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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
...of genomic imprinting. In this review, we examine, for each imprinted domain, the diverse mechanisms by which individual ICRs integrate multiple cis-regulatory activities to regulate both proximal and distal imprinted gene expression throughout the entire domain.Imprinting control regionsICRs are genomic...
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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
..., expanding the applicability of long-read sequencing across diverse genomic studies (Wenger et al. 2019; Koren et al. 2024). Both platforms are capable of DNA and cDNA sequencing and detecting DNA methylation. At the same time, ONT offers additional functionalities such as adaptive sampling and direct RNA...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...of Michigan, Ann Arbor, Michigan 48109, USA Corresponding authors: rmyers@hudsonalpha.org, gcooper@hudsonalpha.orgAbstractTranscription factors (TFs) regulate gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because TF occupancy...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...landscape and the rapid de novo origin of a dosage compensation system.Complete dosage compensation mechanisms have evolved in some organisms with highly diverged sex chromosomes to ameliorate the negative effects of haploinsuffiency (Ohno 1967; Bachtrog 2013). These complex mechanisms act across...
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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: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...into the tissue specificity and developmental dynamics of DNA methylation.DNA methylation, a crucial epigenetic modification, plays an important role in maintaining cell identity across diverse tissue types (Robertson 2005; Ziller et al. 2013). In normal cells, DNA methylation is dependent on local CpG density...
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Method: Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
- Dachang Dang,
- Shao-Wu Zhang,
- Ran Duan,
- and Shihua Zhang
Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122
...to compare domain boundaries across multiple cell types for discovering conserved and divergent topological structures, decipher three types of boundary regions with diverse biological features, and identify consensus TADs (ConsTADs). We illustrate that these analyses could deepen our understanding...
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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
...characterization of their genomic targets. Even though comparisons of zinc fingerprints across KZFPs have been successfully used to establish evolutionary relationships between proteins (Imbeault et al. 2017), complex interactions between ZFs in an array (Wolfe et al. 2001) make in silico predictions of ZF binding...
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Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
- David E. Symer,
- Keiko Akagi,
- Heather M. Geiger,
- Yang Song,
- Gaiyun Li,
- Anne-Katrin Emde,
- Weihong Xiao,
- Bo Jiang,
- André Corvelo,
- Nora C. Toussaint,
- Jingfeng Li,
- Amit Agrawal,
- Enver Ozer,
- Adel K. El-Naggar,
- Zoe Du,
- Jitesh B. Shewale,
- Birgit Stache-Crain,
- Mark Zucker,
- Nicolas Robine,
- Kevin R. Coombes,
- and Maura L. Gillison
Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
...kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute...
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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
...is polymorphically imprinted, and we anticipate that these genes behave Cheong et al. 612 Genome Research www..org Figure 1. Imprinted expression profile in tissues. Individual charts show allelic expression for each gene across the main tissue types examined. (A) Paternally imprinted gene clusters. (B) Maternally...
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