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Method: JACKS: joint analysis of CRISPR/Cas9 knockout screens
- Felicity Allen,
- Fiona Behan,
- Anton Khodak,
- Francesco Iorio,
- Kosuke Yusa,
- Mathew Garnett,
- and Leopold Parts
Genome Res. March 2019 29: 464-471; Published in Advance January 23, 2019, doi:10.1101/gr.238923.118
...: In this window In a new window Figure 1. Joint analysis of several CRISPR/Cas9 knockout screens. (A) JACKS inferred decomposition of median-normalized log2 fold change (heatmap) for six gRNAs targeting the KRAS gene (y-axis, GeCKOv2 library) in 25 cancer cell lines from Aguirre et al. (2016) (x...
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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...Technology, #07922) (see Supplemental Methods; Supplemental Table S11).Preparation of vectors for transfectionTwo vectors were purchased: (1) CMV-rtTA-HygR vector (Addgene, #102423) and (2) CRISPR-Cas9 vectors containing gRNA sequence for TP53 (Addgene, #121917). To generate the pPB-CMVmin-APOBEC (A3A or A3B...
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Method: 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. December 2017 27: 2061-2071; Published in Advance November 16, 2017, doi:10.1101/gr.222521.117
...representation of porcine EML4–ALK rearrangements induced by CRISPR-Cas9. EML4-sgRNA and ALK-sgRNA (red) were designed to target the mutation sites of the porcine EML4 gene intron 14 and porcine ALK gene intron 13. PCR primers are indicated (primers A, B, C, and D). (B) PCRs were performed to analyze ALK–EML4...
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Research: Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- Raquel Ordoñez,
- Marta Kulis,
- Nuria Russiñol,
- Vicente Chapaprieta,
- Arantxa Carrasco-Leon,
- Beatriz García-Torre,
- Stella Charalampopoulou,
- Guillem Clot,
- Renée Beekman,
- Cem Meydan,
- Martí Duran-Ferrer,
- Núria Verdaguer-Dot,
- Roser Vilarrasa-Blasi,
- Paula Soler-Vila,
- Leire Garate,
- Estíbaliz Miranda,
- Edurne San José-Enériz,
- Juan R. Rodriguez-Madoz,
- Teresa Ezponda,
- Rebeca Martínez-Turrilas,
- Amaia Vilas-Zornoza,
- David Lara-Astiaso,
- Daphné Dupéré-Richer,
- Joost H.A. Martens,
- Halima El-Omri,
- Ruba Y. Taha,
- Maria J. Calasanz,
- Bruno Paiva,
- Jesus San Miguel,
- Paul Flicek,
- Ivo Gut,
- Ari Melnick,
- Constantine S. Mitsiades,
- Jonathan D. Licht,
- Elias Campo,
- Hendrik G. Stunnenberg,
- Xabier Agirre,
- Felipe Prosper,
- and Jose I. Martin-Subero
Genome Res. September 2020 30: 1217-1227; Published in Advance August 20, 2020, doi:10.1101/gr.265520.120
...aimed to characterize the pathogenic implication of TXN deregulation in MM cells. TXN inactivation using the CRISPR-Cas9 strategy in MM cell lines (Fig. 3C,D; Supplemental Figs. S12B,C, S13) led to a significant reduction of growth rate as compared to control cells (Fig. 3E; Supplemental Fig. S12D...
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Method: Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing
- Renato Salazar,
- Barbara Arbeithuber,
- Maja Ivankovic,
- Monika Heinzl,
- Sofia Moura,
- Ingrid Hartl,
- Theresa Mair,
- Angelika Lahnsteiner,
- Thomas Ebner,
- Omar Shebl,
- Johannes Pröll,
- and Irene Tiemann-Boege
Genome Res. March 2022 32: 499-511; Published in Advance February 24, 2022, doi:10.1101/gr.275695.121
...DNA, followed by size selection. Like the CRISPR-Cas9 approach (Nachmanson et al. 2018), this also enables the selection of predetermined target fragments, achieving also a low number of off-targets. Further enrichment of targeted regions is performed by two rounds of hybridization capture followed...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...in these samples (two-sided Fisher's exact test, P-value = 9.9 × 10−21), with only four fusions (2× FGFR2-COL14A1, 1× DNAJB1-PRKACA, 1× KANK1-NTRK3) being found in KRAS mutant tumors (Supplemental Table S5). In 79 tumors, we detected neither a KRAS mutation nor a driving fusion. To rule out the possibility that we...
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Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
.... For this purpose, we combined CRISPR-Cas9 technology with the DNA-damage responsive system to investigate the expression of TP53-regulated lncRNAs, following by ribosome profiles and mass spectrometry (MS) methods to explore the translational potentials of lncRNAs in adriamycin (ADR)-treated HepG2 cells...
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Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...–phenotype relationship describes how genetic variations induce biological change (Manolio et al. 2009). Experimental screens tracking the effect of these variations include RNA interference (RNAi) (Boutros and Ahringer 2008), CRISPR-Cas9 knockouts (Mali et al. 2013; Koike-Yusa et al. 2014; Wang et al. 2014b; Hart et al...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
.... Such screens, if sufficiently unbiased, could in theory capture the entire breadth of genetic resistance mechanisms for any drug. Recent studies have demonstrated the power of both -wide gain- and loss-offunction screens using CRISPR/Cas9, lentiviral shRNA, and largescale open-reading frame technologies...
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