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Title: New CRISPR–Cas systems from uncultivated microbes

Abstract

We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity inmore » Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less

Authors:
 [1];  [2];  [2];  [1];  [1];  [1];  [3];  [4]
  1. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Sciences
  2. Univ. of California, Berkeley, CA (United States). Department of Molecular and Cell Biology
  3. Univ. of California, Berkeley, CA (United States). Department of Molecular and Cell Biology, Howard Hughes Medical Institute, Innovative Genomics Initiative, and MBIB Division
  4. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Sciences and Department of Environmental Science, Policy, and Management
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1379729
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 542; Journal Issue: 7640; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Protein function predictions; RNA; Microbiology; Microbial ecology; Biotechnology

Citation Formats

Burstein, David, Harrington, Lucas B., Strutt, Steven C., Probst, Alexander J., Anantharaman, Karthik, Thomas, Brian C., Doudna, Jennifer A., and Banfield, Jillian F. New CRISPR–Cas systems from uncultivated microbes. United States: N. p., 2016. Web. doi:10.1038/nature21059.
Burstein, David, Harrington, Lucas B., Strutt, Steven C., Probst, Alexander J., Anantharaman, Karthik, Thomas, Brian C., Doudna, Jennifer A., & Banfield, Jillian F. New CRISPR–Cas systems from uncultivated microbes. United States. https://doi.org/10.1038/nature21059
Burstein, David, Harrington, Lucas B., Strutt, Steven C., Probst, Alexander J., Anantharaman, Karthik, Thomas, Brian C., Doudna, Jennifer A., and Banfield, Jillian F. Thu . "New CRISPR–Cas systems from uncultivated microbes". United States. https://doi.org/10.1038/nature21059. https://www.osti.gov/servlets/purl/1379729.
@article{osti_1379729,
title = {New CRISPR–Cas systems from uncultivated microbes},
author = {Burstein, David and Harrington, Lucas B. and Strutt, Steven C. and Probst, Alexander J. and Anantharaman, Karthik and Thomas, Brian C. and Doudna, Jennifer A. and Banfield, Jillian F.},
abstractNote = {We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.},
doi = {10.1038/nature21059},
journal = {Nature (London)},
number = 7640,
volume = 542,
place = {United States},
year = {2016},
month = {12}
}

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Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli
journal, August 2018


Recruitment of CRISPR-Cas systems by Tn7-like transposons
journal, August 2017

  • Peters, Joseph E.; Makarova, Kira S.; Shmakov, Sergey
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 35
  • DOI: 10.1073/pnas.1709035114

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a)
journal, May 2018

  • Singh, Digvijay; Mallon, John; Poddar, Anustup
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 21
  • DOI: 10.1073/pnas.1718686115

Prediction and diversity of tracrRNAs from type II CRISPR-Cas systems
journal, June 2018


Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
journal, January 2019

  • Dombrowski, Nina; Lee, Jun-Hoe; Williams, Tom A.
  • FEMS Microbiology Letters, Vol. 366, Issue 2
  • DOI: 10.1093/femsle/fnz008

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
journal, September 2018

  • Wyres, Kelly L.; Wick, Ryan R.; Judd, Louise M.
  • PLOS Genetics
  • DOI: 10.1101/414235

PAM recognition by miniature CRISPR nucleases triggers programmable double-stranded DNA target cleavage
preprint, February 2020

  • Karvelis, Tautvydas; Bigelyte, Greta; Young, Joshua K.
  • Nucleic Acids Research
  • DOI: 10.1101/654897

Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue
journal, June 2019

  • Martin‐Cuadrado, Ana‐Belen; Senel, Ece; Martínez‐García, Manuel
  • Environmental Microbiology, Vol. 21, Issue 10
  • DOI: 10.1111/1462-2920.14680

Interkingdom microbial consortia mechanisms to guide biotechnological applications
journal, July 2018

  • Zhang, Shu; Merino, Nancy; Okamoto, Akihiro
  • Microbial Biotechnology, Vol. 11, Issue 5
  • DOI: 10.1111/1751-7915.13300

