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Research: Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals
- Yoshihito Niimura,
- Atsushi Matsui,
- and Kazushige Touhara
Genome Res. September 2014 24: 1485-1496; Published in Advance July 22, 2014, doi:10.1101/gr.169532.113
...Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals Yoshihito Niimura 1 , 2 , Atsushi Matsui 1 , 2 and Kazushige Touhara 1 , 2...
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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
...). One key insight from comparative studies is that the well-characterized genomic organization seen in mice and humans (the long-standing gold standard for MHC genomic research) is actually a derived state, specific to placental mammals. In humans, the MHC spans 4–5 Mb and contains well over 200 genes...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...under the “innovation–amplification–divergence” model of neofunctionalization (Näsvall et al. 2012). In essence, a tumor may increase its adaptability to a dynamic landscape of selection pressures by exploiting an expanded repertoire of potential functional modifications. Gene duplication, allowing...
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Method: Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
- Artem Mikelov,
- George Nefediev,
- Alexander Tashkeev,
- Oscar L. Rodriguez,
- Diego Aguilar Ortmans,
- Valeriia Skatova,
- Mark Izraelson,
- Alexey N. Davydov,
- Stanislav Poslavsky,
- Souad Rahmouni,
- Corey T. Watson,
- Dmitriy Chudakov,
- Scott D. Boyd,
- and Dmitry Bolotin
Genome Res. December 2024 34: 2293-2303; Published in Advance October 21, 2024, doi:10.1101/gr.278775.123
....Divergent allele frequency distribution in IGHV genes in the African populationThe considered IGH AIRR-seq data sets included repertoires from African, Asian, European, and Hispanic/Latino individuals (Fig. 3A). We did not observe significant differences in the number of detected novel IGHV alleles per donor...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...that occasional XY recombination may hinder sexualization of gene regulation in L. boringii.Finally, we identified five potential candidate genes on Chr 1 that are involved in gonad development and differentiation. zp3 is critical in the process of sperm—egg interaction in African clawed frogs (Omata and Katagiri...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...-order conservation across lineages. We computed 5162 groups of single-copy orthologs present in the six s, and visualized them with strand-independent macrosynteny dot plots, which showed the positions of the same gene in a pair of s (Fig. 2A; Supplemental Fig. S3). This confirmed that gene-order rearrangements were...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...sequence, and one is immediately adjacent to orthologous sequence that is ampliconic in human (∼135 Mb), although the cat sequence is not ampliconic (Supplemental Table S4). One of these novel genes encodes a putative olfactory receptor (98% similarity to an annotated cheetah gene), and a second shares 91...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...because it can increase the DHT-induced chromatin accessibility and BRD4 chromatin occupancy.Coactivation of AR and GR leads to synergistic expression of a subset of target genesBecause GR at AR-assisted GRBs has added effect on chromatin accessibility, we next measured if coactivation of both receptors...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...RNAs) and individual studies that concentrate either on a limited number of TFs or on specific groups of genes. Once again, the best practical path to easily accessing these types of data is via curated integrating databases, especially Harmonizome and GTRD. It is important to remember that although...
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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
...implications in the field of comparative functional genomics.Most phenotypic changes across mammals are thought to arise from differences in gene regulation. African mole-rats are a group of rodents displaying unusual longevity (Emmrich et al. 2022) and evolutionary adaptations to their subterranean...
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