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Research: The evolution of sex-biased gene expression in the Drosophila brain
- Samuel Khodursky,
- Nicolas Svetec,
- Sylvia M. Durkin,
- and Li Zhao
Genome Res. June 2020 30: 874-884; Published in Advance June 18, 2020, doi:10.1101/gr.259069.119
...of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA Corresponding author: lzhao@rockefeller.eduAbstractGenes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However...
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Method: Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases
- Renan Sauteraud,
- Jill M. Stahl,
- Jesica James,
- Marisa Englebright,
- Fang Chen,
- Xiaowei Zhan,
- Laura Carrel,
- and Dajiang J. Liu
Genome Res. September 2021 31: 1629-1637; Published in Advance August 23, 2021, doi:10.1101/gr.275677.121
...escape genes is significantly increased in female-biased diseases. Our results, for the first time, quantitate the importance of variable escape genes for the etiology of sex-biased disease, and our pipeline allows analysis of larger data sets for a broad range of phenotypes.The human X Chromosome...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...(Rödelsperger et al. 2021), KEGG pathways (Kanehisa and Goto 2000), and previous gene expression studies focusing on sex-biased genes (Rödelsperger et al. 2018), intestinal transcriptome (Lightfoot et al. 2016), and developmental oscillations (Supplemental Table S7; Sun et al. 2021). This allowed the labeling...
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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
..., Sweden Corresponding authors: maria.warnefors@gmail.com, h.kaessmann@zmbh.uni-heidelberg.deAbstractSexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we map caQTLs in liver tissue from 138 human donors and identify caQTLs for 35,361 regulatory elements, including population-specific caQTLs driven...
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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
...-random proportion of genes with sex-biased expression, the expression breadth of X-linked genes also differs from that of autosomal genes: TheD. melanogasterX chromosome contains a deficiency of narrowly expressed genes (Mikhaylova and Nurminsky 2011), while there is an excess of X-linked narrowly expressed human...
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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
...-9822(02)00448-7 ↵Charlesworth B, Coyne JA, Barton NH. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am Nat 130: 113–146. doi:10.1086/284701 ↵Chauhan P, Swaegers J, Sánchez-Guillén RA, Svensson EI, Wellenreuther M, Hansson B. 2021. Genome assembly, sex-biased gene expression and dosage compensation...
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Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
.... Furthermore, the genes affected by individual sex-biasing factors and interactions among factors are associated with human disease traits such as coronary artery disease, diabetes, and inflammatory bowel disease. Our study offers a tissue-specific account of the individual and interactive contributions...
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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
...assessed if the sex-biased gene expression we observed in the cancer cell lines is replicated in an independent data set of human tissues. We compared the differentially expressed genes between the XX and XY cell lines to sex-biased genes reported based on the Genotype-Tissue Expression project (GTEx...
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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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