Searching journal content for articles similar to Luedi et al. 17 (12): 000.

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  1. Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
    • Yangyang Liu,
    • Bingqiang Liu,
    • and Juntao Liu
    Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
    ...structures, hierarchical TADs play important roles in epigenetic organization, transcriptional activity, gene regulation, and cell differentiation. Currently, it remains a highly challenging task to accurately identify hierarchical TADs in a computational manner. The key bottleneck for existing TAD callers...
  2. Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
    • Bertille Montibus,
    • James A. Cain,
    • Rocio T. Martinez-Nunez,
    • and Rebecca J. Oakey
    Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
    ...). This was shown for example at two independent imprinted loci, where the expression of a nested gene is associated with “premature” alternative polyadenylation of the host gene upstream of the nested gene, whereas its silencing is associated with polyadenylation at the canonical 3′ UTR (Wood et al. 2008; Cowley...
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  3. 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
    ..., the -wide pattern of DNA methylation in human oocytes was not known (Guo et al. 2014), preventing the definitive identification of novel primary imprints in humans. In this study, we describe the dynamics of known imprinted DMRs throughout human development in somatic and extraembryonic tissues and identify...
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  4. 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
    ...of expressionwasmost dissimilar to that of IGs, displayed the exact reverse behavior (Fig. 6E). Discussion Parental genomic imprinting has commanded attention over the past three decades as a prototypical epigenetic gene regulation mechanism. The identification of mechanisms governing parentof...
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  5. 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
    ...approaches have been used previously in mice to identify imprinted genes and their associatedDMRs.One approach that led to the identification of the first imprinted gene, Igf2r, linked phenotypes that were transmitted in a parent of origin-specific manner to a specific genomic region (Barlow et al. 1991...
  6. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...2003; Giritharan et al. 2007; Rivera et al. 2008; Kohda 2013; Tan et al. 2016). These molecular changes are associated with increased rates of imprinting-related disorders (Cortessis et al. 2018; Hattori et al. 2019) and may contribute to higher rates of adverse pregnancy, perinatal, neonatal, and long...
  7. 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
    ...Genome-wide prediction of imprinted murine genes Philippe P. Luedi 1 , Alexander J. Hartemink 1 , 2 , and Randy L. Jirtle 3 , 4 1 Center for Bioinformatics and Computational Biology, Duke University, Durham, North Carolina 27708, USA...
  8. 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...
  9. 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
    ...discuss current challenges and future directions in the field, emphasizing the need for innovative computational tools and robust, reproducible approaches to fully harness the capabilities of LRS in molecular diagnostics.What is methylation?Cytosine DNA methylation (5mC) involves the covalent modification...
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  10. ARTICLE: Identification of Novel Imprinted Genes in a Genome-Wide Screen for Maternal Methylation
    • Rachel J. Smith,
    • Wendy Dean,
    • Galia Konfortova,
    • and Gavin Kelsey
    Genome Res. April 1, 2003 13: 558-569; doi:10.1101/gr.781503
    ...Identification of Novel Imprinted Genes in a Genome-Wide Screen for Maternal Methylation Rachel J. Smith , Wendy Dean , Galia Konfortova , and Gavin Kelsey 1 Developmental Genetics Program, The Babraham Institute, Cambridge CB2 4AT, UK...
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