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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
...in more data sets.The location of chimeric fusion locations observed is intriguing. Although age-associated mtDNA deletions are most frequently observed to occur within the mitochondrial major arc, recent studies have demonstrated deletion events involving other areas of the (Bua et al. 2006; Lujan et al...
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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...are collectively known as nuclear organelle DNA (NORG) (Leister 2005). The consistent and frequent occurrence of organelle-to-nucleus transfer of DNA has been demonstrated by many experimental studies (Thorsness and Fox 1990; Huang et al. 2003; Stegemann et al. 2003).To date, NUMT has been ubiquitously found...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...(Fig. 1E; Supplemental Figs. S21–S23) display expected genomic features in which more gene-poor chromosomes are located more frequently toward the nuclear periphery (Supplemental Figs. S24–S26). Our 3D modeling of all three cell types reveals major differences between 10A cells versus T1 and C1 cells...
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Corrigendum: Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells
- Young Seok Ju,
- Jose M.C. Tubio,
- William Mifsud,
- Beiyuan Fu,
- Helen R. Davies,
- Manasa Ramakrishna,
- Yilong Li,
- Lucy Yates,
- Gunes Gundem,
- Patrick S. Tarpey,
- Sam Behjati,
- Elli Papaemmanuil,
- Sancha Martin,
- Anthony Fullam,
- Moritz Gerstung,
- ICGC Prostate Cancer Working Group,
- ICGC Bone Cancer Working Group,
- ICGC Breast Cancer Working Group,
- Jyoti Nangalia,
- Anthony R. Green,
- Carlos Caldas,
- Åke Borg,
- Andrew Tutt,
- Ming Ta Michael Lee,
- Laura J. van't Veer,
- Benita K.T. Tan,
- Samuel Aparicio,
- Paul N. Span,
- John W.M. Martens,
- Stian Knappskog,
- Anne Vincent-Salomon,
- Anne-Lise Børresen-Dale,
- Jórunn Erla Eyfjörd,
- Ola Myklebost,
- Adrienne M. Flanagan,
- Christopher Foster,
- David E. Neal,
- Colin Cooper,
- Rosalind Eeles,
- G. Steven Bova,
- Sunil R. Lakhani,
- Christine Desmedt,
- Gilles Thomas,
- Andrea L. Richardson,
- Colin A. Purdie,
- Alastair M. Thompson,
- Ultan McDermott,
- Fengtang Yang,
- Serena Nik-Zainal,
- Peter J. Campbell,
- and Michael R. Stratton
Genome Res. May 2016 26: 717.2; doi:10.1101/gr.206557.116
...: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells Genome Research 26: 291–300 (2016) Corrigendum: Model-based analyses of whole- data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies PingHsunHsieh, August E...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...DNA samples. Leveraging somatic SNVs and fusions, LongSom found subclones with different predicted treatment outcomes. In summary, LongSom enables de novo variant detection without the need for normal samples, facilitating the study of cancer evolution, clonal heterogeneity, and treatment resistance...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...its genetics and genomics fully reproducible by C. elegans laboratories over many years. CGC1 is available at the Caenorhabditis Genetics Center stock center (https://cgc.umn.edu/strain/CGC1).Genome sequencing and assemblyWe harvested genomic DNA (gDNA) from CGC1 and sequenced it in two sets apiece...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...data in light of these studies (Banigan et al. 2020). Our results suggest that frequent loading results in the collision of loop-extruding cohesin molecules when these molecules are not removed from the DNA template by WAPL-1 (Fig. 6). The resulting structure suggests cohesin continues to loop extrude...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...). Given the binary nature of the EDD analysis in calling LADs, we also identified LADs using circular binary segmentation (CBS) to segment DNA with the DNAcopy package (Seshan and Olshen 2023) and the methods in LADetector (Harr et al. 2015; Luperchio et al. 2017). We used this method to assign...
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Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
- Ryan O'Hara,
- Enzo Tedone,
- Andrew Ludlow,
- Ejun Huang,
- Beatrice Arosio,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
...efficiencies between mtDNA and nuclear reference genes. This also has a critical upside in preventing biased results due to copy number variants of nuclear reference genes, which occur frequently in cancer. Results are presented as D-Loop molecules per cell equivalent, corresponding to number of mtDNA...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
..., transcriptional regulation frequently involves long-range interactions between distal CREs and their target promoter, often spanning dozens of kilobases. However, numerous successful reporter lines have been generated in Hydra using only 500–2000 bp of flanking sequence upstream of a gene of interest, motivating...

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