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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
...the reporters are expressed at low level in spite of a euchromatic environment. Our model of birth-diffusion-death on chromatin suggests that some ratelimiting factor is released near the promoters and especially the terminators of active genes. The RNA polymerase itself is a poor candidate for this role...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...RNAs (17%) are lineage-specific (P < 10#2;10, Fisher’s exact test). Furthermore, the new loci detected here are characterized by low expression levels (see also below), which likely explains why they have previously remained undetected. Birth and death rates of miRNAs in mammals With our sets of miRNA gene...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...adaptive immunity, and MHC genes serve as key models in evolutionary genomics, offering insight into birth-and-death evolution, gene duplication, and the maintenance of genetic diversity. However, the organization and evolution of the MHC in species with giant s, such as salamanders, remain poorly...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...to chromosomes, whether spontaneous or induced by external agents, often result in abnormal cell division and aneuploidy, conditions frequently observed in cancer cells (Bakhoum and Cantley 2018). Moreover, chromosome rearrangements post-DNA breakage are well-documented and contribute significantly to evolution...
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REVIEW: Clusters of Resistance Genes in Plants Evolve by Divergent Selection and a Birth-and-Death Process
- Richard W. Michelmore and
- Blake C. Meyers
Genome Res. November 1, 1998 8: 1113-1130; doi:10.1101/gr.8.11.1113
...Clusters of Resistance Genes in Plants Evolve by Divergent Selection and a Birth-and-Death Process Richard W. Michelmore 1 and Blake C. Meyers Department of Vegetable Crops, University of California, Davis, California 95616 USA Abstract Classical...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...and contractions along the Pezizales phylogeny. At each node, the top number indicates the number of gene-family expansions, and the bottom number indicates the number of contractions. The numbers in parentheses represent the significantly expanded and contracted gene families. (λ) Birth–death model rates fitted...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...-Robertson 2012) include epigenetic events such as methylation turnover (Ginno et al. 2020), replication and spatial chromatin changes (Candelli et al. 2018), the birth and death of promoters or their interconversion into enhancers (Majic and Payne 2020) and their putative bidirectional functioning (Young et al...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
.... First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...with high-quality long-read assemblies. We perform annotations of ovary piCs and -wide TE content in each strain. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...). Similarly, engineering of human dicentric chromosomes lead to a variety of consequences, including centromere inactivation (Higgins et al. 2005). Together, these studies indicate that chromosome rearrangements can be associated with the rapid birth and death of centromeres in plants and animals, further...
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