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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
.... Notably, we find that many autosomal genes, including cohesin Rad21, are dysregulated in Xist-upstream-deleted cells. Additionally, we demonstrate that Xist-upstream deletion leads to alterations of topological contacts of the Xist locus with its upstream positive regulator Ftx and across the inactive X...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...al. 2024). However, whether genomic mechanisms govern these slow rates of molecular evolution, and whether they are restricted to a subset of the , such as protein-coding genes (Takezaki 2018; Brownstein et al. 2024) and fourfold degenerate sites (Venkatesh et al. 2014; Gemmell et al. 2020), remain...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
...compilation study of Alu-involved gene rearrangements (Rudiger et al. 1995). (E) Adapted from a comparative genomic study on chimpanzee and human reference (Han et al. 2007). The blue line describes 492 human-specific breakpoint junctions of Alu/Alu-mediated deletions, and the red line depicts 663 chimpanzee...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...Genetics, Sapienza University, Rome 00185, Italy Corresponding author: joris.vermeesch@kuleuven.beAbstractThe 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short...
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
...it is maintained, gene function is commonly inferred from the phenotypic effects of deleting the gene. Because some of the deletion effects are byproducts of other effects, they may not reflect the gene's selected-effect function. To evaluate the degree to which the phenotypic effects of gene deletion inform gene...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
.... 2013), including mitochondrial dysfunction, genomic instability, and cellular senescence. The stochastic development of mtDNA deletion mutations has implications for the role of these mutations in somatic mosaicism (Campbell et al. 2015) and aging in postmitotic tissues. The relative lack of genetic...
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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
...sufficient. Combining tools with awareness of their limitations allows researchers to design experiments with high-confidence hypotheses. However, one of the major steps when trying to identify functional regions of a gene involves systematic perturbation of its regulatory DNA through deletion, linker...
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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
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
..., gene absence/presence, etc. (Computational Pan-Genomics Consortium 2018).Recent works propose the use of pan references to improve genotyping accuracy from short-read sequencing data (Eggertsson et al. 2017; Sibbesen et al. 2018; Hickey et al. 2020; Letcher et al. 2021; Bradbury et al. 2022; Ebler et...
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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...is generated with jsTree view.Estimate HLA gene deletion frequency in The 1000 Genome Project dataTo detect the deletion of HLA genes in The 1000 Genome Project data populations, we calculated the median read depth of the target gene region and 2000 randomly selected regions within Chr 6:20 Mb–50 Mb...

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