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Research: Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code
- Marina Murillo,
- Marina Salvadores,
- Aina Vaquer Picó,
- Lina Tsapanou,
- Adrian Gabriel Torres,
- Fran Supek,
- and Lluis Ribas de Pouplana
Genome Res. April 15, 2026 gr.281022.125; Published in Advance April 15, 2026, doi:10.1101/gr.281022.125
...mutations in BLCA 325 are the consequence of the high levels of APOBEC activity in these tumors, and opens the possibility 326 of a functional relationship between mutated tRNAs and BLCA development. In contrast, brain 327 cancer lays at the opposite spectrum in terms of tDNA somatic mutations, which...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...of one modality from another. However, existing methods for cross-modality translation between single-cell RNA sequencing (scRNA-seq) and single-cell DNA methylation (scDNAm) data face limitations, including unidirectionality, inadequate modeling of context-specific DNA methylation...
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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
...Kenzie D, Teitell MA, Timp W, Wanagat J. 2023. Nanopore sequencing identifies a higher frequency and expanded spectrum of mitochondrial DNA deletion mutations in human aging. Aging Cell 22: e13842. doi:10.1111/acel.13842 ↵Wong S, Witte ON. 2004. The BCR-ABL story: bench to bedside and back. Annu Rev...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...-associated factor CHD8 during cortical development. Mol Autism 12: 16. doi:10.1186/s13229-020-00409-3 ↵Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, et al. 2014. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...-cell DNA sequencing and forensics, the amount of DNA available is low and requires amplification (Butler 2006; Evrony et al. 2015). Although high-depth whole- sequencing (WGS) of PCR-amplified libraries could achieve large-scale, high-fidelity profiling of microsatellites, this is not feasible to scale...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...in otherwellestablished complex singular cellular eukaryotes, like S. cerevisiae and S. pombe, Tetrahymena has a family of 16 proteins containing a Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger domain (Citarelli et al. 2010; Xiong et al. 2013; Ashraf et al. 2019). This provides a unique opportunity to study...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...-induced DNA damage (Andrade-Lima et al. 2015; Williamson et al. 2017; Cugusi et al. 2022). In addition, dysregulated transcriptional elongation has been implicated in developmental defects as well as disease and aging (Aoi and Shilatifard 2023; Debès et al. 2023).RNAPII elongation rates not only reflect...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
...of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial (mtDNA). Here, we present a pipeline to call mtDNA variants...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...investigation is required to fully understand the complete spectrum of new mutations, which will depend on the development of improved and more accessible long-read sequencing technologies, along with tools for analyzing large tandem repeats.MethodsBiological samples, high-molecular-weight DNA extraction...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...to cause LCA when homozygous, but only mild late-onset CoRD when heterozygous (Swaroop et al. 1999; Chen et al. 2002). Pathogenic missense variants have been identified in both the DNA-binding domain and transcriptional effector domain (Fig. 1A).View larger version: In this window In a new window Figure 1...
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