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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
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- 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 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...to similar consequences to 46 A-to-G mutations, diversifying the transcriptome (Eisenberg and Levanon 2018; Duan 47 2025). Editing events taking place in coding sequence (CDS) might alter the genomically 48 encoded amino acid and lead to nonsynonymous changes, namely “recoding” (Alon et al. 49 2015). Genome...
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Method: A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
- Yarui Diao,
- Bin Li,
- Zhipeng Meng,
- Inkyung Jung,
- Ah Young Lee,
- Jesse Dixon,
- Lenka Maliskova,
- Kun-liang Guan,
- Yin Shen,
- and Bing Ren
Genome Res. March 2016 26: 397-405; Published in Advance January 26, 2016, doi:10.1101/gr.197152.115
...A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening Yarui Diao 1 , 7 , Bin Li 1 , Zhipeng Meng 2 , Inkyung Jung 1 , Ah Young Lee 1 , Jesse Dixon 1 , 3 , 4 , Lenka Maliskova...
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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
....swart@tuebingen.mpg.de, aditi.singh@tuebingen.mpg.deAbstractOne of the most extensive forms of natural editing occurs in ciliates, a group of microbial eukaryotes. Ciliate germline and somatic s are contained in distinct nuclei within the same cell. During the massive reorganization process of somatic development, ciliates...
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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
...gene is initially frameshifted owing to the insertion of a CRISPR target site adjacent to the “ATG” start codon. CRISPR-Cas9 mediated editing results in insertions and deletions (indels) that restore the correct reading frame of the reporter gene. (B) Workflow for assessing the correlation between...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
...). Here we report CRISPR/Cas9-mediated knock-in of DNA cassettes into the zebrafish genome at a very high rate by homology-independent double-strand break (DSB) repair pathways. After co-injection of a donor plasmid with a short guide RNA (sgRNA) and Cas9 nuclease mRNA, concurrent cleavage of donor...
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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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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
...are transcribed, assess whether such originates from intermolecular dsRNA structures, and evaluate evidence for coordinated editing activity on both strands. Results We employed a genomic-based approach to identify candidate regions in the human where both strands are expressed and edited concurrently (Figure 1...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...generating crucial control data sets: the 1000 Genomes Project ONT Sequencing Consortium is producing LRS data from 1kGP samples to aid in filtering and prioritizing SNVs and SVs (Gustafson et al. 2024), while the All of Us (AoU) initiative has begun a long-read arm to sequence blood samples from Americans...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...Bafna1,4 1Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA; 2Bionano Genomics, Incorporated, San Diego, California 92121, USA; 3Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090...
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