GE Journal Club (genome engineering/gene editing) at Harvard Medical School

*Meetings on hiatus until Sept. 14th*

Meetings are by Zoom, Mondays at 1pm. Meetings are announced via the mailing list. Contact jabosch@hms.harvard.edu to be added to the list.

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Meetings are Mondays, 12:30 PM – 1:30 PM in NRB 354 unless otherwise noted
Pizza and soda generously provided by the HMS Dept. of Genetics

Advances in genome editing occur at a blazing speed, and reading the high volume of papers is too difficult for one person. To address this, we run a Gene Editing Journal Club. By presenting papers in a group setting, we stay up to date on recent technologies, stimulate critical discussion, and establish new contacts for collaboration. We are always looking for new members in the Longwood Medical and Boston area. Everyone is welcome to attend, from postdocs and PIs to students and techs, with any level of experience.

GE Journal Club Flier

CURRENT SCHEDULE

DATE PRESENTERS PAPERS
9/14/20 1) TBD
2) Liz Lane
1) TBD
2) Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells.
https://www.sciencedirect.com/science/article/pii/S2451945620300684
9/21/20 1) Lucia Sereni
2) Devon Stork
1) TBD
2) Total synthesis of Escherichia coli with a recoded genome
https://www.nature.com/articles/s41586-019-1192-5
9/28/20 1) Takashi Enomoto
2) Afroditi Petsakou
1) TBD
2) TBD
10/5/20 1) Ankita Singh
2) Fu-Kai Hsieh
1) TBD
2) TBD
10/12/20 HOLIDAY HOLIDAY
10/19/20 1) Sara Nunes
2) Ah-Ram Kim
1) TBD
2) TBD
10/26/20 1) Erik Aznauryan
2) Vanitha Nithianandam
1) TBD
2) TBD
11/02/20 1) Patrick Griffin
2) Ram Viswanatha
1) TBD
2) TBD
11/09/20 1) Justin Bosch
2) Ben Ewen-Campen
1) TBD
2) TBD

PAST MEETINGS

DATE PRESENTERS PAPERS
6/1/20 1) Nirmalya Chatterjee
2) Li Li
1) Glia-to-Neuron Conversion by CRISPR-CasRx Alleviates Symptoms of Neurological Disease in Mice
https://www.cell.com/cell/fulltext/S0092-8674(20)30286-5
2) An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells
https://www.cell.com/cell/fulltext/S0092-8674(20)30554-7
5/11/20 1) Shannon Knight
2) Enzo Mameli
1) Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity
https://linkinghub.elsevier.com/retrieve/pii/S0896-6273(20)30004-0
2) Massively parallel Cas13 screens reveal principles for guide RNA design
https://www.nature.com/articles/s41587-020-0456-9

5/4/20

1) Jonathan Zirin
2) Stephanie Mohr
1) Multiplexed conditional genome editing with Cas12a in Drosophila
https://www.biorxiv.org/content/10.1101/2020.02.26.966333v1
​​​​​​​2) Capturing RNA–protein interaction via CRUIS
https://academic.oup.com/nar/article/doi/10.1093/nar/gkaa143/5788206
4/27/20 1) Baolong Xia
2) Navdar Sever
1) Development of CRISPR as an antiviral strategy to combat SARSCoV-2 and influenza
https://www.cell.com/pb-assets/products/coronavirus/CELL_CELL-D-20-00736...
​​​​​​​2) In Utero Gene Editing for Monogenic Lung Disease
https://stm.sciencemag.org/content/11/488/eaav8375

4/20/20

1) Tracy Zhang
2) Pedro Saavedra

1) CRISPR–Cas12-based detection of SARS-CoV-2
https://www.nature.com/articles/s41587-020-0513-4
​​​​​​​2) Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming
https://www.nature.com/articles/s41467-020-14397-8

4/13/20

1) Ram Viswanatha
2) Hassan Bukhari
1) CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities
https://www.nature.com/articles/s41586-020-2099-x
​​​​​​​2) Fast and efficient generation of knock-in human organoids using homology-independent CRISPR–Cas9 precision genome editing
https://www.nature.com/articles/s41556-020-0472-5
4/6/20 1) Russell Walton
2) Cole Peters
1) Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants
https://science.sciencemag.org/content/early/2020/03/25/science.aba8853....
​​​​​​​2) Immune-orthogonal orthologues of AAV capsids and of Cas9 circumvent the immune response to the administration of gene therapy.
https://www.nature.com/articles/s41551-019-0431-2

3/30/20

1) Sarah Bowling
2) Jun Xu

1) A CRISPR-Cas9-based reporter system for single-cell detection of extracellular vesicle-mediated functional transfer of RNA
https://www.nature.com/articles/s41467-020-14977-8
​​​​​​​2) CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa177/580...
3/23/20