A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits
journal, November 2018

  • Zhou, Qun; Zhan, Hengji; Liao, Xinhui
  • Cell Proliferation, Vol. 52, Issue 2
  • DOI: 10.1111/cpr.12552

The rapidly advancing Class 2 CRISPR‐Cas technologies: A customizable toolbox for molecular manipulations
journal, March 2020

  • Wang, Jingyi; Zhang, Chenzi; Feng, Bo
  • Journal of Cellular and Molecular Medicine, Vol. 24, Issue 6
  • DOI: 10.1111/jcmm.15039

New variants of CRISPR RNA-guided genome editing enzymes
journal, May 2017

  • Murovec, Jana; Pirc, Žan; Yang, Bing
  • Plant Biotechnology Journal, Vol. 15, Issue 8
  • DOI: 10.1111/pbi.12736

The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists
journal, May 2018

  • Wolter, Felix; Puchta, Holger
  • The Plant Journal, Vol. 94, Issue 5
  • DOI: 10.1111/tpj.13899

Clinical applications of CRISPR-based genome editing and diagnostics: CLINICAL APPLICATIONS OF CRISPR ENZYMES
journal, January 2019

  • Foss, Dana V.; Hochstrasser, Megan L.; Wilson, Ross C.
  • Transfusion, Vol. 59, Issue 4
  • DOI: 10.1111/trf.15126

In vivo genome editing improves motor function and extends survival in a mouse model of ALS
journal, December 2017

  • Gaj, Thomas; Ojala, David S.; Ekman, Freja K.
  • Science Advances, Vol. 3, Issue 12
  • DOI: 10.1126/sciadv.aar3952

Systematic discovery of natural CRISPR-Cas12a inhibitors
journal, September 2018


Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
journal, October 2018

  • Harrington, Lucas B.; Burstein, David; Chen, Janice S.
  • Science, Vol. 362, Issue 6416
  • DOI: 10.1126/science.aav4294

History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology
journal, January 2018

  • Ishino, Yoshizumi; Krupovic, Mart; Forterre, Patrick
  • Journal of Bacteriology, Vol. 200, Issue 7
  • DOI: 10.1128/jb.00580-17

Protein Engineering Strategies to Expand CRISPR-Cas9 Applications
journal, August 2018

  • Ribeiro, Lucas F.; Ribeiro, Liliane F. C.; Barreto, Matheus Q.
  • International Journal of Genomics, Vol. 2018
  • DOI: 10.1155/2018/1652567

CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering
journal, September 2018

  • Lone, Bilal Ahmad; Karna, Shibendra Kumar Lal; Ahmad, Faiz
  • Genetics Research International, Vol. 2018
  • DOI: 10.1155/2018/3797214

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts
journal, February 2020


Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks
journal, June 2019


HH-suite3 for fast remote homology detection and deep protein annotation
journal, September 2019


Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants
journal, January 2019


CRISPR-like sequences in Helicobacter pylori and application in genotyping
journal, November 2017

  • Bangpanwimon, Khotchawan; Sottisuporn, Jaksin; Mittraparp-arthorn, Pimonsri
  • Gut Pathogens, Vol. 9, Issue 1
  • DOI: 10.1186/s13099-017-0215-8

Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease
journal, January 2020


Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
journal, April 2019


CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci
journal, August 2017

  • Rossi, Ciro C.; Souza-Silva, Thaysa; Araújo-Alves, Amanda V.
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.01545

Schizosaccharomyces pombe Can Reduce Acetic Acid Produced by Baijiu Spontaneous Fermentation Microbiota
journal, November 2019


Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
journal, January 2020


Characterization of Cas proteins for CRISPR‐Cas editing in streptomycetes
journal, May 2019

  • Yeo, Wan Lin; Heng, Elena; Tan, Lee Ling
  • Biotechnology and Bioengineering, Vol. 116, Issue 9
  • DOI: 10.1002/bit.27021

CRISPR/Cas9: Nature's gift to prokaryotes and an auspicious tool in genome editing
journal, November 2019

  • Khanzadi, Manzoor N.; Khan, Abid A.
  • Journal of Basic Microbiology, Vol. 60, Issue 2
  • DOI: 10.1002/jobm.201900420

