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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...affect the amount of host neurotransmitters (Zhang et al. 2022b) and modulate the social network (Liberti et al. 2022) as well as foraging-related behavior in bees (Liberti et al. 2024; Vernier et al. 2024). Honeybees are a model organism for gut microbiota research (Zheng et al. 2018) and have a simple...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...expression in biological systems. At the core of these networks lies the inference of gene regulation, which reflects the binding of transcription factors (TFs) to specific DNA sequences to either activate or repress target gene expression. This regulation directs crucial cellular processes...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...in pancreatic cancer tumors, while also being essential for pancreatic cancer cell proliferation. Using comparative nanopore direct RNA sequencing, we identify potential METTL2A-mediated m3C sites in poly(A) RNA. These m3C sites are mapped in both messenger RNA and mitochondrial RNA and are enriched in the CC...
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Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
- William R. Thomas,
- Cecilia Baldoni,
- Yuanyuan Zeng,
- David Carlson,
- Julie Holm-Jacobsen,
- Marion Muturi,
- Dominik von Elverfeldt,
- Tue B. Bennike,
- Dina K.N. Dechmann,
- John Nieland,
- Angelique P. Corthals,
- and Liliana M. Dávalos
Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
...) data set being smaller than the gene expression set (n = 24,205 transcripts), there was substantial overlap in direction, significance, and pathway enrichment of changes between the two (Supplemental Fig. S6; Supplemental Fig. S3). Using a linear model to estimate the correlation between differential...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...), but direct biochemical assessment of each variant in every relevant cell type and state remains impractical.An alternative approach is to train machine learning models on reference genomic sequence and then apply them to genetic variation data. Recent machine learning models including gkmSVM (Lee et al. 2015...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...basecalling models—arises from the fact that the DNA barcode is sequenced using the “RNA” chemistry, which exhibits several key differences to the DNA chemistry, preventing the use existing DNA basecalling models: (1) RNA is sequenced from its 3′ end (in 3′ > 5′ direction), while DNA is sequenced from its 5...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...over large physical distances, including action-at-a-distance, which suggests allostery between transcriptional regulators within a liquid droplet space (Bialek et al. 2019), and the transcription factor activity gradient model, which suggests a gradient-directed flow of activated transcription factors...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...directed GRNs by manually distinguishing TFs from target genes. More recently, deep learning has been introduced into GRN inference, with methods such as CNNGRN, which leverages convolutional neural networks to analyze bulk time-series gene expression data and infer regulatory interactions between TFs...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...Sat02/TCsat15 repeat. From this, we conclude that the major satellite TfSat01 is evolutionarily younger and that it emerged from TfSat02. A direct comparison of the TfSat01 consensus with the corresponding 166-bp segments of TfSat02 and TCsat15 showed that the TfSat02 and TCsat15 segments are more...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
..., in regulating alternative splicing in the brain. However, the underlying molecular mechanisms through which chromatin regulates signal-induced alternative splicing remain elusive.Direct membrane depolarization of primary neurons using potassium chloride (KCl) serves as a widely used model of neuronal activity...

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