1) Ben Ewen-Campen
2) Justin Bosch

1) A protocol for detection of COVID-19 using CRISPR diagnostics
https://www.broadinstitute.org/files/publications/special/COVID-19%20det...(updated).pdf
2) GO: a functional reporter system to identify and enrich base editing activity
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa124/576...
03/02/2020 1) Jon Rodiger
2) Gabriel Birchak
1) Bradford J, Perrin D (2019) A benchmark of computational CRISPR-Cas9 guide design methods. PLoS Comput Biol 15(8): e1007274. https://doi.org/10.1371/journal.pcbi.1007274
2) Logsdon, G.L., Gambogi, C.W., Liskovykh, M.A., Barrey, E.J., Larionov, V., Miga, K.H., Heun, P., Black, B.E.: Human artificial chromosomes that bypass centromeric DNA. Cell 178: 624-639, 2019.
https://www.ncbi.nlm.nih.gov/pubmed/31348889
02/10/2020 1) Patrick Griffin
2) Cole Peters
1) CRISPR-engineered T cells in patients with refractory cancer
https://science.sciencemag.org/content/early/2020/02/05/science.aba7365
2) Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses.
https://www.nature.com/articles/s41551-019-0501-5
01/27/2020

1) Erik Aznauryan

2) Ah-Ram Kim

1) Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
https://www.nature.com/articles/s41587-019-0387-5
2) A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells.
https://www.nature.com/articles/s41589-019-0443-y
1/13/2020 1) Giulia Ceglie
2) Sara Nunes

1) Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res. Sep. 2019
https://academic.oup.com/nar/article/47/15/7955/5506860

2) De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. Oct 2019
https://www.nature.com/articles/s41467-019-12489-8

12/09/2019 1) Charlotte Bellamy
2) Kyle McCracken
1) MacLeod et al. Genome-Wide CRISPR-Cas9 Screens Expose Genetic Vulnerabilities and Mechanisms of Temozolomide Sensitivity in Glioblastoma Stem Cells. Cell Rep. 2019 Apr 16;27(3):971-986.e9
2) Abudayyeh et al. A cytosine deaminase for programmable single-base RNA editing. Science. 2019 Jul 26;365(6451):382-386
12/02/2019 1) Ankita Singh
2) Zhenfei Xie
1) Loveless et al. DNA writing at a single genomic site enables lineage tracing and analog recording in mammalian cells. bioRxiv. Sept. 29, 2019.
2) Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems

https://www.sciencedirect.com/science/article/pii/S1097276519308020?via%...
11/25/2019 NO MEETING – – – – – – – –
11/18/2019 1) Shannon Knight
2) Enzo Mameli
1) Tian et al. CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons. Neuron. 2019 Aug 5. pii: S0896-6273(19)30640-3.
2) Freije et al. 
Programmable Inhibition and Detection of RNA Viruses Using Cas13. Mol Cell. 2019 Oct 2. pii: S1097-2765(19)30698-7
11/11/2019 NO MEETING (Holiday) – – – – – – – –
11/04/2019 1) Jonathan Zirin
2) Stephanie Mohr
1) Lin et al. Microhomology based CRISPR tagging tools for protein tracking, purification, and depletion. J Biol Chem. 2019 May 28.
2) Smits et al.
Biological Plasticity Rescues Target Activity in CRISPR Knockouts. Nat Methods. 2019 Oct 28.
10/28/2019 1) Baolong Xia
2) Ben Ewen-Campen
1) Anzalone et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019 Oct 21. 
2) Ihry et al. 
p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med. 2018 Jul;24(7):939-946. 
10/21/2019 1) Pedro Saavedra
2) Amit Choudhary
1) Hanlon et al. High levels of AAV vector integration into CRISPR-induced DNA breaks. Nat Commun. 2019 Sep 30;10(1):4439.
2) Maji et al.
A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell. 2019 May 2;177(4):1067-1079.e19.
10/14/2019 NO MEETING (Holiday) – – – – – – – –
10/07/2019 1) Hassan Bukhari
2) Tracy Zhang
1) Jayavaradhan et al. CRISPR-Cas9 fusion to dominant-negative 53BP1 enhances HDR and inhibits NHEJ specifically at Cas9 target sites. Nat Commun. 2019 Jun 28;10(1):2866.
2) Kemaladewi et al.
A mutation-independent approach for muscular dystrophy via upregulation of a modifier gene. Nature. 2019 Aug;572(7767):125-130.
09/30/2019 1) Ram Viswanatha
2) Cole Peters
1) Pickar-Oliver et al. Targeted transcriptional modulation with type I CRISPR–Cas systems in human cells. Nat Biotechnol. 2019 Sept 23.
2) Villiger et al. 
Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nat Med. 2018 Oct;24(10):1519-1525.
09/23/2019 1) Afroditi Petsakou
2) Jun Xu
1) Xu et al. CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia. N Engl J Med. 2019 Sep 11.
2) Xu et al.
Mass spider silk production through targeted gene replacement in Bombyx mori. Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8757-8762.
09/16/2019 Justin Bosch
Sarah Bowling
1) Strecker et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science. 2019 Jun 6. pii: eaax9181.
2) Dong et al.
Genome-Wide Off-Target Analysis in CRISPR-Cas9 Modified Mice and Their Offspring. G3 (Bethesda). 2019 Sep 6. pii: g3.400503.2019
09/09/2019 Navdar Sever
Ah-Ram Kim
1) Quadros et al. Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol. 2017 May 17;18(1):92. 
2) Wang et al. 
Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly. Science. 2019 Aug 30;365(6456):922-926.

