| Related to the history and evolution of CRISPR Cas9 technology for gene knockout / genome editing |
Rewriting a genome. Nature. 2013 Mar 7; 495(7439):50-1. Charpentier & Doudna, 2013. Biotechnology:
Summary: One of the first descriptions of the CRISPR complex to target mammalian cells for gene editing |
Multiplex Genome Engineering Using CRISPR/Cas Systems. Vol. 339(6121): 819-823. Cong, L. et al. (2013).
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795411/
Summary: Cas9 nucleases can be directed by gRNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells to allow editing. |
High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs. Nucleic Acids Res. Jun 1, 2014; 42(10): e84. Duda, K. et al. (2014).
Additional Links:
https://www.ncbi.nlm.nih.gov/pubmed/24753413
Summary: Describes the co-expression of a fluorescent protein to enable the detection of the gRNA expression. |
A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol. 649:247-56. Guschin, DY et al. (2010).
Summary: Description of a functional assays to determine the occurrence of gene modification - The assay is based on the ability of the Surveyor nuclease to selectively cleave distorted duplex DNA formed via cross-annealing of mutated and wild-type sequence. |
DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology 31(9): 827–832. Hsu, PD et al. (2013).
Additional Links:
https://www.researchgate.net/publication/250924204_DNA_targeting_specificity_of_RNA-guided_CAS9_nucleases
Summary: One of the first descriptions of the CRISPR complex to target mammalian cells for gene editing |
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 17 August 2012: Vol. 337 no. 6096 pp. 816-821. Jinek, M et al. (2012).
Summary: Describes the original use of CRISPR – to defend against viruses by using Cas9, tracrRNA and CrRNA. Also the subsequent engineering of tracrRNA:crRNA in one molecule for a commercial CRISPR system. |
| Related to the evolving algorithms of gRNA designs for CRISPR Cas9 gene knockout / genome editing |
| An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout. Molecular Cell, 2017. Erard, N., Knott S., & Hannon, G. |
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology, 34, 184-191, 2016. Doench, J. G. et al.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744125/ (Free Access)
Summary: Describes nucleotide to nucleotide interactions selected to support more efficient gRNA binding to the genomic DNA. |
Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology, 32, 1262-1267, 2014. Doench, J. G. et al.
Summary: Describes nucleotide to nucleotide interactions selected to support more efficient gRNA binding to the genomic DNA. |
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nature Methods, 12, 823-826, 2015. Chari, R., Mali, P., Moosburner, M. & Church, G. M.
Additional Links:
http://escholarship.org/uc/item/7qt804sf#page-1
Summary: Describes sequence optimization to enable more effective Cas9 binding |
Microhomology-based choice of Cas9 nuclease target sites. Nature Methods, 11, 705-706, 2014. Bae, S., Kweon, J., Kim, H. S. & Kim, J. S.
Additional Links:
https://www.researchgate.net/publication/263513198_Microhomology-based_choice_of_Cas9_nuclease_target_sites
Summary: Describes the identification of micro-homology regions that ensure a greater chance of frame-shift mutations. |
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nature Biotechnology, 33, 661-667, 2015. Shi, J. et al.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529991/
Summary: Describes the identification of conserved amino acid domains to enable targeting of regions more likely to disrupt protein function |
| Related to using multiple gRNAs in a single transfection or transduction / Combinatorial gRNA CRISPR Cas9 screening |
| An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout. Molecular Cell, 2017. Erard, N., Knott S., & Hannon, G. |
One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering. Cell 153(4): 910–918. Wang, H et al. (2013).
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3969854/
Summary: The ability of CRISPR/Cas9 mediated gene editing to be multiplexed; and enable studies simultaneously disrupting more than one gene at a time |
Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions. John Paul Shen, Dongxin Zhao, Roman Sasik, Jens Luebeck, Amanda Birmingham, Ana Bojorquez-Gomez, Katherine Licon, Kristin Klepper, Daniel Pekin, Alex N Beckett, Kyle Salinas Sanchez, Alex Thomas, Chih-Chung Kuo, Dan Du, Assen Roguev, Nathan E Lewis,,Aaron N Chang, Jason F Kreisberg, Nevan Krogan, Lei Qi, Trey Ideker and Prashant Mali.
Summary: A systematic approach to map human genetic growth kinetics. Pairs of 73 cancer genes with dual guide RNAs in three cell lines were targeted. Numerous relevant interactions were identified.
