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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
...enriched on the X Chromosome (Wilcox test, P < 0.001), in which it is nearly twice as dense compared with the autosomes.Next, we calculated the Kimura two-parameter (K2P) (Kimura 1980) distance of all transposons (Supplemental Fig. S5). The profile of the X Chromosome is similar to the small chromosomes...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...inactivation (XCI) is a dosage-compensation mechanism equalizing the expression of the majority of X-linked genes between males and females (Van den Veyver 2001). In 46, XX females, one X Chromosome is chosen stochastically as the inactive X (Xi) in a small number of cells early in embryonic development...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...in shaping evolution of retroelement-associated TE-CRE landscapes in Atlantic salmon.Although retroelements dominate the salmon TE-CRE landscape, the role of DNA transposons such as DTA and DTT elements in TE-CRE evolution cannot be neglected owing to their high genomic copy numbers (Figs. 1, 3A). Indeed...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
..., it is unclear what physical constraints or functional loci may drive the large reduction in recombination rate over such a large portion of the X Chromosome. Whether the conserved recombination landscape represents an additional consequence of constraints on dosage compensation has not been previously addressed...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...the preservation of centromere function and structural remodeling. These results illustrate how centromere evolution is driven by the interplay of DNA repair, transcriptional regulation, and epigenetic reprogramming (Graham and Esashi 2024) and enhance our understanding of the structural and functional plasticity...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...I:C), a synthetic viral mimic, and 19 profile transcriptomic and epigenomic responses in the primary haematopoietic and 20 lymphoid tissue. We used ATAC-seq and ChIP-seq (H3K27ac and H3K27me3), combined 21 with mRNA-seq, to comprehensively examine modifications in gene regulation following 22...
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Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
- Adrian Janiszewski,
- Irene Talon,
- Joel Chappell,
- Samuel Collombet,
- Juan Song,
- Natalie De Geest,
- San Kit To,
- Greet Bervoets,
- Oskar Marin-Bejar,
- Caterina Provenzano,
- Lotte Vanheer,
- Jean-Christophe Marine,
- Florian Rambow,
- and Vincent Pasque
Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
...of the two X Chromosomes is induced to establish dosage compensation in the epiblast (Lyon 1961).The XCI process is initiated by the lncRNA Xist and leads to the removal of active histone marks such as histone acetylation and the accumulation of repressive histone marks such as histone H3 lysine 27...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...different preferences. Transposable elements are a source of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored. Here, we perform genomic and transcriptomic analyses in six s of cactophilic species...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...is a critical mechanism in XCI, a dosage compensation process ensuring a single active X Chromosome in both XY and XX individuals (Lyon 1962). In typical XX individuals, one X is randomly silenced in each cell during development, with methylation maintaining gene repression on the inactive X (Xi). This random...
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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
...copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins show dosage compensation and fail to change by the degree expected...

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