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GE Journal Club (genome engineering/gene editing)

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SCHEDULE

**NEW TIME / NEW ROOM** Meetings are Mondays, 12:30 PM – 1:30 PM in NRB 354 unless otherwise noted
Pizza and soda generously provided by the Department of Genetics
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DATE PRESENTERS PAPERS
05/27 NO MEETING – – – – – – – –
05/20 Chiao-Lin Chen
Joel Sohn 		TBD
05/13 Maria Clara Ingaramo
TBA 		TBD
05/06 NO MEETING – – – – – – – –
04/29 Justin Bosch
Stephanie Mohr 		TBD
04/22 NO MEETING – – – – – – – –
04/15 Baolong Xia
Tracy Zhang 		TBD
04/08 Ankita Singh
Arpan Ghosh 		TBD
04/01 Pedro Saavedra
Ram Viswanatha 		TBD
03/25 Afroditi Petsakou
Ben Ewen-Campen 		TBD
03/18 NO MEETING – – – – – – – –
03/11 Ricky Brathwaite
Henrique Camara 		TBD
  NO MEETING 02/18, 02/25, 03/04
02/11 Julio Sainz de Aja
Sarah Bowling 		TBD
02/04 NO MEETING – – – – – – – –
01/28 Ah-Ram Kim
Enzo Mameli 		TBD
  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


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?
4:00 - 5:00 PM Mondays, Room 335 “The Fishbowl”, New Research Building. (see schedule)

What’s the format?
Presenter chooses and presents a paper. We suggest PowerPoint to show figure panels. 2x presentations per meeting (30min each). Presenters are chosen by a rotating schedule.

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.

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)

Yan WX, et al. Functionally diverse type V CRISPR-Cas systems. Science. 2018 Dec 6. eaav7271

Yang S, et al. Shortening the Half-Life of Cas9 Maintains Its Gene Editing Ability and Reduces Neuronal Toxicity. Cell Rep. 2018 Dec 04. 25:10, P2653-2659.E3.

Poe et al. Robust CRISPR/Cas9-mediated tissue specific mutagenesis reveals gene redundancy and perdurance in Drosophila. Genetics. 2018 Nov 30.

Ikeda K, et al. Efficient scarless genome editing in human pluripotent stem cells. Nat Methods 2018 Nov 30. 

Chen B, et al. Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag. Nat Commun. 2018 Nov 29;9(1):5065.

Chen W, et al. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. bioRxiv [Internet]. Nov. 28, 2018.

Allen F, et al. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol. 2018 Nov 27. 

Hoffmann MD, et al. Cell-specific CRISPR/Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. bioRxiv [Internet]. Nov. 27, 2018.

Yang Y, et al. Base editing generates substantial off-target single nucleotide variants. bioRxiv [Internet]. Nov. 27, 2018.

Gao Z, et al. Improvement of the CRISPR-Cpf1 system with ribozyme-processed crRNA. RNA Biol. 2018 Nov 23.

Buchmuller BC, et al. Pooled clone collections by multiplexed CRISPR/Cas12a-assisted gene tagging in yeast. bioRxiv [Internet]. Nov. 22, 2018.

Bolukbasi MF, et al. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat Commun. 2018 Nov 19;9(1):4856. 

Lee HK, et al. Targeting fidelity of adenine and cytosine base editors in mouse embryos. Nat Commun. 2018 Nov 15;9(1):4804.

Burg L, et al. Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish. PLoS Genet. 2018 Nov 14;14(11):e1007754.

Wienert B, et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. bioRxiv [Internet]. Nov. 14, 2018.

Zhu H, et al. Spatial control of in vivo CRISPR–Cas9 genome editing via nanomagnets. Nature Biomed Engineer. 2018 Nov 12.

Kim D, et al. DIG-seq: a genome-wide CRISPR off-target profiling method using chromatin DNA. Genome Res. 2018 Nov 9. 

Liu Y, et al. Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites. Nat Biotechnol. 2018 Nov 5. 