07/01/2019-
09/02/2019

No Meetings – – – – – – – –
06/24/2019 Claire Hu
Ricky Brathwaite
1a) Dandage et al. beditor: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing. Genetics. 2019 Jun;212(2):377-385. 
1b) Erard et al.
A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout. Mol Cell. 2017 Sep 21;67(6):1080.
2) Dolan et al.
Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell. 2019 Apr 5. pii: S1097-2765(19)30217-5.
06/17/2019 NO MEETING – – – – – – – –
06/10/2019 Josh Li 
Zhenfei Xie
1) Meltzer, et al. Tissue-specific (ts)CRISPR as an efficient strategy for in vivo screening in Drosophila. Nat Commun. 2019 May 8;10(1):2113.
2) Li, et al. 
CRISPR–Cas9-mediated base-editing screening in mice identifies DND1 amino acids that are critical for primordial germ cell development. Nat Cell Biol. 2018 Nov;20(11):1315-1325.
06/04/2019 Stephanie Mohr
Shannon Knight
1) Port et al. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. bioRxiv May 13, 2019.
2) Back et al.
Neuron-Specific Genome Modification in the Adult Rat Brain Using CRISPR-Cas9 Transgenic Rats. Neuron. 2019 Feb 8. pii: S0896-6273(19)30062-5
05/27/2019 NO MEETING – – – – – – – –
05/20/2019 NO MEETING – – – – – – – –
05/13/2019 Julian Grunewald
Clarita Ingaramo
1) Grunewald J, et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature. 2019 Apr 17. 
2) Pan et al.
Near-infrared upconversion-activated CRISPR-Cas9 system: A remote-controlled gene editing platform. Sci Adv. 2019 Apr 3;5(4):eaav7199. 
05/06/2019 Jonathan Zirin
Ben Ewen-Campen
1) Hoffmann MD, et al. Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic Acids Res. 2019 Apr 15. pii: gkz271.
2) Guichard A, et al.
Efficient allelic-drive in Drosophila. Nat Commun. 2019 Apr 9;10(1):1640.
04/29/2019 Justin Bosch
Chiao-Lin Chen
1) Kocak DD, et al. Increasing the specificity of CRISPR systems with engineered RNA secondary structures. Nat Biotechnol. 2019 Apr 15.
2) Bian WP, et al.
A knock-in strategy for editing human and zebrafish mitochondrial DNA using mito-CRISPR/Cas9 system. ACS Synth Biol. 2019 Apr 10.
04/22/2019 NO MEETING – – – – – – – –
04/15/2019 Baolong Xia
Tracy Zhang
1) Ma Z, et al. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature. 2019 Apr 3.
2) El-Brolosy MA, et al.
Genetic compensation triggered by mutant mRNA degradation. Nature. 2019 Apr 3.
3) Iyer S, et al.
Precise therapeutic gene correction by a simple nuclease-induced double-stranded break. Nature. 2019 Apr 3.
04/08/2019 Cory Smith
Ankita Singh
1) Smith CJ, et al. Enabling large-scale genome editing by reducing DNA nicking. bioRxiv. Mar. 15, 2019.
2) Tuladhar R, et al. 
CRISPR/Cas9-based mutagenesis frequently provokes on-target mRNA misregulation. bioRxiv. Mar. 20, 2019.
04/01/2019 Pedro Saavedra
Ram Viswanatha

1) Min YL, et al. CRISPR-Cas9 corrects Duchenne muscular dystrophy exon 44 deletion mutations in mice and human cells. Sci Adv. 2019 Mar 6;5(3):eaav4324.
2) Hwang B, et al.
Lineage tracing using a Cas9-deaminase barcoding system targeting endogenous L1 elements. Nat Commun. 2019 Mar 15;10(1):1234

