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Genome editing

Guest Editors: Jennifer Doudna and Charles Gersbach

Advances in the development of genome engineering tools — such as zinc finger proteins, TALEs, and more recently the CRISPR/Cas9 system — are allowing us to study the genomes of diverse organisms at the functional level with unprecedented ease and accuracy.

Genome Biology highlights this young, dynamic field with a special issue covering the applications of genome editing technologies in all kingdoms of life, both wet-lab and computational methodological advances, novel insights into the biology of naturally occurring CRISPR/Cas systems, discussions on the challenges and opportunities of these new techniques, and more.

In addition to the selection of articles below, here you can also find a series of blogs and Author Q&As on Genome Biology articles and other interesting studies from the field of genome editing.

  1. Research

    Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design

    Genome-scale CRISPR interference (CRISPRi) has been used in human cell lines; however, the features of effective guide RNAs (gRNAs) in different organisms have not been well characterized. Here, we define rule...

    Justin D. Smith, Sundari Suresh, Ulrich Schlecht, Manhong Wu, Omar Wagih, Gary Peltz, Ronald W. Davis, Lars M. Steinmetz, Leopold Parts and Robert P. St.Onge

    Genome Biology 2016 17:45

    Published on: 8 March 2016

  2. Review

    Towards a new era in medicine: therapeutic genome editing

    Genome editing is the process of precisely modifying the nucleotide sequence of the genome. It has provided a powerful approach to research questions but, with the development of a new set of tools, it is now ...

    Matthew H. Porteus

    Genome Biology 2015 16:286

    Published on: 22 December 2015

  3. Method

    Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR

    High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VI...

    Wei Li, Johannes Köster, Han Xu, Chen-Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown and X. Shirley Liu

    Genome Biology 2015 16:281

    Published on: 16 December 2015

  4. Research

    Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency

    Single-guide RNA (sgRNA) is one of the two key components of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome-editing system. The current commonly used sgRNA structure has a s...

    Ying Dang, Gengxiang Jia, Jennie Choi, Hongming Ma, Edgar Anaya, Chunting Ye, Premlata Shankar and Haoquan Wu

    Genome Biology 2015 16:280

    Published on: 15 December 2015

  5. Research

    Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease

    The RNA-guided Cas9 system represents a flexible approach for genome editing in plants. This method can create specific mutations that knock-out or alter target gene function. It provides a valuable tool for p...

    Tom Lawrenson, Oluwaseyi Shorinola, Nicola Stacey, Chengdao Li, Lars Østergaard, Nicola Patron, Cristobal Uauy and Wendy Harwood

    Genome Biology 2015 16:258

    Published on: 30 November 2015

  6. Review

    Resources for the design of CRISPR gene editing experiments

    CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tool...

    Daniel B. Graham and David E. Root

    Genome Biology 2015 16:260

    Published on: 27 November 2015

  7. Research

    Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications

    CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the s...

    Ari E. Friedland, Reshica Baral, Pankhuri Singhal, Katherine Loveluck, Shen Shen, Minerva Sanchez, Eugenio Marco, Gregory M. Gotta, Morgan L. Maeder, Edward M. Kennedy, Anand V. R. Kornepati, Alexander Sousa, McKensie A. Collins, Hari Jayaram, Bryan R. Cullen and David Bumcrot

    Genome Biology 2015 16:257

    Published on: 24 November 2015

  8. Method

    Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements

    To expand the repertoire of Cas9s available for genome targeting, we present a new in vitro method for the simultaneous examination of guide RNA and protospacer adjacent motif (PAM) requirements. The method relie...

    Tautvydas Karvelis, Giedrius Gasiunas, Joshua Young, Greta Bigelyte, Arunas Silanskas, Mark Cigan and Virginijus Siksnys

    Genome Biology 2015 16:253

    Published on: 19 November 2015

  9. Research Highlight

    Boosting plant immunity with CRISPR/Cas

    CRISPR/Cas has recently been transferred to plants to make them resistant to geminiviruses, a damaging family of DNA viruses. We discuss the potential and the limitations of this method.

