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Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
- Amit Blumberg,
- Edward J. Rice,
- Anshul Kundaje,
- Charles G. Danko,
- and Dan Mishmar
Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
...: In this window In a new window Figure 4. Identification of mtDNA nascent transcript across evolution: (A) PRO-seq experiment performed in four mammalian CD4+ cells: chimpanzee, rhesus macaque, rat, and mouse. x- and y-axes are identical to those in Figure 2, and “horizontal T” sign designates the pausing site...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...suggests a greater level of convergent evolution within a single rodent family, Murinae, than in the total data set. One possible reason is that Murinae have recently diverged and thus share a common genomic background. Another reason may be that their transitions all occurred in a more similar time frame...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...(Fig. 4A), followed by TE-terminated transcripts with 10.63% and 9.45% and in TE-initiated transcripts with 1.79% and 1.51%. All species have a similar number of expressed genes (heads: x¯ = 9508, σ = 300; larvae: x¯ = 11,375, σ = 117), but we observed on average 11-fold fewer chimeric transcripts in D...
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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
...(Pol II) -wide. These approaches provide a high-resolution view of transcription initiation, pausing, and elongation, enabling rapid detection of transcriptional changes following TF perturbation.Other methods survey Pol II–associated chromatin-bound RNAs, such as chromatin-associated RNA-seq (Chr...
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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: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...at a chromosome extremity is associated with shorter telomeres in cis, but (2) the overall Y′ element content in a strain correlates with longer telomeres. Finally, we show that the length of the shortest telomeres remains relatively constant across strains, suggesting a selective constraint at the species level...
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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
...; and neofunctionalization, in which duplicates evolve new functions (Taylor and Raes 2004; Hahn 2009; Kondrashov 2012; Kuzmin et al. 2022). Genome sequencing has supported the view that whole- duplication (WGD) events frequently occur during evolution across all domains of life, with many plant species retaining polyploid...
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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
...motif densities of viruses and their hosts.Genomic distribution of G4s in genomic subcompartments across organismal sG4s are unevenly distributed in the human and are enriched in specific subcompartments in which they have functional roles associated with transcription and translation (Huppert et al...
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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
...of Michigan, Ann Arbor, Michigan 48109, USA Corresponding authors: rmyers@hudsonalpha.org, gcooper@hudsonalpha.orgAbstractTranscription factors (TFs) regulate gene expression by facilitating or disrupting the formation of transcription initiation machinery at particular genomic loci. Because TF occupancy...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...related to S. cerevisiae, follows an initiation pattern similar to that of classic-model species in TATA-containing promoters (Choi et al. 2002). Thus, the most parsimonious explanation posits that the scanning model may have originated during the evolution of S. cerevisiae after it diverged from S. pombe...

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