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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...-ornstein@primemedicine.comAbstractGene editing makes precise changes in DNA to restore normal function or expression of genes; however, the advancement of gene editing to the clinic is limited by the potential genotoxicity of off-target editing. To comprehensively identify potential sites in the that may be recognized by gene editing agents...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...Highly efficient and scarless editing via essential gene-coupled 1 homology-directed repair 2 Running title: Efficient scarless editing via essential gene HDR 3 4 Joo Hye Yeo1,2,3, Hyongbum Henry Kim2,3,4,5,6,7,8,9, Sang Ho Oh10, Jinu Lee1,* 5 6 1College of Pharmacy, Yonsei Institute...
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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
...to construct RNA-seq libraries, and bodies were subjected to DNA resequencing. The reliable RNA–DNA differences (RDDs) were regarded as RNA editing sites. (B) The number of different types of mismatches in the RDDs. Only the RDDs in the genic region were considered. A-to-G RDDs represent A-to-I RNA editing...
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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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Resource: DEAD box RNA helicases are pervasive protein kinase interactors and activators
- Alexander Hirth,
- Edoardo Fatti,
- Eugen Netz,
- Sergio P. Acebron,
- Dimitris Papageorgiou,
- Andrea Švorinić,
- Cristina-Maria Cruciat,
- Emil Karaulanov,
- Alexandr Gopanenko,
- Tianheng Zhu,
- Irmgard Sinning,
- Jeroen Krijgsveld,
- Oliver Kohlbacher,
- and Christof Niehrs
Genome Res. June 2024 34: 952-966; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123
...helicases, a protein array profiling for direct DDX binding partners, and a kinome-wide in vitro kinase activity screen. Taken together, these screens support a pervasive function of DDX proteins as kinetic modifiers of protein kinases and provide a resource to explore the underlying regulatory relationship...
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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: A 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 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
....1016/S00222836(05)80360-2 Athanasiadis A, Rich A,Maas S. 2004.Widespread A-to-I RNA editing of Alucontaining mRNAs in the human transcriptome. PLoS Biol 2: e391. doi:10.1371/journal.pbio.0020391 Azad MTA, Bhakta S, Tsukahara T. 2017. Site-directed RNA editing by adenosine deaminase acting on RNA...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
..., and cap analysis gene expression (CAGE-seq) data, by rescuing non-uniquely mapped reads. An average of 15% more reads can be rescued using this algorithm for constructing epigenomic or expression profiles on TEs (Supplemental Figure S1). The front-end of the WashU Repeat Browser provides intuitive data...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...PCR and high-throughput sequencing. No significant off-target effects were detected by this method (Supplemental Fig. S5). RNA-seq analysis of seven-gene-edited cells revealed increased expression of genes involved in DNA replication, repair pathways, p53 signaling, and cancer-related pathways...
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Method: Global quantification exposes abundant low-level off-target activity by base editors
- Ilana Buchumenski,
- Shalom Hillel Roth,
- Eli Kopel,
- Efrat Katsman,
- Ariel Feiglin,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. December 2021 31: 2354-2361; Published in Advance October 19, 2021, doi:10.1101/gr.275770.121
....levanon@biu.ac.ilAbstractBase editors are dedicated engineered deaminases that enable directed conversion of specific bases in the or transcriptome in a precise and efficient manner, and hold promise for correcting pathogenic mutations. A major concern limiting application of this powerful approach is the issue of off-target edits...

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