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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
....“Tissue-independent” genes are strongly biased wherever they are expressed. Most parent-of-origin-dependent ASE genes (67%) have this expression profile—all of which are related to genomic imprinting, a well-characterized epigenetic phenomenon that results in uniparental expression and is often conserved across tissues...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...).DiscussionIn this report, we have collected and analyzed epigenetic data from diverse genomic assays to characterize the overall chromatin state of adult hermaphrodite germ cells in C. elegans. The distribution of chromatin states across the captures known and novel features of organization in the germline and identifies...
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Research: Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline
- Toshiaki Watanabe,
- Ee-chun Cheng,
- Mei Zhong,
- and Haifan Lin
Genome Res. March 2015 25: 368-380; Published in Advance December 5, 2014, doi:10.1101/gr.180802.114
...Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline Toshiaki Watanabe , Ee-chun Cheng , Mei Zhong and Haifan Lin Yale Stem Cell Center and Department of Cell Biology, Yale University School...
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Research: Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
- Michael S. Werner,
- Bogdan Sieriebriennikov,
- Neel Prabh,
- Tobias Loschko,
- Christa Lanz,
- and Ralf J. Sommer
Genome Res. November 2018 28: 1675-1687; Published in Advance September 19, 2018, doi:10.1101/gr.234872.118
...structure and epigenetic signature of orphan genes in the satellite model nematode Pristionchus pacificus. Consistent with previous findings, we find young genes are shorter, contain fewer exons, and are on average less strongly expressed than older genes. However, the subset of orphan genes...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate . Cancer cells are characterized by the acquisition...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...resolution, as well as to identify their chromosomal origin and formation mechanism. Here, we apply long-read sequencing (lrGS) in combination with the telomere-to-telomere (T2T-CHM13) assembly to characterize the structure and genomic content of 10 clinically detected sSMCs. We use sequencing data...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...error rates are in the range of 0.1% (PacBio HiFi) to 0.5% (ONT Q20+). Finally, LRS is believed to be nearly bias-free in terms of sequence composition (e.g., Ross et al. 2013), although a few exceptions have been noted. Nurk et al. (2020, 2022) reported a lack of PacBio HiFi sequencing coverage across...
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Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
..., 56124 Pisa, Italy; 5Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy ↵6 These authors contributed equally to this work. Corresponding authors: albertomagi@gmail.com, gianluca.mattei@unifi.it, marta.baragli@unifi.itAbstractIn epigenetic analysis, the identification...
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Research: Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications
- Artur Veloso,
- Killeen S. Kirkconnell,
- Brian Magnuson,
- Benjamin Biewen,
- Michelle T. Paulsen,
- Thomas E. Wilson,
- and Mats Ljungman
Genome Res. June 2014 24: 896-905; Published in Advance April 8, 2014, doi:10.1101/gr.171405.113
...a potential mechanism by which cells can fine-tune the temporal gene expression and alternative splicing patterns despite fixed gene lengths. Future studies are needed to define the mechanisms by which cells regulate elongation rates through epigenetic modification and characterize pathological states whereby...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
...of multiple random samples. Accurate and thorough characterization of the MHC haplotypes will enable further studies on the epigenetic and 3D genomic characteristics of this crucial genomic region, ultimately shedding light on the mechanisms affected by variants within both coding and noncoding regions...
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