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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...coding-like NUMTs within nuclear regions, particularly in areas of low recombination (Gossmann et al. 2014). This selective pressure could further suppress the rate of mutation accumulation in NUMTs.MethodsData collection and selectionGenome assemblies for all mammalian species (available before November...
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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
...to a specific chromosome. Because the initial mapping of MHC transcripts to s indicated that automatic annotation of MHC genes was, in many cases, not accurate, MHC-I and MHC-II genes were annotated manually (Supplemental Data). The following description incorporates key observations informed by expression data...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...↵11 These authors contributed equally to this work. Corresponding authors: pavlopoulos@fleming.gr, izg5139@psu.eduAbstractG-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...suggests a novel, non-XCI role of XIST in peripheral Schwann cells that is mediated by a newly recognized transcript.X-inactive specific transcript (XIST) is a long noncoding RNA (lncRNA) that serves as an important regulator of X Chromosome inactivation (XCI) in mammalian XX females (Loda and Heard 2019...
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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
...by the coding region (exons and introns); and ending with a terminator and polyadenylation signals that ensure proper transcript processing and stability. Before we can determine proteins that directly regulate GOI expression, we must identify the regulatory DNA sequences relevant to the GOI such as its...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...Uncovering methylation-dependent genetic effects on regulatory element function in diverse s Rachel M. Petersen1,2, Christopher M. Vockley3 and Amanda J. Lea1,2,4 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA; 2Evolutionary Studies Initiative, Vanderbilt...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...regions (Christmas et al. 2023).Here, to identify reliable mammalian UCEs (mUCEs) and avian UCEs (aUCEs) using numerous species, we developed a comparative genomics approach that considers potential species-specific mutations and assembly errors without compromising length or quantity (Fig. 1). First, we...
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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
.... The robustness of the association between eusociality and high recombination rates can therefore be addressed by assessing mean genomic recombination rates in social Blattodea (termites).In addition to variation between species, the rate of recombination also varies along chromosomes. In mammals, crossover...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...decided to use the GENCODE consortium genomic annotation. We used the “comprehensive” set which includes the highest number of transcripts associated with protein-coding genes, pseudogenes, long noncoding RNAs and small noncoding RNAs genes (Frankish et al. 2019). Transcripts with “to be experimentally...
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