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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 cells. Thus, to evaluate this response in a global manner, comprehensive DDR studies utilizing omics methods are essential. Here, we studied DNA damage repair kinetics from a global transcriptomic and proteomic perspective in the ciliate Tetrahymena thermophila (Tetrahymena) (Orias et al. 2011; Ruehle...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...of defense systems on HGT. From a taxonomic perspective, working at or below the species level is a natural choice because species represent genetically cohesive units (Bobay and Ochman 2017; Konstantinidis 2023; Conrad et al. 2024), and as a result, uncontrolled confounding factors are less likely to affect...
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Research: Systems genetics of the Drosophila metabolome
- Shanshan Zhou,
- Fabio Morgante,
- Matthew S. Geisz,
- Junwu Ma,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 392-405; Published in Advance November 6, 2019, doi:10.1101/gr.243030.118
...-phenotype relationships of complex traits requires systems genetic analyses that incorporate genetic variation with variation in gene expression traits, the metabolome, and complex trait phenotypes in a population with replicated genotypes. Such comprehensive studies are challenging in human populations but can...
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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...Table S6). Taken together, our data identify unique signatures in retina and brain microglia and highlight the molecular diversity despite the common origin.Retina and brain microglia are dominant pathogenic cell type for AMD and ADAs our understanding of immune system dysfunction in relation to AMD...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...that may be countered by underdeveloped lung and breathing control systems (Salmaso et al. 2014). Outside of these pathological but common scenarios, recent studies using in vivo oxygen biosensors have also observed regions of local tissue hypoxia in rodent brains, both at rest and during demanding tasks...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
..., Germany Corresponding author: christian.roedelsperger@tuebingen.mpg.deAbstractAll animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Bacterial feeding nematodes are powerful systems to study host-microbe interactions...
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In memoriam: Sydney Brenner—a personal perspective
- Byrappa Venkatesh
Genome Res. June 2019 29: vii-ix; doi:10.1101/gr.251918.119
...AND TECHNOLOGY)Sydney Brenner (1927–2019), a pioneering molecular biologist and scientific giant, passed away recently at the age of 92. This is a personal perspective on Sydney based on my association with him during the last 28 years.Sydney was born on January 13, 1927 in Germiston, a small town in South...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...), and gene retrocopy variants (Zhang et al. 2021; Zhang and Tautz 2022). This made the house mouse an ideal system to directly trace the origin and pattern of alternative isoforms in natural populations.Here, we use mice brains as the source tissue for the transcriptome analysis. The brain harbors...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...is driven in part by recognition of DNA sequence, genetic variation can influence TF–DNA associations and gene regulation. To identify variants that impact TF binding in human brain tissues, we assessed allele-specific binding (ASB) at heterozygous variants for 94 TFs in nine brain regions from two donors...
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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
...-neuronal lineage genes during fibroblast-to-neuron direct differentiation. However, MYT1L's molecular and cellular functions in the adult mammalian brain have not been fully characterized. Here, we found that MYT1L loss leads to up-regulated deep layer (DL) gene expression, corresponding to an increased ratio...
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