Developmental progress of CRISPR/Cas9 and its therapeutic applications for HIV-1 infection
journal, July 2018

  • Deng, Qiudi; Chen, Zisheng; Shi, Lei
  • Reviews in Medical Virology, Vol. 28, Issue 5
  • DOI: 10.1002/rmv.1998

A load driver device for engineering modularity in biological networks
journal, November 2014

  • Mishra, Deepak; Rivera, Phillip M.; Lin, Allen
  • Nature Biotechnology, Vol. 32, Issue 12
  • DOI: 10.1038/nbt.3044

Diversity and evolution of class 2 CRISPR–Cas systems
journal, January 2017

  • Shmakov, Sergey; Smargon, Aaron; Scott, David
  • Nature Reviews Microbiology, Vol. 15, Issue 3
  • DOI: 10.1038/nrmicro.2016.184

The emerging and uncultivated potential of CRISPR technology in plant science
journal, July 2019


Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy
journal, July 2019

  • Moreno, Ana M.; Palmer, Nathan; Alemán, Fernando
  • Nature Biomedical Engineering, Vol. 3, Issue 10
  • DOI: 10.1038/s41551-019-0431-2

The next generation of CRISPR–Cas technologies and applications
journal, May 2019

  • Pickar-Oliver, Adrian; Gersbach, Charles A.
  • Nature Reviews Molecular Cell Biology, Vol. 20, Issue 8
  • DOI: 10.1038/s41580-019-0131-5

Clades of huge phages from across Earth’s ecosystems
journal, February 2020


Broad-spectrum enzymatic inhibition of CRISPR-Cas12a
journal, April 2019

  • Knott, Gavin J.; Thornton, Brittney W.; Lobba, Marco J.
  • Nature Structural & Molecular Biology, Vol. 26, Issue 4
  • DOI: 10.1038/s41594-019-0208-z

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems
journal, June 2018


PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures
journal, September 2018


A new statistic for efficient detection of repetitive sequences
journal, April 2019


Multiplex genome editing of microorganisms using CRISPR-Cas
journal, April 2019

  • Adiego-Pérez, Belén; Randazzo, Paola; Daran, Jean Marc
  • FEMS Microbiology Letters, Vol. 366, Issue 8
  • DOI: 10.1093/femsle/fnz086

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery
journal, February 2018

  • Bernard, Guillaume; Pathmanathan, Jananan S.; Lannes, Romain
  • Genome Biology and Evolution, Vol. 10, Issue 3
  • DOI: 10.1093/gbe/evy031

Structural insights into the modulatory role of the accessory protein WYL1 in the Type VI-D CRISPR-Cas system
journal, April 2019

  • Zhang, Heng; Dong, Cheng; Li, Li
  • Nucleic Acids Research, Vol. 47, Issue 10
  • DOI: 10.1093/nar/gkz269

Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium
posted_content, February 2019

  • Schmidt, Stephanie Tzouanas; Yu, Feiqiao Brian; Blainey, Paul C.
  • DOI: 10.1101/555169

HH-suite3 for fast remote homology detection and deep protein annotation
journal, February 2019

  • Steinegger, Martin; Meier, Markus; Mirdita, Milot
  • BMC Bioinformatics
  • DOI: 10.1101/560029

Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy
journal, January 2017

  • Gee, Peter; Xu, Huaigeng; Hotta, Akitsu
  • Stem Cells International, Vol. 2017
  • DOI: 10.1155/2017/8765154

On the global CRISPR array behavior in class I systems
journal, August 2017


Building a genome engineering toolbox in nonmodel prokaryotic microbes
journal, May 2018

  • Freed, Emily; Fenster, Jacob; Smolinski, Sharon L.
  • Biotechnology and Bioengineering, Vol. 115, Issue 9
  • DOI: 10.1002/bit.26727

Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum
journal, July 2019

  • Wang, Yu; Liu, Ye; Li, Junwei
  • Biotechnology and Bioengineering, Vol. 116, Issue 11
  • DOI: 10.1002/bit.27121

A highly specific SpCas9 variant is identified by in vivo screening in yeast
journal, January 2018

