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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...6BT, United Kingdom; 2Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; 3Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 4University College London Cancer...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
..., transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate...
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Research: ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
- Lili Tang,
- Fei Huang,
- Wuxin You,
- Ansgar Poetsch,
- Rafael Henrique Nóbrega,
- Deborah Mary Power,
- Tengfei Zhu,
- Kaiqiang Liu,
- Hong-Yan Wang,
- Qian Wang,
- Xiwen Xu,
- Bo Feng,
- Manfred Schartl,
- and Changwei Shao
Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
...of circdmrt1 and AMSDT in tongue sole testisGenome analysis revealed that the dmrt1 gene generated circdmrt1, which was from exon 4 and flanked by long introns. Sanger sequencing confirmed circdmrt1 in testis and the back-splicing junction (Fig. 3A). PCR analysis of the testis of tongue sole confirmed...
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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain; 2Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain; 3Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain; 4Division of Genetics, Department of Medicine...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...the maize shoot apex as a paradigm, we address this question on a -wide scale and highlight how the complexity inherent within the miRNA pathway allows regulation of these small RNAs and their action on targets to be tailored to bring about the gene expression versatility needed during development.ResultsSubfunctionalization...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; 7CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; 8National Center for Mathematics...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
.... These subsequent mutational changes likely nonfunctionalized SRGAP2B and are consistent with the fixation of the granddaughter duplicate SRGAP2C in the human population.Similarly, splicing patterns differ between FCGR1A and FCGR1B, despite their shared 99.0% nucleotide identity at the genomic level (Supplemental...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
...terms were omitted for clarity. Guschanski et al. 1464 Genome Research www..org 2011), in line with the neo- and subfunctionalization models of gene duplication. However, to understand why tissue specificity is elevated in paralogs, it is necessary to study the contribution of expression levels...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...sub- or neofunctionalization. Thus, when subfunctionalization or neofunctionalization occurs, a difference Chang and Liao 1520 Genome Research www..org in ΔEA-B.max between two ortholog sets is not expected. However, we found that the ortholog sets characterized by NA = 1 and NB > 1 consistently...

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