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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: 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
...these markers with green fluorescent protein (GFP) in 238 the sgRNA–Cas9 expression constructs (Supplemental Fig. S4A–C). The detection of 239 transient GFP expression enabled the rapid and non-toxic isolation of transfected cells 240 by FACS, which allows for precision gating based on fluorescence intensity...
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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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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
...).PCRs on genomic DNA from the cells that completed MAC development were used to check whether the ICOP KDs affect IES excision (Fig. 4C). Longer fragments containing IESs (IES+) were amplified in all KD permutations, suggesting ICOPs are essential during editing.Next, we investigated the -wide effect of ICOP KDs...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...To comprehensively profile alternative polyadenylation across pig tissues, we analyzed 10x Genomics single-nucleus RNA sequencing (10x snRNA-seq) data from our previous study as a preprint on bioRxiv (Chen et al. 2023), which identified 261 cell subtypes spanning 19 distinct pig tissues (Supplemental Table S1...
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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
.... Science (1979) 309: 1564–1566. doi:10.1126/science.1112009 Katrekar D, Yen J, Xiang Y, Saha A, Meluzzi D, Savva Y, Mali P. 2022. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Nat Biotechnol 40: 938–945. doi:10 .1038/s41587-021-01171-4 Kim DDY...
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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
...consumption, while41 reducing the sensitivity of decomposition results to parameter settings. These improvements enable more robust,42 accurate, and efficient analysis of TR reads and assemblies.43 1 1 1 1 AA A T T A A A Input Output AA A T T A A A Tandem Repeat Sequence: R AA A TT T STRs LTRs Template...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...six different genomic deletions spanning RE1–3 (Supplemental Fig. S48B) or sgRNAs for mCherry or EGFP as controls. The Cas9 protein was equally expressed from all vectors in C1 cells compared with GAPDH (Supplemental Fig. S48C). After 2 days of puromycin selection for Cas9-expressing C1 cells, we...
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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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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
...for graphs. Bioinformatics 37: i460–i467. doi:10.1093/bioinformatics/btab302 ↵Letcher B, Hunt M, Iqbal Z. 2021. Gramtools enables multiscale variation analysis with graphs. Genome Biol 22: 259. doi:10.1186/s13059-021-02474-0 ↵Li H. 2022. Sample graphs and sequences for testing sequence-to-graph alignment...

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