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Insights from Genome Editing

Guest Editors: Jin-Soo Kim and Fyodor Urnov

InsightsfromGenomeEditingSIPageResized

We are pleased to announce the publication of our special issue on Insights from Genome Editing, guest edited by  Jin-Soo Kim of the Seoul National University and Fyodor Urnov of the Altius Institute for Biomedical Sciences.

Genome editing-based technology not only provides efficient tools for editing the genome in cell lines, model organisms and agriculturally important species, but has also found application in imaging genome compartments, regulation of gene expression and as an additional means of experimental validation. New findings in genome editing are advancing genome studies at an unprecedented pace.

We highlight insights into these fields that use genome editing methods in this special issue, including new Research, Method, Reviews, Research Highlights, and more. 

  1. Content type: Short Report

    Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we ...

    Authors: Christopher L. Nobles, Shantan Reddy, January Salas-McKee, Xiaojun Liu, Carl H. June, J. Joseph Melenhorst, Megan M. Davis, Yangbing Zhao and Frederic D. Bushman

    Citation: Genome Biology 2019 20:14

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  2. Content type: Research

    Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis ele...

    Authors: Shuai Wei, He Chen, Emmanuel Enoch Dzakah, Bin Yu, Xiaolin Wang, Tao Fu, Jingxin Li, Lei Liu, Shucheng Fang, Weihong Liu and Ge Shan

    Citation: Genome Biology 2019 20:7

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  3. Content type: Research

    The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild...

    Authors: Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Paul D. Donohoue, Alexander H. Settle, Alexandra M. Lied, Kyle McGovern, Chris K. Fuller, Peter Cameron, Thomas G. Fazzio…

    Citation: Genome Biology 2018 19:214

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  4. Content type: Review

    Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism’s genome. Genome-editing systems have been utilized in a wide variet...

    Authors: Yi Zhang, Karen Massel, Ian D. Godwin and Caixia Gao

    Citation: Genome Biology 2018 19:210

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    The Correction to this article has been published in Genome Biology 2019 20:13

  5. Content type: Review

    The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impa...

    Authors: Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J. McGrew, Alan L. Archibald, Helen M. Sang, Ross D. Houston, C. Bruce Whitelaw and Mick Watson

    Citation: Genome Biology 2018 19:204

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  6. Content type: Short report

    The CRISPR/Cas9 system has recently been engineered to confer resistance to geminiviruses in plants. However, we show here that the usefulness of this antiviral strategy is undermined by off-target effects ide...

    Authors: Xiang Ji, Xiaomin Si, Yi Zhang, Huawei Zhang, Feng Zhang and Caixia Gao

    Citation: Genome Biology 2018 19:197

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  7. Content type: Short report

    CRISPR/dCas9 is a versatile tool that can be used to recruit various effectors and fluorescent molecules to defined genome regions where it can modulate genetic and epigenetic markers, or track the chromatin d...

    Authors: Jinzhi Duan, Guangqing Lu, Yu Hong, Qingtao Hu, Xueying Mai, Jing Guo, Xiaofang Si, Fengchao Wang and Yu Zhang

    Citation: Genome Biology 2018 19:192

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  8. Content type: Research

    Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA dou...

    Authors: Tao Guo, Yi-Li Feng, Jing-Jing Xiao, Qian Liu, Xiu-Na Sun, Ji-Feng Xiang, Na Kong, Si-Cheng Liu, Guo-Qiao Chen, Yue Wang, Meng-Meng Dong, Zhen Cai, Hui Lin, Xiu-Jun Cai and An-Yong Xie

    Citation: Genome Biology 2018 19:170

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  9. Content type: Method

    CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis...

    Authors: Vivien A. C. Schoonenberg, Mitchel A. Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello and Daniel E. Bauer

    Citation: Genome Biology 2018 19:169

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  10. Content type: Research

    Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the func...

    Authors: Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie and Peggy J. Farnham

    Citation: Genome Biology 2018 19:160

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  11. Content type: Research Highlight

    Two articles recently described the development of CRISPR technologies that have the potential to fundamentally transform the barcoding and tracing of mammalian cells.

    Authors: Thomas Gaj and Pablo Perez-Pinera

    Citation: Genome Biology 2018 19:143

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  12. Content type: Research

    Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) ...

    Authors: Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue and Erik J. Sontheimer

    Citation: Genome Biology 2018 19:137

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  13. Content type: Research

    Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncoge...

    Authors: Ruiqi Han, Li Li, Alejandro Piñeiro Ugalde, Arieh Tal, Zohar Manber, Eric Pinto Barbera, Veronica Della Chiara, Ran Elkon and Reuven Agami

    Citation: Genome Biology 2018 19:118

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  14. Content type: Method

    CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the s...

    Authors: Michael Gapinske, Alan Luu, Jackson Winter, Wendy S. Woods, Kurt A. Kostan, Nikhil Shiva, Jun S. Song and Pablo Perez-Pinera

    Citation: Genome Biology 2018 19:107

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