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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
...of Plant Protection, China Agricultural University, Beijing 100193, China ADAR-mediated adenosine-to-inosine (A-to-I) mRNA editing contributes to the proteomic diversity and behavioral complexity of animals. Although recent studies indicate that the gut microbiome influences various aspects of animal...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
..., Israel 3Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv, University, Tel Aviv 6997801, Israel *These authors contributed equally to this work. Corresponding authors: Eli Eisenberg, elieis@post.tau.ac.il and Erez Y. Levanon, erez.levanon@biu.ac.il. Abstract A-to-I RNA editing...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels Brigitta Szabo, Therese C. Mandl, Bernhard Woldrich, Gregor Diensthuber, David Martin, Michael F. Jantsch and Konstantin Licht Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical...
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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
...). The chromosome-level assemblies are masked using RepeatMasker (Tarailo-Graovac and Chen 2009) and their corresponding repeat libraries. We used STAR (Dobin et al. 2013) to align RNA-seq reads to the repeat-masked as transcriptome evidence for gene prediction in BRAKER2. For protein homology evidence, we used...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...for biases introduced by LD, by including both SNP-based relationship and haplotype-based IBD matrices (Supplemental Fig. S6). A previous study predicted mRNA abundance for each haplotype in the NAM population, similar to our prediction of protein structures (Giri et al. 2021). Importantly, in this study...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...and predictors based on DEGs identified in our study and across multiple published data sets, which predict disease across SOD1 mutations and species.DiscussionWe conducted RNA sequencing analysis of MNs displaying differential vulnerability to degeneration in ALS to unveil mechanisms of protection...
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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...authors: Michael.Jantsch@meduniwien.ac.at, Konstantin.Licht@meduniwien.ac.atAbstractPre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs...
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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
...to eliminate 557 them from the transcriptome. Why would cells expend time and energy transcribing 558 genes into pre-mRNA that is not spliced and destined for degradation? A possible 559 explanation is that this excessive transcription is utilized for DNA damage scanning in a 560 mutation-suppressing mechanism...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...cosilencing. Allowing no mismatches and searching the “Paramecium tetraurelia strain 51 transcript (v2.0)” database, ParameciumDB's off-target tool (Arnaiz et al. 2020) predicted a 24 bp window in the ICOPb RNAi construct that could cosilence the endogenous ICOPa gene (Paramecium siRNAs are typically 23 nt...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...Chimeric mitochondrial RNA transcripts predict mitochondrial deletion mutations in mitochondrial genetic diseases and aging Amy R. Vandiver1,2, Allen Herbst3,5, Paul Stothard3 and Jonathan Wanagat2,4 1Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los...

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