03/25/2019 Kendell Clement
Afroditi Petsakou
1) Clement K, et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol. 2019 Feb 26.
2) Katrekar D, et al. 
In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat Methods. 2019 Feb 8.
03/18/2019 NO MEETING – – – – – – – –
03/11/2019 Benjamin Kleinstiver
Henrique Camara
1) Kleinstiver BP, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 Feb 11.   
2) Wang XW, et al. 
A microRNA-inducible CRISPR-Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool. Nat Cell Biol. 2019 Feb 25.
03/04/2019   NO MEETING – – – – – – – –
02/25/2019 NO MEETING – – – – – – – –
02/18/2019 NO MEETING – – – – – – – –
02/11/2019 Julio Sainz de Aja
Sarah Bowling
1) Grunwald HA, et al. Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature. 2019 Jan 23.
2) Salvador-Martinez I, et al. 
Is it possible to reconstruct an accurate cell lineage using CRISPR recorders? Elife. 2019 Jan 28;8. pii: e40292.
02/04/2019 NO MEETING – – – – – – – –
01/28/2019 Ah-Ram Kim
Enzo Mameli

1) Matharu N, et al. CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science. 2019 Jan 18;363(6424). pii: eaau0629.
2) Oakes BL, et al.
CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell. 2019 Jan 10;176(1-2):254-267.e16

  NO MEETING 2018: 12/17, 12/24, 12/31
2019: 01/07, 01/14, 01/21
12/10/2018 Henrique Camara
Maria Clara Ingaramo
1) Garcia-Marques J, et al. Unlimited genetic switches for cell-type specific manipulation. bioRxiv [Internet]. Nov. 14, 2018.
2) Farzadfard F, et al.
Single-Nucleotide-Resolution Computing and Memory in Living Cells. bioRxiv [Internet]. Feb. 16, 2018.
12/03/2018 Stephanie Mohr
Justin Bosch
1) Chong Z-S, et al. Pooled extracellular receptor-ligand interaction screening using CRISPR activation. Genome Biol. 2018 Nov 26;19(1):205. 
2) Fueller J, et al.
CRISPR/Cas12a-assisted PCR tagging of mammalian genes. bioRxiv [Internet]. Nov. 20, 2018.
11/26/2018 Baolong Xia
Tracy Zhang
1) Sanson KR, et al. Up, down, and out: optimized libraries for CRISPRa, CRISPRi, and CRISPR-knockout genetic screens. bioRxiv [Internet]. July 2, 2018.
2) Shen MW, et al.
Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018 Nov 7. 
11/19/2018 Johana Vásquez
Chiao-Lin Chen

1) Haney MS, et al. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet. 2018 Nov 5. 
2) Harrington LB, et al. 
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 18 Oct 2018: eaav4294.

11/12/2018 NO MEETING – – – – – – – –
11/05/2018 Pedro Saavedra
Ram Viswanatha

1) Wroblewska A, et al. Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell. 2018 Oct 18.
2) Nishimasu H, et al.
Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science. 2018 Aug 30.

10/29/2018 Afroditi Petsakou
Ben Ewen-Campen

1) Schmidt F, et al. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature. 2018 Oct 3.
2) Zafra MP, et al. 
Optimized base editors enable efficient editing in cells, organoids and mice. Nat Biotechnol. 2018 Oct;36(9):888-893. 

10/22/2018 Justin Bosch
Stephanie Mohr

1) Akcakaya P, et al. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature. 2018 Sep 12.
2) Findlay GM, et al.
Accurate classification of BRCA1 variants with saturation genome editing. Nature. 2018 Sep 12.

10/15/2018

Baolong Xia
Charles Xu

1) Sharon E,  et al. Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing. Cell. 2018 Sep 18. pii: S0092-8674(18)31118-8.
2) Alemany A, et al.
Whole-organism clone tracing using single-cell sequencing. Nature. 2018 Apr 5;556(7699):108-112.

10/08/2018 NO MEETING – – – – – – – –
10/01/2018

Ankita Singh
Chiao-Lin Chen

1) Swings T, et al. CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing. Nat Commun. 2018 Jun 8;9(1):2231.
2)  Allen FR, et al. 
Mutations generated by repair of Cas9-induced double strand breaks are predictable from surrounding sequence. bioRxiv [Internet]. Aug. 25, 2018.

  NO MEETING 09/04, 09/10, 09/17, 09/24

08/27/2018

Pedro Saavedra
Ram Viswanatha

1) Horlbeck MA, et al. Mapping the Genetic Landscape of Human Cells. Cell. 2018 Aug 9;174(4):953-967.e22. 
2) Roche PJR, et al. 
Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells. bioRxiv [Internet]. Aug. 6, 2018. 

