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Corrigendum: Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing
- Kepin Wang,
- Qin Jin,
- Degong Ruan,
- Yi Yang,
- Qishuai Liu,
- Han Wu,
- Zhiwei Zhou,
- Zhen Ouyang,
- Zhaoming Liu,
- Yu Zhao,
- Bentian Zhao,
- Quanjun Zhang,
- Jiangyun Peng,
- Chengdan Lai,
- Nana Fan,
- Yanhui Liang,
- Ting Lan,
- Nan Li,
- Xiaoshan Wang,
- Xinlu Wang,
- Yong Fan,
- Pieter A. Doevendans,
- Joost P.G. Sluijter,
- Pentao Liu,
- Xiaoping Li,
- and Liangxue Lai
Genome Res. June 2025 35: 1472-2; doi:10.1101/gr.280849.125
...Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo editing Kepin Wang, Qin Jin, Degong Ruan, Yi Yang, Qishuai Liu, Han Wu, Zhiwei Zhou, Zhen Ouyang, Zhaoming Liu, Yu Zhao, Bentian Zhao, Quanjun Zhang, Jiangyun Peng, Chengdan Lai, Nana Fan, Yanhui Liang, Ting Lan, Nan Li...
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Method: Precise and efficient nucleotide substitution near genomic nick via noncanonical homology-directed repair
- Kazuhiro Nakajima,
- Yue Zhou,
- Akiko Tomita,
- Yoshihiro Hirade,
- Channabasavaiah B. Gurumurthy,
- and Shinichiro Nakada
Genome Res. February 2018 28: 223-230; Published in Advance December 22, 2017, doi:10.1101/gr.226027.117
...-sequence homology between the target gene and repair template, but does not require CtIP, RAD51, or RAD52. Thus, it is considered that noncanonical homology-directed repair regulates the SNGD-mediated gene editing. In summary, SNGD promotes precise and efficient gene editing and may be a promising strategy...
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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
...for substrate recognition (Grüne et al. 2003). ISWI complex partners determine the context of the complex activity and alter its remodeling efficiency (Längst et al. 1999; Toto et al. 2014). ISWI complexes have been shown to regulate DNA replication, transcription, DNA repair, and V(D)J cleavage...
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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
...the transcriptome (Eisenberg and Levanon 2018; Duan 2025). Editing events taking place in coding sequences (CDSs)might alter the genomically encoded amino acid and lead to nonsynonymous changes, namely, “recoding” (Alon et al. 2015). Genome-wide profiling of RNA editing sites has been performed in several metazoans...
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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
...source of dsRNA is cotranscription of sense and antisense strands of the same genomic region. Binding of these complementary, naturally occurring, antisense transcripts (NATs) results in a perfect RNA duplex, which may be targeted by ADARs. To explore the scope of ADAR editing of NAT-derived dsRNA, we...
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Method: Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases
- Séverine Remy,
- Laurent Tesson,
- Séverine Menoret,
- Claire Usal,
- Anne De Cian,
- Virginie Thepenier,
- Reynald Thinard,
- Daniel Baron,
- Marine Charpentier,
- Jean-Baptiste Renaud,
- Roland Buelow,
- Gregory J. Cost,
- Carine Giovannangeli,
- Alexandre Fraichard,
- Jean-Paul Concordet,
- and Ignacio Anegon
Genome Res. August 2014 24: 1371-1383; Published in Advance July 2, 2014, doi:10.1101/gr.171538.113
...-specific nucleases, such as ZFNs, TALE nucleases, and CRISPR/Cas9 have allowed the creation of rat knockout models. Genetic engineering by homology-directed repair (HDR) is utilized to create animals expressing transgenes in a controlled way and to introduce precise genetic modifications. We applied TALE nucleases...
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Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
- Junhai Qi,
- Zhidong Yang,
- Ting Yu,
- and Guojun Li
Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
...annotation of centromere with centroanno. bioRxiv doi: 10.1101/123456 .362 Ren J, Gu B, and Chaisson MJ. 2023. Vamos: variable-number tandem repeats annotation using efficient motif sets. Genome Biology 24: 175.363 Ting DT, Lipson D, Paul S, Brannigan BW, Akhavanfard S, Coffman EJ, Contino G, Deshpande V...
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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
...editing efficiency. This approach led to the successful generation of xenotransplantation pigs with multiple homozygously edited genes in a much shorter time frame than previously achievable.ResultsSurrogate reporters for genomic targetingEfficient selection methods are essential for enhancing multiplex...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...@bham.ac.ukAbstractA single guide RNA (sgRNA) directs Cas9 nuclease for gene-specific scission of double-stranded DNA. High Cas9 activity is essential for efficient gene editing to generate gene deletions and gene replacements by homologous recombination. However, cleavage efficiency is below 50...
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Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
- Kristine Bilgrav Saether,
- Angelo Salazar Mantero,
- Marlene Ek,
- Maria Pettersson,
- Elisabeth Syk Lundberg,
- Christopher M. Grochowski,
- Claudia M.B. Carvalho,
- Jesper Eisfeldt,
- and Anna Lindstrand
Genome Res. April 2026 36: 661-670; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
...chromosome arm, followed by direct end-to-end fusion via double-strand break repair mechanisms. However, recently it has been shown that sSRCs may form through mechanisms related to the formation of complex genomic rearrangements, such as breakage–fusion–bridge (BFB) cycles (Nazaryan-Petersen et al. 2018...
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