  • Casini, Antonio; Olivieri, Michele; Petris, Gianluca
  • Nature Biotechnology, Vol. 36, Issue 3
  • DOI: 10.1038/nbt.4066

A decade of discovery: CRISPR functions and applications
journal, June 2017


Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium
journal, October 2019

  • Schmidt, Stephanie Tzouanas; Yu, Feiqiao Brian; Blainey, Paul C.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 46
  • DOI: 10.1073/pnas.1904273116

A new statistic for efficient detection of repetitive sequences
journal, September 2018

  • Chen, Sijie; Sun, Fengzhu; Waterman, Michael S.
  • Bioinformatics
  • DOI: 10.1101/420745

Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes
posted_content, January 2019


Functionally diverse type V CRISPR-Cas systems
journal, December 2018

  • Yan, Winston X.; Hunnewell, Pratyusha; Alfonse, Lauren E.
  • Science, Vol. 363, Issue 6422
  • DOI: 10.1126/science.aav7271

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing
text, January 2018


Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms
text, January 2017


Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease
journal, January 2020


CdpR Inhibits CRISPR-Cas Adaptive Immunity to Lower Anti-viral Defense while Avoiding Self-Reactivity
journal, March 2019


Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein
journal, April 2018


Blossom of CRISPR technologies and applications in disease treatment
journal, December 2018


A highly specific SpCas9 variant is identified by in vivo screening in yeast
journal, January 2018

  • Casini, Antonio; Olivieri, Michele; Petris, Gianluca
  • Nature Biotechnology, Vol. 36, Issue 3
  • DOI: 10.1038/nbt.4066

Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information
journal, February 2019


Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation
journal, November 2018


Increasing the specificity of CRISPR systems with engineered RNA secondary structures
journal, April 2019

  • Kocak, D. Dewran; Josephs, Eric A.; Bhandarkar, Vidit
  • Nature Biotechnology, Vol. 37, Issue 6
  • DOI: 10.1038/s41587-019-0095-1

Broad-spectrum enzymatic inhibition of CRISPR-Cas12a
journal, April 2019

  • Knott, Gavin J.; Thornton, Brittney W.; Lobba, Marco J.
  • Nature Structural & Molecular Biology, Vol. 26, Issue 4
  • DOI: 10.1038/s41594-019-0208-z

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms
journal, June 2017


Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains
journal, December 2017


Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli
journal, August 2018


Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium
journal, October 2019

  • Schmidt, Stephanie Tzouanas; Yu, Feiqiao Brian; Blainey, Paul C.
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 46
  • DOI: 10.1073/pnas.1904273116

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems
journal, June 2018


PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures
journal, September 2018


CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems
journal, April 2018

  • Crawley, Alexandra B.; Henriksen, James R.; Barrangou, Rodolphe
  • The CRISPR Journal, Vol. 1, Issue 2
  • DOI: 10.1089/crispr.2017.0022

Harnessing “A Billion Years of Experimentation”: The Ongoing Exploration and Exploitation of CRISPR–Cas Immune Systems
journal, April 2018


Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
journal, January 2019

  • Dombrowski, Nina; Lee, Jun-Hoe; Williams, Tom A.
  • FEMS Microbiology Letters, Vol. 366, Issue 2
  • DOI: 10.1093/femsle/fnz008

Multiplex genome editing of microorganisms using CRISPR-Cas
journal, April 2019

  • Adiego-Pérez, Belén; Randazzo, Paola; Daran, Jean Marc
  • FEMS Microbiology Letters, Vol. 366, Issue 8
  • DOI: 10.1093/femsle/fnz086

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
journal, October 2017

  • Mitchell, Alex L.; Scheremetjew, Maxim; Denise, Hubert
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx967

Structural insights into the modulatory role of the accessory protein WYL1 in the Type VI-D CRISPR-Cas system
journal, April 2019

  • Zhang, Heng; Dong, Cheng; Li, Li
  • Nucleic Acids Research, Vol. 47, Issue 10
  • DOI: 10.1093/nar/gkz269

Interkingdom microbial consortia mechanisms to guide biotechnological applications
journal, July 2018

