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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 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...2021). In spite of this, comparative genomics analyses indicate 64 that short discrete non-coding regions of the display a high degree of sequence 65 conservation across hundreds of million years of evolution (Elgar 2009; Vavouri and Lehner 66 2009; Nelson and Wardle 2013; Polychronopoulos et al. 2017...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...to annotate cell classes. For UMAP 485 visualization, the IntegrateData function was used to create the co-embedding space. 486 Consensus scores were calculated as the number of nuclei within a cluster annotated as the 487 corresponding cell class in the scRNA-seq data divided by the number of nuclei...
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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
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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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
...6BT, United Kingdom; 2Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; 3Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 4University College London Cancer...
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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
...a moderate signal for habitat-related convergent evolution of gene expression levels, whereas the Murinae_expr data set displays a stronger signal.Transcriptome convergence is associated with convergent shifts in kidney cell compositionTissue bulk RNA-seq data reflect variation in both expression per cell...
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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...16802, USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractCircular RNA (circRNA) is a class of RNA molecules that forms a closed loop with their 5′ and 3′ ends covalently bonded. CircRNAs are known to be more stable than linear RNAs, have distinct...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...Present address: AstraZeneca Discovery Sciences, Translational Genomics, 43183 Mölndal, Sweden Corresponding author: michiel.dehoon@riken.jpAbstractIn eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), with the 3D remodeling of chromatin structures, and with recombination processes, such as gene conversion (Cheetham et al. 2020). These protein-independent functions might explain the conservation of “pseudogenes” that still have biological...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...and identified thousands of endogenous loci representing dozens of unique elements that give rise to mostly low to moderate levels of siRNAs, called 23H-RNAs. These loci include repetitive elements, putative coding genes, pseudogenes, noncoding RNAs, and unannotated features, many of which adopt hairpin (hp...
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Resource: Functional annotation of human long noncoding RNAs via molecular phenotyping
- Jordan A. Ramilowski,
- Chi Wai Yip,
- Saumya Agrawal,
- Jen-Chien Chang,
- Yari Ciani,
- Ivan V. Kulakovskiy,
- Mickaël Mendez,
- Jasmine Li Ching Ooi,
- John F. Ouyang,
- Nick Parkinson,
- Andreas Petri,
- Leonie Roos,
- Jessica Severin,
- Kayoko Yasuzawa,
- Imad Abugessaisa,
- Altuna Akalin,
- Ivan V. Antonov,
- Erik Arner,
- Alessandro Bonetti,
- Hidemasa Bono,
- Beatrice Borsari,
- Frank Brombacher,
- Christopher J.F. Cameron,
- Carlo Vittorio Cannistraci,
- Ryan Cardenas,
- Melissa Cardon,
- Howard Chang,
- Josée Dostie,
- Luca Ducoli,
- Alexander Favorov,
- Alexandre Fort,
- Diego Garrido,
- Noa Gil,
- Juliette Gimenez,
- Reto Guler,
- Lusy Handoko,
- Jayson Harshbarger,
- Akira Hasegawa,
- Yuki Hasegawa,
- Kosuke Hashimoto,
- Norihito Hayatsu,
- Peter Heutink,
- Tetsuro Hirose,
- Eddie L. Imada,
- Masayoshi Itoh,
- Bogumil Kaczkowski,
- Aditi Kanhere,
- Emily Kawabata,
- Hideya Kawaji,
- Tsugumi Kawashima,
- S. Thomas Kelly,
- Miki Kojima,
- Naoto Kondo,
- Haruhiko Koseki,
- Tsukasa Kouno,
- Anton Kratz,
- Mariola Kurowska-Stolarska,
- Andrew Tae Jun Kwon,
- Jeffrey Leek,
- Andreas Lennartsson,
- Marina Lizio,
- Fernando López-Redondo,
- Joachim Luginbühl,
- Shiori Maeda,
- Vsevolod J. Makeev,
- Luigi Marchionni,
- Yulia A. Medvedeva,
- Aki Minoda,
- Ferenc Müller,
- Manuel Muñoz-Aguirre,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Kazuhiro R. Nitta,
- Shuhei Noguchi,
- Yukihiko Noro,
- Ramil Nurtdinov,
- Yasushi Okazaki,
- Valerio Orlando,
- Denis Paquette,
- Callum J.C. Parr,
- Owen J.L. Rackham,
- Patrizia Rizzu,
- Diego Fernando Sánchez Martinez,
- Albin Sandelin,
- Pillay Sanjana,
- Colin A.M. Semple,
- Youtaro Shibayama,
- Divya M. Sivaraman,
- Takahiro Suzuki,
- Suzannah C. Szumowski,
- Michihira Tagami,
- Martin S. Taylor,
- Chikashi Terao,
- Malte Thodberg,
- Supat Thongjuea,
- Vidisha Tripathi,
- Igor Ulitsky,
- Roberto Verardo,
- Ilya E. Vorontsov,
- Chinatsu Yamamoto,
- Robert S. Young,
- J. Kenneth Baillie,
- Alistair R.R. Forrest,
- Roderic Guigó,
- Michael M. Hoffman,
- Chung Chau Hon,
- Takeya Kasukawa,
- Sakari Kauppinen,
- Juha Kere,
- Boris Lenhard,
- Claudio Schneider,
- Harukazu Suzuki,
- Ken Yagi,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- and Piero Carninci
Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
..., Connecticut 06510, USA ↵47 These authors contributed equally to this work. Corresponding authors: michiel.dehoon@riken.jp, jay.shin@riken.jp, carninci@riken.jpAbstractLong noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian s, and yet, their functions remain largely unknown...
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