08/20/2018

Afroditi Petsakou
Ben Ewen-Campen

1) Kundert K, et al. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. bioRxiv [Internet]. May 15, 2018.
2) Chaverra-Rodriguez D, et al. 
Targeted delivery of CRISPR-Cas9 ribonucleoprotein into arthropod ovaries for heritable germline gene editing. Nat Commun. 2018 Aug 1;9(1):3008. 

08/06/2018 Justin Bosch 1) Kosicki M, et al. Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements. Nat Biotechnol. 2018;36 (8) :765-771.

About GE Journal Club

ABOUT GE JOURNAL CLUB


Who are we?
Researchers at HMS (Post-docs, grad students, technicians, PIs, etc).

What do we talk about?
Genome engineering/gene editing – novel methods, technical issues (e.g. off-target analysis), ethical concerns, etc.

Why are we doing this?
To stay up to date on recent techniques, stimulate critical discussions, establish contacts for collaboration

When/where?
12:30 PM – 1:30 PM Mondays, Room 354 New Research Building (see schedule) 

What’s the format?
Presenters choose what they present. 2x presentations per meeting (30min each). Usually, this is a single recent paper in the field, presented as a PowerPoint to show the figure panels. Presenters can present any topic/format they wish, such as multiple papers, reviews, general discussion, chalk talk, etc.

Do I have to read the paper?
No, but it’s recommended.

Will I have to present?
We hope you will! But this is not strictly required.

I’m scheduled to present, what do I do?
Find a paper/topic you are excited about! The topic can be related to your expertise, or not. We provide a list of suggested papers (below) but feel free to consider alternatives. *Send your paper/topic selection to the organizer by the Friday before your presentation.* When you present, 1) introduce yourself, 2) explain why you selected the paper/topic, and 3) give background on the topic. Feel free to cut out panels or entire figures if it improves the presentation. Keep your presentation aimed at a general audience - most people do not read the paper and some will not be familiar with your topic.

CONTACT

Questions? Want to join the mailing list? Want to present? Have paper suggestions? – Contact Justin Bosch (jabosch@hms.harvard.edu) (Perrimon Lab)

HMS Email Accounts: Click here to subscribe yourself to the mailing list.

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SUGGESTED PAPERS (reverse chronological order)

 

Mutation-Independent Allele-Specific Editing by CRISPR-Cas9, a Novel Approach to Treat Autosomal Dominant Disease
https://www.sciencedirect.com/science/article/abs/pii/S1525001620302367

A Redox-Based Electrogenetic CRISPR System to Connect With and Control Biological Information Networks
https://www.nature.com/articles/s41467-020-16249-x Massively parallel assessment of human variants with base editor screens
https://www.biorxiv.org/content/10.1101/2020.05.17.100818v1

Pronuclear Microinjection during S-Phase Increases the Efficiency of CRISPR-Cas9-Assisted Knockin of Large DNA Donors in Mouse Zygotes
https://www.sciencedirect.com/science/article/pii/S2211124720306069

Multiplex enCas12a screens show functional buffering by paralogs is systematically absent from genome-wide CRISPR/Cas9 knockout screens
https://www.biorxiv.org/content/10.1101/2020.05.18.102764v1

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects.
https://www.nature.com/articles/s41592-020-0832-x

Cas9 Activates the p53 Pathway and Selects for p53-inactivating Mutations
https://www.nature.com/articles/s41588-020-0623-4

A Cas9 With PAM Recognition for Adenine Dinucleotides
https://www.nature.com/articles/s41467-020-16117-8

Genome-wide CRISPR Screening Reveals Genes Essential for Cell Viability and Resistance to Abiotic and Biotic Stresses in Bombyx mori
https://genome.cshlp.org/content/early/2020/05/18/gr.249045.119

Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance
https://elifesciences.org/articles/55325

Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells
https://www.sciencedirect.com/science/article/pii/S2451945620300684

Detection of Deleterious On-Target Effects after HDR-Mediated CRISPR Editing
https://www.sciencedirect.com/science/article/pii/S2211124720306422

Enhanced Golic+: Highly effective CRISPR gene targeting and transgene HACKing in Drosophila
https://dev.biologists.org/content/early/2020/05/24/dev.181974
 

 

 

Evaluation of Off-Targets Predicted by sgRNA Design Tools
https://www.sciencedirect.com/science/article/pii/S0888754319307086

BEON: A Functional Fluorescence Reporter for Quantification and Enrichment of Adenine Base-Editing Activity
https://www.sciencedirect.com/science/article/abs/pii/S1525001620301908

Targeted mRNA Demethylation Using an Engineered dCas13b-ALKBH5 Fusion Protein
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa269/582...