    Angela Chaparro-Garcia, Sophien Kamoun and Vladimir Nekrasov

    Genome Biology 2015 16:254

    Published on: 19 November 2015

  10. Research

    Zinc finger nuclease-based double-strand breaks attenuate malaria parasites and reveal rare microhomology-mediated end joining

    Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombinati...

    Mirko Singer, Jennifer Marshall, Kirsten Heiss, Gunnar R. Mair, Dirk Grimm, Ann-Kristin Mueller and Friedrich Frischknecht

    Genome Biology 2015 16:249

    Published on: 17 November 2015

  11. Research Highlight

    The Cpf1 CRISPR-Cas protein expands genome-editing tools

    CRISPR-Cas systems have immense biotechnological utility. A recent study reveals the potential of the Cpf1 nuclease to complement and extend the existing CRISPR-Cas9 genome-editing tools.

    Robert D. Fagerlund, Raymond H. J. Staals and Peter C. Fineran

    Genome Biology 2015 16:251

    Published on: 17 November 2015

  12. Research

    CRISPR/Cas9-mediated viral interference in plants

    The CRISPR/Cas9 system provides bacteria and archaea with molecular immunity against invading phages and conjugative plasmids. Recently, CRISPR/Cas9 has been used for targeted genome editing in diverse eukaryo...

    Zahir Ali, Aala Abulfaraj, Ali Idris, Shakila Ali, Manal Tashkandi and Magdy M. Mahfouz

    Genome Biology 2015 16:238

    Published on: 11 November 2015

  13. Research

    A novel two-step genome editing strategy with CRISPR-Cas9 provides new insights into telomerase action and TERT gene expression

    To facilitate indefinite proliferation, stem cells and most cancer cells require the activity of telomerase, which counteracts the successive shortening of telomeres caused by incomplete DNA replication at the...

    Linghe Xi, Jens C. Schmidt, Arthur J. Zaug, Dante R. Ascarrunz and Thomas R. Cech

    Genome Biology 2015 16:231

    Published on: 10 November 2015

  14. Review

    Diversity of CRISPR-Cas immune systems and molecular machines

    Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genome...

    Rodolphe Barrangou

    Genome Biology 2015 16:247

    Published on: 9 November 2015

  15. Research Highlight

    CRISPR sabotage

    The biological arms race generally involves the rapid co-evolution of anti-virus systems in host organisms and of anti-anti-virus systems in their viral parasites. The CRISPR-Cas system is an example of a prok...

    John van der Oost and Stan J. J. Brouns

    Genome Biology 2015 16:248

    Published on: 9 November 2015

  16. Research

    High-frequency, precise modification of the tomato genome

    The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequ...

    Tomáš Čermák, Nicholas J. Baltes, Radim Čegan, Yong Zhang and Daniel F. Voytas

    Genome Biology 2015 16:232

    Published on: 6 November 2015

  17. Method

    Network analysis of gene essentiality in functional genomics experiments

    Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated...

    Peng Jiang, Hongfang Wang, Wei Li, Chongzhi Zang, Bo Li, Yinling J. Wong, Cliff Meyer, Jun S. Liu, Jon C. Aster and X. Shirley Liu

    Genome Biology 2015 16:239

    Published on: 6 November 2015

  18. Opinion

    The societal opportunities and challenges of genome editing

    The genome editing platforms currently in use have revolutionized the field of genetics. At an accelerating rate, these tools are entering areas with direct impact on human well being. Here, we discuss applica...

    Dana Carroll and R. Alta Charo

    Genome Biology 2015 16:242

    Published on: 5 November 2015

  19. Method

    Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation

    Arabidopsis mutants produced by constitutive overexpression of the CRISPR/Cas9 genome editing system are usually mosaics in the T1 generation. In this study, we used egg cell-specific pro...

    Zhi-Ping Wang, Hui-Li Xing, Li Dong, Hai-Yan Zhang, Chun-Yan Han, Xue-Chen Wang and Qi-Jun Chen

    Genome Biology 2015 16:144

    Published on: 21 July 2015