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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
...to translocation of the distal long arm of the X Chromosome (Xq28) to the long arm of the Y Chromosome show severe mental retardation and developmental defects (Lahn et al. 1994). Most genes in Xq28 are inactivated in 46,XX females but escape inactivation in such X;Y translocations, suggesting that increased...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...addressed whether it is involved in repressing X Chromosome genes in males. We divided the genes on the X Chromosome into groups: genes undergoing X inactivation (X nonescapees), genes escaping inactivation (X escapees) (Wainer Katsir and Linial 2019), and genes in the pseudoautosomal region (PAR) (Weng et...
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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
...forces contributed to some degree to the observed pattern. Refinement of the ‘out of X’ hypothesis of new gene emergence The “out of X” pattern, where genes on the X Chromosome are especially prone to give rise to autosomal retrogenes (Emerson et al. 2004; Potrzebowski et al. 2008), is clearly visible...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...of recapitulating female-/male-biased patterns in each sex-matched time point and cell type. (B) Similar to in A, pairwise comparison of Sunbear prediction and the nearest neighbor baseline in ranking escape genes to be more female-biased than all other genes on the X Chromosome. (C,D) Predicted temporal sex-biased...
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Research: Gene essentiality in cancer cell lines is modified by the sex chromosomes
- Shahar Shohat,
- Ethel Vol,
- and Sagiv Shifman
Genome Res. November/December 2022 32: 1993-2002; Published in Advance November 23, 2022, doi:10.1101/gr.276488.121
...inferred the dosage of the sex chromosomes in 355 female and 408 male cancer cell lines and used it to dissect the contributions of the Y and X Chromosomes to sex-biased gene expression. Furthermore, based on -wide CRISPR screens, we identified genes whose essentiality is different between male and female...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...(P < 5 × 10–3, by permutation; Methods), consistent with their escape from X-Chromosome inactivation (Fig. 6C). In contrast, proteins encoded by X-Chromosome genes that are subject to X-Chromosome inactivation showed no or only modest sex biases in protein abundance (Supplemental Fig. S18...
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Research: Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system
- Dan Sun,
- Donna L. Maney,
- Thomas S. Layman,
- Paramita Chatterjee,
- and Soojin V. Yi
Genome Res. October 2019 29: 1673-1684; Published in Advance September 23, 2019, doi:10.1101/gr.248641.119
...Corresponding author: soojinyi@gatech.eduAbstractIn male heterogametic systems, the X Chromosome is epigenetically differentiated between males and females, to facilitate dosage compensation. For example, the X Chromosome in female mammals is largely inactivated. Relative to well-studied male heterogametic...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...1984; Ellegren and Parsch 2007). This mode of selection can drive the X Chromosome to accumulate and amplify sex-biased genes engaged in sexual antagonism (i.e., beneficial to one sex and detrimental or neutral to the other) (Ross et al. 2005; Ellegren 2011).Their rapid divergence, X...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...with respect to the X chromosome (see below). Our analyses of new mammalian miRNA families revealed several remarkable patterns. Young mammalian miRNA genes are expressed at low levels and are apparently subject to weak or no purifying selection. Given their generally low expression levels, the regulatory...
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