ΔG &lt;–30 kcal/mole were systematically identified within the ∼1-Mb-long imprinted 14q32 region by using RNAfold software from http://www.tbi.univie.ac.at/~ivo/RNA/ . We then retained the conserved hairpin structures between the murine and human orthologous...

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