Wang X, et al. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol. 2018 Nov;36(10):946-949. 

Ma H, et al. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods. 2018 Oct 30.

Bubeck F, et al. Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nat Methods. 2018 Oct 30.

Chatterjee P, et al. Minimal PAM specificity of a highly similar SpCas9 ortholog. Science Advances  24 Oct 2018: Vol. 4, no. 10, eaau0766.

Liu DL, et al. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep. 2018 Oct 23. 25:4, P884-892.E3.

Guo T, et al. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol. 2018 Oct 19;19(1):170. 

Wang D, et al. Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nat Biotechnol. 2018 Oct;36(9):839-842. 

Koblan LW, et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol. 2018 Oct;36(9):843-846. 

Ting PY, et al. Guide Swap enables genome-scale pooled CRISPR-Cas9 screening in human primary cells. Nat Methods. 2018 Oct 8. 

Wang H, et al. CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Cell. 2018 Oct 8. pii: S0092-8674(18)31185-1. 

Shariati A, et al. Reversible disruption of specific transcription factor-DNA interactions using CRISPR/Cas9. bioRxiv [Internet]. Sept. 28, 2018.

Jakimo N, et al. A Cas9 with Complete PAM Recognition for Adenine Dinucleotides. bioRxiv [Internet]. Sept. 27, 2018.

Kyrou K, et al. A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat Biotechnol. 2018 Sep 24.

Yuan J, et al. Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase. Mol Cell. 2018 Sep 21.  pii: S1097-2765(18)30741-X.

Oberhofer G, et al. Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs. Proc Natl Acad Sci U S A. 2018 Sep 17.

Wang H, et al. An Efficient Genome Editing Strategy To Generate Putative Null Mutants in Caenorhabditis elegans Using CRISPR/Cas9. G3 (Bethesda). 2018 Sep 17.

Serebrenik YV, et al. Scalable tagging of endogenous genes by homology-independent intron targeting. bioRxiv [Internet]. Sept. 10, 2018.

Yarrington RM, et al. Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo. Proc Natl Acad Sci USA. 2018 Sep 10. 

Champer J, et al. Molecular safeguarding of CRISPR gene drive experiments. bioRxiv [Internet]. Sept 8, 2018.

Bin Moon S, et al. Highly efficient genome editing by CRISPR-Cpf1 using CRISPR RNA with a uridinylate-rich 3'-overhang. Nat Commun. 2018 Sep 7;9(1):3651. 

Marino ND, et al. Discovery of widespread Type I and Type V CRISPR-Cas inhibitors. Science. 2018 Sep 6. 

Watters KE, et al. Systematic discovery of natural CRISPR-Cas12a inhibitors. Science. 2018 Sep 6. 

Sinha S, et al. A systematic genome-wide mapping of the oncogenic risks associated with CRISPR-Cas9 editing. bioRxiv [Internet]. Sept. 3, 2018.

Lee H, et al. Unexpected CRISPR on-target effects. Nat Biotechnol. 2018 Sep;36(8):703-704. 

Kalhor R, et al. Developmental barcoding of whole mouse via homing CRISPR. Science. 2018 Aug 31;361(6405).

Gutierrez-Triana JA, et al. Efficient single-copy HDR by 5' modified long dsDNA donors. Elife. 2018 Aug 29;7.

Schaefer M, et al. PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation. bioRxiv [Internet]. Aug. 23, 2018.

Gapinske M, et al. CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biol. 2018 Aug 15;19(1):107. 

Sternberg PW, et al. An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9. bioRxiv [Internet]. Aug. 13, 2018.

Chakrabarti AM, et al. Target-specific precision of CRISPR-mediated genome editing. bioRxiv [Internet]. Aug. 9, 2018.

Su K-C, et al. CRISPR/Cas9-based gene targeting using synthetic guide RNAs enables robust cell biological analyses. Mol Biol Cell. 2018 Aug 9:mbcE18040214. 

Kuscu C, et al. Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells. J Mol Biol. 2018 Aug 9. 

Roche PJR, et al. Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells. bioRxiv [Internet]. Aug. 6, 2018.

Lee JK, et al. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun. 2018 Aug 6;9(1):3048. 

Richardson CD, et al. CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat Genet. 2018 Aug;50(8):1132-1139. 

Halperin SO, et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature. 2018 Aug;560(7717):248-252.

Yeo NC, et al. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Aug;15(8):611-616. 

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. 

Gehrke JM, et al. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol. 2018 Jul 30. 

Kandul NP, et al. Transforming Insect Population Control with Precision Guided Sterile Males. bioRxiv [Internet]. July 26, 2018.

Grunwald HA, et al. Super-Mendelian inheritance mediated by CRISPR/Cas9 in the female mouse germline. bioRxiv [Internet]. July 7, 2018.

Suzuki T, et al. Switchable genome editing via genetic code expansion. Sci Rep. 2018 Jul 3;8(1):10051.

Ihry RJ, et al. p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med. 2018 Jul;24(7):939-946. 

Mello C, et al. Robust genome editing with short single-stranded and long, partially single-stranded DNA donors in C. elegans. bioRxiv [Internet]. June 20, 2018.

Noble C, et al. Current CRISPR gene drive systems are likely to be highly invasive in wild populations. Elife. 2018 Jun 19;7.

Knapp DJHF, et al. Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression. bioRxiv [Internet]. June 8, 2018.

Li-Kroeger D, et al. An expanded toolkit for gene tagging based on MiMIC and scarless CRISPR tagging in Drosophila. bioRxiv [Internet]. June 2, 2018.

Savic N, et al. Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife. 2018 May 29;7.

Kurata M, et al. Highly Multiplexed Genome Engineering Using CRISPR/Cas9 gRNA Arrays. bioRxiv [Internet]. May 25, 2018.

Kundert K, et al. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. bioRxiv [Internet]. May 15, 2018.

Liao C, et al. One-step assembly of large CRISPR arrays enables multi-functional targeting and reveals constraints on array design. bioRxiv [Internet]. May 2, 2018.

Chen JS, et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018 Apr 27;360(6387):436-439. 

Tang W, et al. Rewritable multi-event analog recording in bacterial and mammalian cells. Science. 2018 Apr 13;360(6385). 

Hu JH, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity. Nature. 2018 Apr 5;556(7699):57-63.

Tsui C, et al. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci USA. 2018 Mar 20;115(12):E2734-E2741

Chen B, et al. CRISPR-Tag: an Efficient DNA Tagging System in Living Cells. bioRxiv [Internet]. March 12, 2018.

Kim HK, et al. Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity. Nat Biotechnol. 2018 Mar;36(3):239-241. 

Casini A, et al. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotechnol. 2018 Mar;36(3):265-271. 

Zhou H, et al. In vivo simultaneous transcriptional activation of multiple genes in the brain using CRISPR-dCas9-activator transgenic mice. Nat Neurosci. 2018 Mar;21(3):440-446. 

Poe AR, et al. Highly efficient CRISPR/Cas9-mediated tissue specific mutagenesis in Drosophila. bioRxiv [Internet]. Feb. 20, 2018.

Strutt SC, et al. RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 2018 Jan 5;7.

Moreno-Mateos MA, et al. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Commun. 2017 Dec 8;8(1):2024.

Gaudelli NM, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature. 2017 Nov 23;551(7681):464-471. 

Chen JS, et al. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature. 2017 Oct 19;550(7676):407-410. 

Abudayyeh OO, et al. RNA targeting with CRISPR-Cas13. Nature. 2017 Oct 12;550(7675):280-284.

Joung J, et al. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature. 2017 Aug 17;548(7667):343-346.

Gao L, et al. Engineered Cpf1 variants with altered PAM specificities. Nat Biotechnol. 2017 Aug;35(8):789-792. 

Gootenberg JS, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2.. Science. 2017 Apr 28;356(6336):438-442.