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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...I:C), a synthetic viral mimic, and 19 profile transcriptomic and epigenomic responses in the primary haematopoietic and 20 lymphoid tissue. We used ATAC-seq and ChIP-seq (H3K27ac and H3K27me3), combined 21 with mRNA-seq, to comprehensively examine modifications in gene regulation following 22...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...been reported in studies using long-read sequencing of nascent RNA, 91 where transcripts were found to be either fully spliced or completely unspliced , with a 92 smaller group of transcripts showing a mixture of spliced and unspliced introns (Herzel 93 et al. 2018; Drexler et al. 2020). However, after...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...synthesis) and synthesis of precursors for macromolecules (amino acids for proteins and nucleoside triphosphates for DNA and RNA synthesis). In some cases, as studied here, recombination is critical for viral DNA replication, which together produce concatemeric DNA essential for viral packaging...
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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...samples from the Himalaya region and Sri Lanka (2014). For subsocial species, we collected S. lineatus from the Negev Desert in Israel (2020), S. bicolor from Betta in Namibia (2021), and S. tentoriicola from Tierberg in South Africa (2015). S. africanus RNA data were previously published by Bechsgaard et...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
.... 2015; Warburton et al. 2021). Some of these apparent discrepancies may be attributed to differences in the sequencing approaches used (i.e., whole , HPV capture, RNA) (Fan et al. 2023). HPV integration sites are also associated with dense structural alterations, perhaps as a result of unstable HPV...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...-read sequencing technologies in annotation, we acknowledge several limitations in our work. First, we provided AUGUSTUS with relatively simple lrRNA-seq data sets (one cell line in human and two tissues for the manatee) to evaluate prediction accuracy. Genome annotation efforts often use multiple tissue types...
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Research: Genomic insights into metabolic flux in hummingbirds
- Ariel Gershman,
- Quinn Hauck,
- Morag Dick,
- Jerrica M. Jamison,
- Michael Tassia,
- Xabier Agirrezabala,
- Saad Muhammad,
- Raafay Ali,
- Rachael E. Workman,
- Mikel Valle,
- G. William Wong,
- Kenneth C. Welch, Jr.,
- and Winston Timp
Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122
...-read sequencing were generated with the cDNA PCR sequencing kit (SQK-PCS109) from Oxford Nanopore Technologies according to the manufacturer's instructions. Libraries were each sequenced on a PromethION flow cell for 72 h.Genome annotation and transcriptome assemblyIllumina RNA-seq reads were trimmed...
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Method: Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
- Matthew D. Parker,
- Benjamin B. Lindsey,
- Shay Leary,
- Silvana Gaudieri,
- Abha Chopra,
- Matthew Wyles,
- Adrienn Angyal,
- Luke R. Green,
- Paul Parsons,
- Rachel M. Tucker,
- Rebecca Brown,
- Danielle Groves,
- Katie Johnson,
- Laura Carrilero,
- Joe Heffer,
- David G. Partridge,
- Cariad Evans,
- Mohammad Raza,
- Alexander J. Keeley,
- Nikki Smith,
- Ana Da Silva Filipe,
- James G. Shepherd,
- Chris Davis,
- Sahan Bennett,
- Vattipally B. Sreenu,
- Alain Kohl,
- Elihu Aranday-Cortes,
- Lily Tong,
- Jenna Nichols,
- Emma C. Thomson,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Dennis Wang,
- Simon Mallal,
- and Thushan I. de Silva
Genome Res. April 2021 31: 645-658; Published in Advance March 15, 2021, doi:10.1101/gr.268110.120
...: t.desilva@sheffield.ac.ukAbstractWe have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA for most open reading frames (ORFs) occurs via RNA intermediates termed “subgenomic RNAs.” sgRNAs...
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Research: Single-cell discovery of m⁶A RNA modifications in the hippocampus
- Shuangshuang Feng,
- Maitena Tellaetxe-Abete,
- Yujie Zhang,
- Yan Peng,
- Han Zhou,
- Mingjie Dong,
- Erika Larrea,
- Liang Xue,
- Li Zhang,
- and Magdalena J. Koziol
Genome Res. June 2024 34: 822-836; Published in Advance July 15, 2024, doi:10.1101/gr.278424.123
...; Jiang et al. 2021). Cell-specific m6A levels have been noted in the cerebellum and cortex, suggesting potential cell type–specific functions (Chang et al. 2017).To uncover the landscape of m6A RNA methylation in hippocampal cells, we employ single-cell sequencing. Single-cell sequencing technologies...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...-encoded helicases are 91% identical at the amino acid level (Lahn and Page 1997). Although they have significantly diverged in their N- and C-terminal regions, the RNA binding and helicase domains are largely conserved (Rosner and Rinkevich 2007). Early experiments showed that the DDX3Y protein was functionally...
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