Analysis and minimization of cellular RNA editing by DNA adenine base editors.
https://advances.sciencemag.org/content/5/5/eaax5717

Massively Parallel CRISPRi Assays Reveal Concealed Thermodynamic Determinants of dCas12a Binding
https://www.pnas.org/content/early/2020/05/05/1918685117

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform
https://www.nature.com/articles/s41587-020-0437-z

Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes
https://www.nature.com/articles/s41587-020-0428-0

Reply to: Fitness effects of CRISPR/ Cas9-targeting of long noncoding RNA genes
https://www.nature.com/articles/s41587-020-0431-5

Increasing the Efficiency and Targeting Range of Cytidine Base Editors Through Fusion of a Single-Stranded DNA-binding Protein Domain
https://www.nature.com/articles/s41556-020-0518-8

An Engineered ScCas9 With Broad PAM Range and High Specificity and Activity
https://www.nature.com/articles/s41587-020-0517-0

A Male-Biased Sex-Distorter Gene Drive for the Human Malaria Vector Anopheles Gambiae
https://www.nature.com/articles/s41587-020-0508-1

Endogenous CRISPR/Cas9 Arrays for Scalable Whole-Organism Lineage Tracing
https://dev.biologists.org/content/147/9/dev184481

 

 

Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope.
https://www.nature.com/articles/s41467-020-15892-8

Plants with genetically encoded autoluminescence
https://www.nature.com/articles/s41587-020-0500-9

Enhancement of homology-directed repair with chromatin donor templates in cells
https://elifesciences.org/articles/55780

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair
https://www.nature.com/articles/s41467-020-15845-1

Safety and feasibility of CRISPR-edited T cells in patients with refractory non-small-cell lung cancer
https://www.nature.com/articles/s41591-020-0840-5

CRISPR-Cas13 Inhibitors Block RNA Editing in Bacteria and Mammalian Cells
https://www.sciencedirect.com/science/article/abs/pii/S1097276520302252

Massively Multiplexed Nucleic Acid Detection Using Cas13
https://www.nature.com/articles/s41586-020-2279-8

CRISPR/Cas9 mediated genetic resource for unknown kinase and phosphatase genes in Drosophila
https://www.nature.com/articles/s41598-020-64253-4

 

 

ORANGE: A CRISPR/Cas9-based genome editing toolbox for epitope tagging of endogenous proteins in neurons
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.30...

Perturbing Proteomes at Single Residue Resolution Using Base Editing
https://www.nature.com/articles/s41467-020-15796-7

Systematic in Vitro Profiling of Off-Target Affinity, Cleavage and Efficiency for CRISPR Enzymes
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa231/582...

Enabling Large-Scale Genome Editing at Repetitive Elements by Reducing DNA Nicking
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa239/582...

Multiplex secretome engineering enhances recombinant protein production and purity
https://www.nature.com/articles/s41467-020-15866-w

 

 

Glia-to-Neuron Conversion by CRISPR-CasRx Alleviates Symptoms of Neurological Disease in Mice
https://www.sciencedirect.com/science/article/pii/S0092867420302865

Extinction of All Infectious HIV in Cell Culture by the CRISPR-Cas12a System With Only a Single crRNA
https://academic.oup.com/nar/article/doi/10.1093/nar/gkaa226/5819595

Rewiring of Endogenous Signaling Pathways to Genomic Targets for Therapeutic Cell Reprogramming
https://www.nature.com/articles/s41467-020-14397-8

Directed evolution of adenine base editors with increased activity and therapeutic application.
https://www.nature.com/articles/s41587-020-0491-6

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies
https://www.cell.com/cell/fulltext/S0092-8674(20)30332-9?dgcid=raven_jbs_aip_email

 

 

Combinatorial Single-Cell CRISPR Screens by Direct Guide RNA Capture and Targeted Sequencing
https://www.nature.com/articles/s41587-020-0470-y

Quantification of the affinities of CRISPR-Cas9 nucleases for cognate protospacer adjacent motif (PAM) sequences.
https://www.jbc.org/content/early/2020/04/01/jbc.RA119.012239.abstract

CRISPR Screens in Cancer Spheroids Identify 3D Growth-Specific Vulnerabilities
https://www.nature.com/articles/s41586-020-2099-x

Therapeutic base editing of human hematopoietic stem cells
https://www.nature.com/articles/s41591-020-0790-y

Genetic Interaction Mapping and Exon-Resolution Functional Genomics With a Hybrid Cas9-Cas12a Platform
https://www.nature.com/articles/s41587-020-0437-z

Targeted nanopore sequencing with Cas9-guided adapter ligation
https://www.nature.com/articles/s41587-020-0407-5

 

 

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes.
https://www.nature.com/articles/s41467-020-15204-0

Prime genome editing in rice and wheat
https://www.nature.com/articles/s41587-020-0455-x

Conditional Single Vector CRISPR/SaCas9 Viruses for Efficient Mutagenesis in the Adult Mouse Nervous System
https://www.sciencedirect.com/science/article/pii/S2211124720302667

