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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...to the evolution of gene regulatory networks in mammals (Imbeault et al. 2017; Senft and Macfarlan 2021), we first evaluated the amino acid sequence similarity of mouse and human KZFP proteins across mammalian species using the BioMart web tool. Notably, a subset of mouse KZFPs was present only in mice...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
..., these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.MicroRNAs (miRNAs) are small RNAs that mediate posttranscriptional gene regulation by targeting mRNAs for degradation and translational repression. In animals, miRNAs typically recognize their m...
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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
..., a fraction of the transcripts that shape the oocyte methylome originates from species-specific long terminal repeats (LTRs) of endogenous retroviruses (ERVs) (Veselovska et al. 2015; Brind'Amour et al. 2018). This phenomenon contributes to significant differences in the oocyte methylation pattern between...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...well known to be involved in repeat stability, such as Pms2 (Narayanan et al. 1997). This may be because of a lack of segregating functional variants in other relevant genes in this cohort or because of a lack of power to capture certain mutation events such as large expansions.Definitively identifying...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...). (ITR) Inverted terminal repeat sequence. (C) Flow cytometry analysis distinguishing colonies edited in genomic DNA (PE positive) and plasmid DNA (FITC positive). The selection efficiency is calculated by the ratio of GFP and RFP double-positive cells to GFP-positive cells. (D) Workflow for assessing...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...in the evolution of gene regulation previously observed in mammalian s (Pehrsson et al. 2019) to the zebrafish . We found that various TE subfamilies belonging to different classes are enriched for different categories of tissue-specific active regulatory elements (Fig. 3). This suggests that TEs have been able...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...elegans and C. briggsae have revealed powerful insights into the evolution of functional novelty and constraint in phenotypes and genetic pathways (Cutter et al. 2009; Marri and Gupta 2009; Thomas et al. 2012; Haag and Liu 2013; Verster et al. 2014). The high quality C. briggsae assembly facilitated...
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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
...with transcriptional and epigenetic alterations to oocytes (Market-Velker et al. 2010; Lopes et al. 2022; Xie et al. 2024), including changes in the expression of genes implicated in DNA damage repair (Daugelaite et al. 2023). Nonetheless, we cannot exclude the potential influence of other ART-related factors...
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Research: The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes
- Luisa Robbez-Masson,
- Christopher H.C. Tie,
- Lucia Conde,
- Hale Tunbak,
- Connor Husovsky,
- Iva A. Tchasovnikarova,
- Richard T. Timms,
- Javier Herrero,
- Paul J. Lehner,
- and Helen M. Rowe
Genome Res. May 4, 2018 ; Published in Advance May 4, 2018, doi:10.1101/gr.228171.117
.... 2017. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res 27: 1384–1394. Garrick D, Sharpe JA, Arkell R, Dobbie L, Smith AJ, Wood WG, Higgs DR, Gibbons RJ. 2006. Loss of Atrx affects trophoblast development and the pattern of X...
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