  • Zhang, Shu; Merino, Nancy; Okamoto, Akihiro
  • Microbial Biotechnology, Vol. 11, Issue 5
  • DOI: 10.1111/1751-7915.13300

A revolutionary tool: CRISPR technology plays an important role in construction of intelligentized gene circuits
journal, November 2018

  • Zhou, Qun; Zhan, Hengji; Liao, Xinhui
  • Cell Proliferation, Vol. 52, Issue 2
  • DOI: 10.1111/cpr.12552

New variants of CRISPR RNA-guided genome editing enzymes
journal, May 2017

  • Murovec, Jana; Pirc, Žan; Yang, Bing
  • Plant Biotechnology Journal, Vol. 15, Issue 8
  • DOI: 10.1111/pbi.12736

Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy
journal, January 2017

  • Gee, Peter; Xu, Huaigeng; Hotta, Akitsu
  • Stem Cells International, Vol. 2017
  • DOI: 10.1155/2017/8765154

Protein Engineering Strategies to Expand CRISPR-Cas9 Applications
journal, August 2018

  • Ribeiro, Lucas F.; Ribeiro, Liliane F. C.; Barreto, Matheus Q.
  • International Journal of Genomics, Vol. 2018
  • DOI: 10.1155/2018/1652567

CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering
journal, September 2018

  • Lone, Bilal Ahmad; Karna, Shibendra Kumar Lal; Ahmad, Faiz
  • Genetics Research International, Vol. 2018
  • DOI: 10.1155/2018/3797214

CRISPR-Cas Genome Surgery in Ophthalmology
journal, May 2017

  • DiCarlo, James E.; Sengillo, Jesse D.; Justus, Sally
  • Translational Vision Science & Technology, Vol. 6, Issue 3
  • DOI: 10.1167/tvst.6.3.13

Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks
journal, June 2019


HH-suite3 for fast remote homology detection and deep protein annotation
journal, September 2019


Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants
journal, January 2019


On the global CRISPR array behavior in class I systems
journal, August 2017


Correction to: CRISPR-like sequences in Helicobacter pylori and application in genotyping
journal, December 2017

  • Bangpanwimon, Khotchawan; Sottisuporn, Jaksin; Mittraparp-arthorn, Pimonsri
  • Gut Pathogens, Vol. 9, Issue 1
  • DOI: 10.1186/s13099-017-0221-x

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
journal, April 2019


Cas1 and Cas2 From the Type II-C CRISPR-Cas System of Riemerella anatipestifer Are Required for Spacer Acquisition
journal, June 2018

  • He, Yang; Wang, Mingshu; Liu, Mafeng
  • Frontiers in Cellular and Infection Microbiology, Vol. 8
  • DOI: 10.3389/fcimb.2018.00195

CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci
journal, August 2017

  • Rossi, Ciro C.; Souza-Silva, Thaysa; Araújo-Alves, Amanda V.
  • Frontiers in Microbiology, Vol. 8
  • DOI: 10.3389/fmicb.2017.01545

Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
journal, May 2019


Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish
journal, January 2020


Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability
journal, November 2018


Schizosaccharomyces pombe Can Reduce Acetic Acid Produced by Baijiu Spontaneous Fermentation Microbiota
journal, November 2019


“French Phage Network”—Second Meeting Report
journal, April 2017

  • Torres-Barceló, Clara; Kaltz, Oliver; Froissart, Rémy
  • Viruses, Vol. 9, Issue 4
  • DOI: 10.3390/v9040087

CRISPR Genome Engineering for Human Pluripotent Stem Cell Research
journal, January 2017

  • Chaterji, Somali; Ahn, Eun Hyun; Kim, Deok-Ho
  • Theranostics, Vol. 7, Issue 18
  • DOI: 10.7150/thno.18456

Allele-specific genome targeting in the development of precision medicine
journal, January 2020

  • Wu, Junjiao; Tang, Beisha; Tang, Yu
  • Theranostics, Vol. 10, Issue 7
  • DOI: 10.7150/thno.43298

Detection and variability analyses of CRISPR-like loci in the H. pylori genome
journal, September 2018


Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
journal, January 2020