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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...as yeasts, plants, worms, flies, and humans. The rDNA locus is an ideal candidate to harbor fundamental and evolutionarily conserved aging mechanisms as well as yield widely applicable markers of aging. In eukaryotes, the array originates the nucleolus, the site of ribosomal RNA (rRNA) transcription...
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Research: Natural genetic variation in yeast longevity
- Stefan W. Stumpferl,
- Sue E. Brand,
- James C. Jiang,
- Boguslawa Korona,
- Anurag Tiwari,
- Jianliang Dai,
- Jae-Gu Seo,
- and S. Michal Jazwinski
Genome Res. October 2012 22: 1963-1973; Published in Advance September 5, 2012, doi:10.1101/gr.136549.111
...RNA transcripts in C. Standard error bars are shown for n = 3 biological replicates. Natural genetic variation in yeast longevity Genome Research 1969 www..org for other quantitative traits in yeast (Steinmetz et al. 2002; Sinha et al. 2006). The presence of the S96 rDNA cluster leads to increasedmRLS (Fig. 3C...
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Method: Identifying gene function and module connections by the integration of multispecies expression compendia
- Hao Li,
- Daria Rukina,
- Fabrice P.A. David,
- Terytty Yang Li,
- Chang-Myung Oh,
- Arwen W. Gao,
- Elena Katsyuba,
- Maroun Bou Sleiman,
- Andrea Komljenovic,
- Qingyao Huang,
- Robert W. Williams,
- Marc Robinson-Rechavi,
- Kristina Schoonjans,
- Stephan Morgenthaler,
- and Johan Auwerx
Genome Res. December 2019 29: 2034-2045; Published in Advance November 21, 2019, doi:10.1101/gr.251983.119
...of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland; 8Department of Genetics, Genomics and Informatics, University of Tennessee, Memphis, Tennessee 38163, USA Corresponding author: admin.auwerx@epfl.chAbstractThe functions of many eukaryotic genes are still poorly understood...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...are remarkably divergent in structure and gene content. Nature 463: 536–539. doi:10.1038/nature08700 ↵Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves T, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, et al. 2012. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
...conservation and divergence of nematode miRNAs over 400 million years of evolution. Ascaris endo-siRNAs (26G- and 22G-RNAs), particularly in the testis, demonstrate striking adaptability and plasticity in their expression and biogenesis, including the loss of 39 29-Omethylation of small RNAs, when comparedwith...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...the proper folding of proteins (Buhr et al. 2016; Walsh et al. 2020). But again, this is expected to be a local effect, with limited -wide impact on SCU.The intensity of TS varies widely across species, not only in unicellular organisms but also in multicellular eukaryotes (Sharp et al. 2005; Subramanian...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
..., as monitored by single-cell RNA-seq. Our results point toward a role for quiescent-specific RNAPII distribution to ensure a rapid and robust transcriptional response upon return to growth.Eukaryotic organization is dynamic, varying across cell types and conditions, both functionally and spatially...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
..., and also Blattodea, in which all termites (Infraorder: Isoptera) are eusocial but exhibit varying levels of social complexity. These insect orders likely diverged ∼400 million years ago (Misof et al. 2014), and there are substantial differences between social insects from the two orders (Korb 2008; Korb...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...pleiotropic RNA helicases implicated in multiple aspects of RNA metabolism, including splicing, export, stability, translation, and stress response (Soto-Rifo and Ohlmann 2013). DDX3X is widely conserved across eukaryotes, with orthologs in mammals, flies, worms, and yeast (Johnstone et al. 2005; Elbaum...
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Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
...composition (Charlesworth and Charlesworth 2000; Bachtrog 2013). Y Chromosomes are derived from ordinary autosomes, but over time, they often have diverged considerably from their former homolog, the X Chromosome (Charlesworth 1978; Bull 1983).Y Chromosomes are transmitted through males only, which makes them...

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