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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
...be explained by an allelic skew in X-Chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions. We propose a novel approach using nanopore sequencing to quantify...
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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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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
...X Chromosome silencing in mammals (Do Kim et al. 2006; Donohoe et al. 2007; Jeon and Lee 2011; Makhlouf et al. 2014; Chen et al. 2016). In the context of mammalian X inactivation, YY1 binding is regulated by the differences in the epigenetic landscape between the active and inactive X in females...
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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
...unclear how epigenetic memory of stable gene silencing is reversed by transcription factors (TFs) and accompanying chromatin mechanisms. Chromosome-wide transitions between active and inactive chromatin states are excellently modeled by X-Chromosome inactivation (XCI) and reactivation (XCR) in female...
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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
.... Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun 9: 2064. doi:10.1038/s41467-018-04540-x ↵Bird AP. 1986. CpG-rich islands and the function of DNA methylation. Nature 321: 209–213. doi:10.1038/321209a0 ↵Caylor RC. 2023. Nonrandom X chromosome inactivation detection. Curr...
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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
...of the long-range superloops required for formation of the Xi chromatin conformation (Bonora et al. 2018). Second, X-linked satellite arrays are epigenetically distinct in that they reside in euchromatic bands amid the heterochromatic background of the inactive X Chromosome, reflecting the chromosome-wide...
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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
..., Brown CJ. 2017. When the lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 372: 20160355. doi:10.1098/rstb.2016.0355 ↵Carrel L, Willard HF. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...-type-specific transcriptomic and epigenetic changes associated with aging in 88 the substantia nigra, we profiled this brain region in mice at four different age stages: 2 months 89 (adolescent), 6 months (mature adult), 12 months (middle-aged), and 18 months (old) using 10x 90 Genomics Chromium Multiome (Fig. 1A). We...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
.... 2016) and exhibit pronounced variability on the inactive X Chromosome (Liu et al. 2023), suggesting epigenomic compartmentalization of drift. The biological consequences of epigenetic drift are increasingly being explored. Hannum et al. (2013) showed that drift-CpGs in blood are associated...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...ectopic exchange between GGO.3p (Chr2/hsa3) and Chromosome Xp (Fig. 5A). We refined the breakpoints of the sequence exchange and mapped both to different SD-spacer regions, corresponding to the third and 25th SD spacer positions on the short arm of the gorilla X Chromosome (Fig. 5B). Analyzing...
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