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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
...for safeguarding genomic stability. Due to their intricate and fragile nature, centromeres are susceptible to chromosomal rearrangements. However, the mechanisms preserving their functional integrity and supporting nuclear homeostasis following breakages remain enigmatic. In this study, we use wheat ditelosomic...
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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
...high-quality, chromosome-level assembly of P. picta, we were able to identify key elements of the genomic and epigenomic architecture that led to the recent and rapid evolution of a novel dosage compensation system. Our results support the putative model that a recent wave of TE replication led...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
.... S11C). Considering the 80% sequence similarity and wide genomic distribution in both species, we hypothesize that the TCAST transposon-like element was present in the ancestral and gave rise to the 360-bp TCAST satDNA, the current major satellite of T. castaneum (Fig. 5A).The orthologous centromeric...
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Research: Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans
- Christopher A. Desjardins,
- Charles Giamberardino,
- Sean M. Sykes,
- Chen-Hsin Yu,
- Jennifer L. Tenor,
- Yuan Chen,
- Timothy Yang,
- Alexander M. Jones,
- Sheng Sun,
- Miriam R. Haverkamp,
- Joseph Heitman,
- Anastasia P. Litvintseva,
- John R. Perfect,
- and Christina A. Cuomo
Genome Res. July 2017 27: 1207-1219; Published in Advance June 13, 2017, doi:10.1101/gr.218727.116
.... neoformans for human virulence. Genome sequencing and phylogenetic analysis of 387 isolates, representing the global VNI and African VNB lineages, highlighted a deep, nonrecombining split in VNB (herein, VNBI and VNBII). VNBII was enriched for clinical samples relative to VNBI, while phenotypic profiling...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...in C. albicans. Together, these findings highlight that SVs and TEs are common across diverse clinical isolates of C. albicans and that the centromeres of this organism are important sites of rearrangement.Genomes are under constant evolutionary pressure from environmental stressors. Populations...
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Letter: Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability
- Mark D. Pertile,
- Alison N. Graham,
- K.H. Andy Choo,
- and Paul Kalitsis
Genome Res. December 2009 19: 2202-2213; Published in Advance September 8, 2009, doi:10.1101/gr.092080.109
..., Paul Choo K.H. Andy Choo, KH Andy KA Choo K.A. Choo M Pertile Alison N K Choo Andy Pertile 10.1101/gr.092080.109 genome;gr.092080.109 1088-9051 Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability Letter Rapid evolution of mouse Y centromere repeat DNA belies recent...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...of electrophoretic mobility shift assays (EMSA) (Hellman and Fried 2007). In an EMSA, labeled probes corresponding to the DNA of interest are synthesized or isolated and are consequently incubated with a purified protein of interest or with a mixture of proteins (e.g., a nuclear extract). To determine if direct...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...via dual-luciferase reporter assays. These findings align with those of previous studies on the TERT promoter (Péneau et al. 2022). Notably, HBV-Enh I sequences are highly conserved and functionally active in vivo, and their integration may contribute to the amplification of genomic regions harboring...
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Research: Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
- Jitendra Thakur and
- Kaustuv Sanyal
Genome Res. April 2013 23: 638-652; Published in Advance February 25, 2013, doi:10.1101/gr.141614.112
...221 1620 ND J222 1600 ND J223 1570 ND J224 2306 ND J225 3298 ND J226 5269 ND CdJ3/cen7D J201 2369 ND J202 1483 ND J203 2892 ND J204 1830 ND J205 1492 ND (ND) Not detected. Gene conversion maintains native centromere loci Genome Research 641 www..org Chr7. CENPC1 ChIP assays in resulting strain J193...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...point, cells were harvested and their gDNA extracted for use in library preparation or alkaline gel electrophoresis assay. To create a fully deaminated control, isolated gDNA from the 48 h time point was further incubated for 16 h at 67°C. In vitro control libraries were prepared by isolating genomic...
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