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants
https://science.sciencemag.org/content/early/2020/03/25/science.aba8853

A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01989-2

 

 

Cas9-Mediated Gene-Editing in the Malaria Mosquito Anopheles stephensi by ReMOT Control.
https://www.g3journal.org/content/early/2020/03/02/g3.120.401133.long

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling.
https://www.pnas.org/content/117/11/5853.abstract

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR-Cas9 precision genome editing.
https://www.nature.com/articles/s41556-020-0472-5

Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches.
https://www.nature.com/articles/s41589-020-0490-4

A CRISPR-Cas9-based reporter system for single-cell detection of extracellular vesicle-mediated functional transfer of RNA
https://www.nature.com/articles/s41467-020-14977-8

Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly.
https://science.sciencemag.org/content/365/6456/922

RNA-guided retargeting of Sleeping Beauty transposition in human cells.
https://elifesciences.org/articles/53868

OffScan: a universal and fast CRISPR off-target sites detection tool.
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6241-9

Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures
https://www.ncbi.nlm.nih.gov/pubmed/32160537

Capturing RNA-protein interaction via CRUIS.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa143/578...

CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects.
https://www.jbc.org/content/early/2020/03/11/jbc.RA120.012933.abstract

CAS9 is a genome mutator by directly disrupting DNA-PK dependent DNA repair pathway.
https://link.springer.com/article/10.1007%2Fs13238-020-00699-6

CRISPR-Cas12b enables efficient plant genome engineering.
https://www.nature.com/articles/s41477-020-0614-6

Small molecule regulated sgRNAs enable control of genome editing in E. coli by Cas9
https://www.nature.com/articles/s41467-020-15226-8

Extracellular nanovesicles for packaging of CRISPR-Cas9 protein and sgRNA to induce therapeutic exon skipping
https://www.nature.com/articles/s41467-020-14957-y

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants.
https://www.sciencedirect.com/science/article/pii/S0092867420302087

Highly Parallel Profiling of Cas9 Variant Specificity.
https://www.sciencedirect.com/science/article/abs/pii/S109727652030143X

CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa177/580...

 

 

 

 

Deep learning improves the ability of sgRNA off-target propensity prediction.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-...

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors.
https://www.nature.com/articles/s41587-020-0414-6

Targeted nanopore sequencing with Cas9-guided adapter ligation.
https://www.nature.com/articles/s41587-020-0407-5

Continuous evolution of SpCas9 variants compatible with non-G PAMs.
https://www.nature.com/articles/s41587-020-0412-8

Synthetic CRISPR/Cas9 reagents facilitate genome editing and homology directed repair.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa085/573...

CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank.
https://www.sciencedirect.com/science/article/pii/S1934590920300199

Multiplexed and tunable transcriptional activation by promoter insertion using nuclease-assisted vector integration.
https://academic.oup.com/nar/article/47/12/e67/5424073

MagnEdit-interacting factors that recruit DNA-editing enzymes to single base targets.
https://www.life-science-alliance.org/content/3/4/e201900606

SpCas9-NG self-targets the sgRNA sequence in plant genome editing.
https://www.nature.com/articles/s41477-020-0603-9

Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes
https://www.nature.com/articles/s41587-020-0428-0

Pervasive head-to-tail insertions of DNA templates mask desired CRISPR-Cas9-mediated genome editing events.
https://advances.sciencemag.org/content/6/7/eaax2941

Multiplexed conditional genome editing with Cas12a in Drosophila
https://www.biorxiv.org/content/10.1101/2020.02.26.966333v1

Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01956-x

Spatial and temporal control of gene manipulation in Drosophila via drug-activated Cas9 nucleases.
https://www.sciencedirect.com/science/article/pii/S0965174820300254

A toxin-antidote CRISPR gene drive system for regional population modification.
https://www.nature.com/articles/s41467-020-14960-3

GO: a functional reporter system to identify and enrich base editing activity
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa124/576...

BIG-TREE: Base-Edited Isogenic hPSC Line Generation Using a Transient Reporter for Editing Enrichment
https://www.sciencedirect.com/science/article/pii/S2213671119304527

A CRISPR-Cas9-based reporter system for single-cell detection of extracellular vesicle-mediated functional transfer of RNA.
https://www.nature.com/articles/s41467-020-14977-8

 

 

 

Tandem Paired Nicking Promotes Precise Genome Editing with Scarce Interference by p53
https://www.sciencedirect.com/science/article/pii/S2211124719317218

Multiplex CRISPR/Cas screen in regenerating haploid limbs of chimeric Axolotls.
https://elifesciences.org/articles/48511

