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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...to Muller element F in Drosophila melanogaster (the ancestral fly X Chromosome; 55.6% of fly Muller F genes, chi-squared test, 1 d.f., P = 3.84 × 10−31) (Vicoso and Bachtrog 2013) despite 400 million years of divergence. Through functional enrichment analysis, we show that these conserved X-linked genes...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
...transcribed from their own promoters (Ozsolak et al. 2008) and would require targeted sex-biased regulation, for example by hormones, to become differentially expressed between males and females. In Drosophila, hormonal regulation by ecdysone promotes sex-biased expression of the miRNA locus let-7-C, which...
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Research: Sex-biased genetic effects on gene regulation in humans
- Antigone S. Dimas,
- Alexandra C. Nica,
- Stephen B. Montgomery,
- Barbara E. Stranger,
- Towfique Raj,
- Alfonso Buil,
- Thomas Giger,
- Tuuli Lappalainen,
- Maria Gutierrez-Arcelus,
- MuTHER Consortium,
- Mark I. McCarthy,
- and Emmanouil T. Dermitzakis
Genome Res. December 2012 22: 2368-2375; Published in Advance September 7, 2012, doi:10.1101/gr.134981.111
...-cholesterol have been detected, respectively, inDrosophila (Nuzhdin et al. 1997) andmouse (Korstanje et al. 2004). Sex-specific eQTLs have also been detected in mice (Yang et al. 2006), but whether such effects on expression regulation are also seen in humans has not been explored to date. To address the above...
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Research: Disentangling the relationship between sex-biased gene expression and X-linkage
- Richard P. Meisel,
- John H. Malone,
- and Andrew G. Clark
Genome Res. July 2012 22: 1255-1265; Published in Advance April 12, 2012, doi:10.1101/gr.132100.111
...expressed genes, or some combination of the two. To address this problem, we measured sex-biased expression in multiple Drosophila species and at different developmental time points. These data were combined with available expression measurements from Drosophila melanogaster and mouse to reconcile...
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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
...via the accumulation of epigenomic marks (Sahakyan et al. 2018). In Drosophila, dosage compensation of the X Chromosome in somatic cells is achieved through the male-specific lethal (MSL) complex, which acetylates histone H4, resulting in hyperexpression of X-linked genes in males (Lucchesi and Kuroda...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...) and Drosophila (Kaiser et al. 2011). Human X- and chicken Z-linked genes that show the strongest signatures of dosage compensation in either lineage also show signs of dosage sensitivity as measured by membership in large protein complexes (Pessia et al. 2012) or evolutionary patterns of gene duplication...
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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
...expression. In addition, unless the up-regulation mechanism is specific to males (like in Drosophila) (Fig. 2E; Conrad and Akhtar 2012), the overabundance of X transcripts in females, which results from the combined activity of the two up-regulated X Chromosomes, would lead to the evolution of a compensation...
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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
.... 2010. Co-option of the hormone-signalling module dafachronic acid–DAF-12 in nematode evolution. Nature 466: 494–497. ↵Betrán E, Long M. 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164: 977–988. ↵Brand M, Rampalli S...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...in Drosophila (MARS2 [Bayat et al. 2012] and RNF113A [Carney et al. 2013]) or perform the same enzymatic process as the endogenous copy in yeast (TRMT12) (Rodriguez et al. 2012). These studies support a substantial functional overlap between orphan and parent, suggesting that new retrogenes can evolve to carry...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...with motifs for transcription factors (TFs) associated with immune response and hematopoietic maintenance (Fig. 4E; Supplemental File S2), such as RFX5, SMAD1, and EOMES. The rapid evolution of immune response genes and TFs is supported by many studies in vertebrates and in Drosophila melanogaster...
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