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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
.... Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Corresponding authors: jianhaichen@uchicago.edu, mlong@uchicago.edu, bairong.shen@scu.edu.cnAbstractNew genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
.... 2009). Unlike DNA-based duplicates, functional retrocopies or retrogenes inherently lack the ancestral regulatory sequences, having to recruit new ones from the vicinity and/or by evolving them de novo (Kaessmann et al. 2009; Carelli et al. 2016). The contribution of retrogenes to phenotypic evolution...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...mechanism warrants further work. Nevertheless, we used the transcriptome data to illuminate the functional evolution of Anolis Y and X gametologs. We compared current XY expression patterns in adult organs to those inferred for their proto-sex chromosomal precursors based on median expression levels...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...studies have provided insights into the complexity of alternative isoforms at a deep evolutionary timescale. However, the diversity and pattern of the alternative isoform landscape within natural populations remain largely unexplored (Verta and Jacobs 2022).Owing to its well-defined evolutionary history...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...with somatic cells.Mammalian spermatogenesis is the process by which germ cells undergo progressive differentiation to generate mature male gametes. In the mouse, a pool of undifferentiated spermatogonia is recruited with regular periodicity into this process (de Rooij and Russell 2000). Once committed...
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Research: Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters
- Shrutii Sarda,
- Avinash Das,
- Charles Vinson,
- and Sridhar Hannenhalli
Genome Res. April 2017 27: 553-566; Published in Advance February 21, 2017, doi:10.1101/gr.212050.116
...for this article.] In mammalian DNA, cytosines within CpG dinucleotides are heavily methylated throughout the , yet there are several discrete “islands” that contain a high frequency of unmethylated CpG sites. These are called CpG islands (CGI), and their identification has long been considered important...
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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
...potentially be large. Indeed, a recent analysis of mammalian ChIP-seq data sets found 51% of expressed mouse retrogenes (mRNAs that are reverse transcribed and inserted into the ) exhibit robust H3K4 trimethylation (Carelli et al. 2016), and transcription of the new gene QQS in Arabidopsis thaliana...
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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
...lacking the transcriptional corepressor TIF1β are defective in early postimplantation development. Development 127: 2955–2963. Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. 2016. The life history of retrocopies illuminates the evolution of newmammalian genes. Genome Res 26: 301...
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