Additional Links:
http://mali.ucsd.edu/uploads/3/1/0/0/31002267/nature_methods_2017b.pdf |
Combinatorial CRISPR-Cas9 Knockout Screen -Protocol. Zhao Dongxin, Shen John Paul, Sasik Roman, Ideker Trey, Mali Prashant
Summary: Simultaneous mutation of two genes can produce a phenotype that is unexpected in light of each mutation’s individual effect. This describes a method using the CRISPR-Cas9 system to knockout pairs of genes, enabling high-throughput, systematic mapping of these genetic interactions. |
| Related to CRISPR Cas9 gene knockout / genome editing for in vivo or ex vivo pooled screening |
Simple and Rapid In Vivo Generation of Chromosomal Rearrangements using CRISPR/Cas9 Technology. Cell Reports, Volume 9, Issue 4, 1219 – 1227. Rafael B. Blasco, Elif Karaca, Chiara Ambrogio, Taek-Chin Cheong, Emre Karayol, Valerio G. Minero, Claudia Voena, and Roberto Chiarle. Department of Pathology, Boston Children’s Hospital.
Additional Links:
http://www.cell.com/cell-reports/abstract/S2211-1247(14)00920-6
Summary: Use of direct in vivo CRISPR/Cas9 injection of the gRNAs against two genes directly into the animal. Of additional interest is the fact that they also created a chromosomal translocation between two chromosome implicated in non-small-cell lung cancers |
| Related to CRISPR Cas9 pooled multiplex library screening |
A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Oren Parnas, Marko Jovanovic, Thomas M. Eisenhaure, Rebecca H. Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski, Randall J. Platt, Itay Tirosh, Neville E. Sanjana, Ophir Shalem, Rahul Satija, Raktima Raychowdhury, Philipp Mertins, Steven A. Carr, Feng Zhang, Nir Hacohen, Aviv Regev.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522370/
Summary: The use of a pooled gRNA strategy to identify targets and their associated regulators, ex vivo in cells obtained from a Cas9 positive mouse line. |
Enzymatically Generated CRISPR Libraries for Genome Labeling and Screening. Andrew B. Lane, Magdalena Strzelecka, Andreas Ettinger, Andrew W. Grenfell, Torsten Wittmann, Rebecca Heald.
Additional Links:
http://www.cell.com/developmental-cell/abstract/S1534-5807(15)00392-5
Summary: The use of pooled gRNAs and a fluorescently labeled dead-Cas9 to label larger stretches of chromosomal implicated in certain cellar pathways and function. |
| Related to CRISPR Cas9 gene knockout / genome editing confirmation (Surveyor assay, etc.) |
Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nature Biotechnology, 33, 661-667, 2015. Shi, J. et al.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529991/
Summary: Describes the identification of conserved amino acid domains to enable targeting of regions more likely to disrupt protein function. |
| Related to CRISPR Cas9 Nickase gene knockout / genome editing |
Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell 154(6): 1380–1389. Ran, FA et al. (2013).
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856256/
Summary: Cas9 mutant (knickase, D10A) cuts the DNA in two disparate places on the DNA target and thereby is less likely to promote undesired off-target mutagenesis |
| Related to the comparison of shRNA and CRISPR multiplex pooled library screening |
Systematic comparison of CRISPR-Cas9 and RNAi screens for essential genes. Nature Biotechnology 34, 634–636 (2016). David W Morgens, Richard M Deans, Amy Li, and Michael Bassik.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4900911/
Summary: A comparison of the ability of short hairpin RNA (shRNA) and CRISPR/Cas9 screens to identify essential genes.in the human chronic myelogenous leukemia cell line K562. It was found that the precision of the two libraries in detecting essential genes was similar and that combining data from both screens improved performance. Notably, results from the two screens showed little correlation when dealing with essential genes. shRNA screening picked up hits that CRISPR/Cas9 didn’t. Thus combining the results from the two methods could reveal information that neither could on its own. |
| Related to CRISPR/CAS9 knockout of using transOMIC pCLIP-All-EFS-Puro lentivirus |
PTRF/Cavin-1 promotes efficient ribosomal RNA transcription in response to metabolic challenges. Liu, L., and Pilch, P. F. (2016). eLife, 5, e17508.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987143/
Summary: Describes the generation of PTRF null 3T3-L1 stable cell lines by CRISPR/Cas9 genome editing using lentiviral plasmid based CRISPR/Cas9 from transOMIC technologies (Huntsville, AL). The researchers used pCLIP-All-EFS-Puro to express the 3 gRNA against mouse Ptrf and Cas9 as well as a NTC. Lentivirus were packing used third generation packing system. The 3T3-L1 fibroblast stable cell lines were obtained after lentivirus transduction and puromycin selection. |
| Related to the use of ssODNs with CRIPSR/Cas9 |
High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nature Methods, 8(9), 753–755.
Chen, F., Pruett-Miller, S. M., Huang, Y., Gjoka, M., Duda, K., Taunton, J. Davis, G. D. (2011).
Summary: Using ssDNA oligonucleotides with ZFNs to efficiently produce human cell lines to create point mutations, genomic deletions up to 100 kb and insertion of small genetic elements e.g: Tags.
Additional Links:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617923/ |