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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...genes, with an average of more than 10 FIEs per gene. Only seven genes had FIEs identified in more than five tumors, all of which were known cancer genes: TP53 (n = 74 FIEs), PIK3CA (28), CDKN2A (13), KRAS (90), SMARCA4 (7), LUAD-specific EGFR (10), and BRAF (8). Using driver mutations classified...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...gene receptor clusters found within this region (Giglio et al. 2001). Individuals affected by 8p syndrome present with a variety of clinical phenotypes, including agenesis of the corpus callosum, epilepsy, and other neurodevelopmental delays (Vibert et al. 2022).Over the past several decades...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...-prioritized target genes for 58.1% of the duplication hotspots in the five cancer types, of which 61.5% are not harbored within the hotspots per se (Fig. 4A–D; Supplemental Fig. S3C,D), suggesting long-distance gene regulation. The GC content of promoters of the RENC-prioritized genes is not significantly different...
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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
...of X-linked genes across five insect orders: (SPX) S. piceifrons X, (TCX) T. castaneum X, (APX) A. pisum X, (CCX) C. carnea X, and (HIX) H. illucens X.Next, we asked if the X Chromosome gene order is also conserved across insect orders. Cross-order collinearity is usually weak owing to the long...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig , which has a functional implication -wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene...
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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
.../subspecies to investigate how TEs interact with genes associated with host shift. Our results reveal enrichment of TEs at promoter regions of host shift–related genes, with ∼39% of the odorant receptors containing their transcription factor binding sites within TEs. We observe that ∼50% of these TEs are Helitrons...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...–D; Table 1; Supplemental Table S3). Further, several chromatin-associated complexes contain multiple components, all significantly differentially expressed in GSC-like cells (Table 1). For example, genes encoding both FACT complex subunits, five minichromosome maintenance 2–7 (MCM2-7) complex components...
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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
...is important for understanding the molecular and evolutionary processes that regulate chromosome structure and gene regulatory processes (Dekker and Mirny 2016; Kuroda et al. 2016) and how the evolution of X-linked genes influences local adaptation (Lasne et al. 2017).The extensive analysis of dosage...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...1:1 orthologs in vertebrate s, including marmoset and mouse lemur (Table 1, GENCODE v44 and Ensembl release 110). The remaining 10 copies map on Chromosome 10, with the majority (7/10) at the q-arm pericentromeric region, precisely 10q11.22 (Table 1). They consist in four protein-coding genes, five...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...of 2308 gene families with more than seven arid and nine mesic species, corresponding to five transitions. Differentially expressed genes as well as five GO terms showed an enrichment (adjusted P-value < 0.1) (Fig. 5E). Here again, we did not observe sites with convergent evolution at all five transitions...
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