A Small Molecule-Controlled Cas9 Repressible System.
https://www.cell.com/molecular-therapy-family/nucleic-acids/fulltext/S21...(20)30006-8

Quality Control Strategy for CRISPR-Cas9-Based Gene Editing Complicated by a Pseudogene.
https://www.frontiersin.org/articles/10.3389/fgene.2019.01297/full

Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity.
https://linkinghub.elsevier.com/retrieve/pii/S0896-6273(20)30004-0

Efficient and flexible tagging of endogenous genes by homology-independent intron targeting.
https://genome.cshlp.org/content/early/2019/06/25/gr.246413.118?top=1

Cell-cell contact-induced gene editing/activation in mammalian cells using a synNotch-CRISPR/Cas9 system.
https://link.springer.com/article/10.1007/s13238-020-00690-1

Expanding the genome-targeting scope and the site selectivity of high-precision base editors.
https://www.nature.com/articles/s41467-020-14465-z

Identification of functional regulatory elements in the human genome using pooled CRISPR screens.
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6497-0

Multiple Input Sensing and Signal Integration Using a Split Cas12a System
https://www.sciencedirect.com/science/article/pii/S109727652030037X

Genetic screens in isogenic mammalian cell lines without single cell cloning
https://www.nature.com/articles/s41467-020-14620-6

Universal and Naked-Eye Gene Detection Platform Based on CRISPR/Cas12a/13a System.
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.9b05597

 

 

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells.
https://www.nature.com/articles/s41551-019-0505-1

Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses.
https://www.nature.com/articles/s41551-019-0501-5

A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment.
https://www.nature.com/articles/s41467-019-13977-7

CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish.
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6493-4

Single-cell analysis of a mutant library generated using CRISPR-guided deaminase
https://www.biorxiv.org/content/10.1101/610725v2

Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency.
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioi...

High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation
https://www.biorxiv.org/content/10.1101/2020.01.22.916064v1

Production of genetically engineered mice with higher efficiency, lower mosaicism, and multiplexing capability using maternally expressed Cas9.
https://www.nature.com/articles/s41598-020-57996-7

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1928-4

Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice.
https://www.nature.com/articles/s41467-019-14181-3

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing.
https://www.nature.com/articles/s41467-020-14362-5

 

 

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform.
https://www.nature.com/articles/s41467-019-14012-5

Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies.
https://www.nature.com/articles/s41422-019-0267-z

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons.
https://www.nature.com/articles/s41588-019-0555-z

A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells.
https://www.nature.com/articles/s41589-019-0443-y

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
https://www.nature.com/articles/s41587-019-0387-5

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors.
https://www.nature.com/articles/s41587-019-0393-7

CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos
https://www.biorxiv.org/content/10.1101/2020.01.13.904763v1

 

Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9.
https://elifesciences.org/articles/51662

CRISPR-Cas3 induces broad and unidirectional genome editing in human cells.
https://www.nature.com/articles/s41467-019-13226-x

Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency.
https://www.nature.com/articles/s41587-019-0325-6

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases.
https://www.nature.com/articles/s41586-019-1786-y

Synthetic chimeric nucleases function for efficient genome editing.
https://www.nature.com/articles/s41467-019-13500-y

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1136/565...

Expanding the editable genome and CRISPR-Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking.
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1121/565...

Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
https://genome.cshlp.org/content/early/2019/12/12/gr.248559.119.abstract

A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus
https://www.nature.com/articles/s41467-019-13649-6

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
https://www.nature.com/articles/s41592-019-0392-0

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq
https://www.biorxiv.org/content/10.1101/503367v1

Structural basis of DNA targeting by a transposon-encoded CRISPR–Cas system
https://www.nature.com/articles/s41586-019-1849-0

Multi-functional genome-wide CRISPR system for high throughput genotype-phenotype mapping.
https://www.nature.com/articles/s41467-019-13621-4

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.
https://www.nature.com/articles/s41467-019-13805-y

Cas12a mediates efficient and precise endogenous gene tagging via MITI: microhomology-dependent targeted integrations.
https://link.springer.com/article/10.1007/s00018-019-03396-8

Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing.
https://www.nature.com/articles/s41467-019-11454-9

A transient reporter for editing enrichment (TREE) in human cells.
https://academic.oup.com/nar/article/47/19/e120/5552066

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor.
https://www.nature.com/articles/s41587-019-0331-8

Expanding C-T base editing toolkit with diversified cytidine deaminases.
https://www.nature.com/articles/s41467-019-11562-6

Conditional control of RNA-guided nucleic acid cleavage and gene editing.
https://www.nature.com/articles/s41467-019-13765-3

Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes.
https://www.g3journal.org/content/early/2019/12/27/g3.119.400985

An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms
https://www.nature.com/articles/s41589-019-0432-1

 

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