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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. 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
    Content type: Research Published on:

  2. 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...

    Authors: 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
    Citation: Genome Biology 2016 17:45
    Content type: Research Published on:

  5. 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...

    Authors: Wei Li, Johannes Köster, Han Xu, Chen-Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown and X. Shirley Liu
    Citation: Genome Biology 2015 16:281
    Content type: Method Published on:

  6. 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...

    Authors: Ying Dang, Gengxiang Jia, Jennie Choi, Hongming Ma, Edgar Anaya, Chunting Ye, Premlata Shankar and Haoquan Wu
    Citation: Genome Biology 2015 16:280
    Content type: Research Published on:

  7. 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...

    Authors: Tom Lawrenson, Oluwaseyi Shorinola, Nicola Stacey, Chengdao Li, Lars Østergaard, Nicola Patron, Cristobal Uauy and Wendy Harwood
    Citation: Genome Biology 2015 16:258
    Content type: Research Published on:

  8. 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...

    Authors: Daniel B. Graham and David E. Root
    Citation: Genome Biology 2015 16:260
    Content type: Review Published on:

  9. 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...

    Authors: 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
    Citation: Genome Biology 2015 16:257
    Content type: Research Published on:

  10. P16 DNA methylation is well known to be the most frequent event in cancer development. It has been reported that genetic inactivation of P16 drives cancer growth and metastasis, howeve...

    Authors: Chenghua Cui, Ying Gan, Liankun Gu, James Wilson, Zhaojun Liu, Baozhen Zhang and Dajun Deng
    Citation: Genome Biology 2015 16:252
    Content type: Research Published on:

  12. 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.

    Authors: Angela Chaparro-Garcia, Sophien Kamoun and Vladimir Nekrasov
    Citation: Genome Biology 2015 16:254
    Content type: Research Highlight Published on:

  13. 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...

    Authors: Tautvydas Karvelis, Giedrius Gasiunas, Joshua Young, Greta Bigelyte, Arunas Silanskas, Mark Cigan and Virginijus Siksnys
    Citation: Genome Biology 2015 16:253
    Content type: Method Published on:

  14. 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.

    Authors: Robert D. Fagerlund, Raymond H. J. Staals and Peter C. Fineran
    Citation: Genome Biology 2015 16:251
    Content type: Research Highlight Published on:

  15. 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...

    Authors: Mirko Singer, Jennifer Marshall, Kirsten Heiss, Gunnar R. Mair, Dirk Grimm, Ann-Kristin Mueller and Friedrich Frischknecht
    Citation: Genome Biology 2015 16:249
    Content type: Research Published on:

  16. 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...

    Authors: Zahir Ali, Aala Abulfaraj, Ali Idris, Shakila Ali, Manal Tashkandi and Magdy M. Mahfouz
    Citation: Genome Biology 2015 16:238
    Content type: Research Published on:

  18. 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...

    Authors: Linghe Xi, Jens C. Schmidt, Arthur J. Zaug, Dante R. Ascarrunz and Thomas R. Cech
    Citation: Genome Biology 2015 16:231
    Content type: Research Published on:

  19. 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...

    Authors: John van der Oost and Stan J. J. Brouns
    Citation: Genome Biology 2015 16:248
    Content type: Research Highlight Published on:

  21. 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...

    Authors: 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
    Citation: Genome Biology 2015 16:239
    Content type: Method Published on:

  22. 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...

    Authors: Tomáš Čermák, Nicholas J. Baltes, Radim Čegan, Yong Zhang and Daniel F. Voytas
    Citation: Genome Biology 2015 16:232
    Content type: Research Published on:

  23. 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...

    Authors: Dana Carroll and R. Alta Charo
    Citation: Genome Biology 2015 16:242
    Content type: Opinion Published on:

  26. 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...

    Authors: Zhi-Ping Wang, Hui-Li Xing, Li Dong, Hai-Yan Zhang, Chun-Yan Han, Xue-Chen Wang and Qi-Jun Chen
    Citation: Genome Biology 2015 16:144
    Content type: Method Published on: