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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...or translationDetecting de novo gene birth need not rely only on the identification of new ORFs originating from noncoding regions. New genes can also arise as a result of transcription and/or translation of pre-existing ORFs that were previously unexpressed, a process that represents one of the more frequently...
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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
...-like), Rpb3-FLAG is partially retained within the gene body while accumulating outside the ORF specifically in Q cells (Fig. 3A,C, gray boxes).To ask whether RNAPII was enriched in Q in all intergenes alike, we sorted them based on the orientation of their surrounding annotations (convergent, divergent...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...to control gene expression during early organogenesis across vertebrate evolution. HCNEs bearing hallmarks of functionality in human and zebrafish endoderm are enriched for binding sites of endoderm TFs To determine which TFs are likely to be acting via the endodermal HCNEs, we performed de novo and known...
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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
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...of allele-depth ratios for dnSNVs between animals conceived via ART and those conceived naturally (two-tailed Wilcoxon rank-sum test, P = 0.29) (Supplemental Fig. 11), indicating no evidence of differences in the developmental origin of dnSNVs between cohorts.No detectable difference in de novo structural...
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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
..., even in some cases, alleles. A phylogenetic effect is visible in the coexpression modules, which can be considered as the mark of this common background in gene expression. Our analysis also shows that changes in kidney structural composition increase with time, which will blur the evolution of bulk...
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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
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...domain derived from RTE-1; however, its molecular function remains unknown (Iwashita et al. 2006). Although these few LINE-derived genes have been identified in mammals, their evolution and diversity are poorly understood.In the present study, we report the co-option of L1 ORF1 as alternative exons...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...haploid s.De novo assembly provides essential insights into organism's biology and evolution by reconstructing its from short DNA fragments (or reads), without the access to the original genomic sequence. The assembly process is based on intricate methods on strings and graphs which were first introduced...
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Research: Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
- Éléonore Durand,
- Isabelle Gagnon-Arsenault,
- Johan Hallin,
- Isabelle Hatin,
- Alexandre K. Dubé,
- Lou Nielly-Thibault,
- Olivier Namy,
- and Christian R. Landry
Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
...process of de novo gene birth has been described with two hypotheses that consider selection as acting at different timepoints. The continuum hypothesis involves a gradual change of coding properties from nongenic to genic and was used to explain patterns related to the size of intergenic ORFs (Carvunis...
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