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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
...Bertille Montibus, Franck Court and Philippe Arnaud Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, 63000 Clermont-Ferrand, France Corresponding author: philippe.arnaud@uca.frAbstractGenomic imprinting is a specialized mechanism...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...to genetic variants (Cheung et al. 2023). DNA methylation patterns captured by long-read sequencing can help reveal the parent of origin of genetic variation extending to chromosome-length haplotypes, as well as detect parent-specific methylation patterns to help resolve genomic imprinting and disease...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...Medhat Mahmoud1,4, Daniel P. Agustinho1,4 and Fritz J. Sedlazeck1,2,3 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3Department of Computer Science, Rice...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
.... Corresponding author: jlai@cau.edu.cnAbstractGenomic imprinting refers to allele-specific expression of genes depending on their parental origin. Nucleosomes, the fundamental units of chromatin, play a critical role in gene transcriptional regulation. However, it remains unknown whether differential nucleosome...
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Research: The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
...10013, USA; 18Department of Systems Biology, Columbia University, New York, New York 10032, USA Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from...
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Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...These authors contributed equally to this work. ↵4 Present addresses: Neochromosome Inc., Long Island City, NY 11101, USA; 5BlueRock Therapeutics, New York, NY 10016, USA Corresponding author: maurano@nyu.eduAbstractThe specificity of interactions between genomic regulatory elements and potential target genes...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey...
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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
...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 1 , 2 , 3 , 4 , 6 , Brendan Evano 1 , 2 , 3 , 4 , 7...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...methyltransferases (DNMT1, DNMT3A, DNMT3B) (Goll and Bestor 2005) and plays important roles in transcriptional repression. For example, DNA methylation is known to regulate imprinted genes (Kaneda et al. 2004), some tissue-restricted genes (De Smet et al. 1999; Maatouk et al. 2006; Borgel et al. 2010...
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Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
...Corresponding author: afsmith@mole.bio.cam.ac.uk ↵ Present addresses: 3 Crown Bioscience, Inc., Santa Clara, CA 95054, USA; 4 Health Sciences Authority, Singapore 138623; 5 Syngenta APAC Pte Ltd., Singapore 117406. Abstract Genomic imprinting is an epigenetic mechanism resulting...
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