Undergraduate CRISPR Journal Club

Fall 2021

September 8^th | The basics of CRISPR-Cas

Presenter

Valeri Vasquez, Graduate Student & Journal Club Coordinator

September 15^th | The CRISPR-Cas patent war

Presenter

Ben Rubin, Postdoctoral Researcher & Journal Club Coordinator

September 22^nd | Biohacking

Guest Speaker	Richard Fuisz, Founder of Strandbase
Paper	Caveat creator Journal of Law and the Biosciences \| Fuisz \| January 2018

September 29^th | CRISPR-associated transposases

Presenter	Sarp Kurtoglu, Journal Club Member
Paper	Dual modes of CRISPR-associated transposon homing Cell \| Saito, Ladha, Strecker, Faure, et al. \| April 2021

October 6^th | CRISPR for selection of edited viruses

Presenter	Vindhya Kilaru, Journal Club Member
Paper	Rapid poxvirus engineering using CRISPR/Cas9 as a selection tool Communications Biology \| Gowripalan & Smith et al. \| November 2020

October 13^th | Prime editing

Presenter	Kenneth Loi, Journal Club Member
Paper	Search-and-replace genome editing without double-strand breaks or donor DNA Nature \| Anzalone et al. \| October 2019

October 20^th | Cas9 structural dynamics

Guest Speaker	Josh Cofsky, Graduate Student in the Doudna Lab
Paper	CRISPR-Cas9 bends and twists DNA to read its sequence bioRxiv \| Cofsky et al. \| September 2021

October 27^th | High-throughput Cas protein engineering

Guest Speaker

David Savage, IGI Investigator and Associate Professor at UC Berkeley

Papers

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification
Cell | Oakes et al. | January 2019

Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules
Nature Communications | Shams & Higgins et al. | September 2021

November 3^rd | CRISPR screening to improve immunotherapy

Presenter	Chang Liu, Journal Club Member
Paper	Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy Nature \| Wei & Long et al. \| December 2019

November 10^th | Therapeutic delivery of CRISPR tools

Guest Speaker	Niren Murthy, IGI Investigator and Professor at UC Berkeley
Related Project	Development of novel technologies for delivery of base editors to the airway epithelium IGI Project Profile

November 17^th | Using anti-CRISPRs to control gene drives

Presenter	Russell Brown, Journal Club Member
Paper	A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression Nature Communications \| Taxiarchi et al. \| June 2021

November 24^th | Thanksgiving: No meeting

December 1^st | Career panel

December 8^th | Dinner at Jupiter (final meeting of the semester!)

Spring 2021

February 3^rd | CRISPR basics — Prokaryotic immunity and Cas9

Presenter	Megan Hochstrasser, IGI Education Program Manager & Journal Club Coordinator
Supporting Material	Apps: Phage Invaders and CRISPR-3D (IGI) Video: The CRISPR-Cas9 Experiment that Led to Genome Editing (XBio) Textbook chapter: CRISPR-Cas9: A New Tool for Genome Editing (XBio) Interactive visualization: CRISPR-Cas9 "Click & Learn" (HHMI Biointeractive)

February 10^th | CRISPR basics — Genome editing and applications

Presenter	Megan Hochstrasser, IGI Education Program Manager & Journal Club Coordinator
Review Paper	The Promise and Challenge of Therapeutic Genome Editing Nature \| Doudna \| February 2020

February 17^th | Cas9 structure and function

Guest Speaker

Ross Wilson, Adjunct Professor at UC Berkeley and IGI Director of Therapeutic Delivery

February 24^th | CRISPR-based genome editing in human cells

Presenter	Megan Hochstrasser, IGI Education Program Manager & Journal Club Coordinator
Paper	Multiplex Genome Engineering Using CRISPR/Cas Systems Science \| Cong et al. \| February 2013

March 3^rd | CRISPR and the coronavirus

Presenter	Eli McAmis, Student Leader for CRISPR Journal Club
Paper	Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses Cell \| Wang & Simoneau et al. \| January 2021

March 10^th | Discovering new CRISPR enzymes through metagenomics

Presenter	Leighton Pu, CRISPR Journal Club member
Paper	New CRISPR-Cas systems from uncultivated microbes Nature \| Burstein, Harrington, & Strutt et al. \| February 2017

March 17^th | CRISPR in agriculture: Golden rice

Presenter	Alex Gueorguieva, Student Leader for CRISPR Journal Club
Paper	Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9 Nature Communications \| Dong et al. \| March 2020
Supporting Material	Twitter thread paper summary @igisci \| March 2020

March 24^th | Spring break: No meeting

March 31^st | CRISPR in the clinic

Guest Speaker

Dan Hostetter, Principal Scientist at CRISPR Therapeutics

Paper

'Off-the-shelf' allogeneic CAR T cells: development and challenges

Nature Reviews Drug Discovery | Depil et al. | January 2020

CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia

NEJM | Frangoul et al. | December 2020

Supporting Material

Meet Victoria Gray, The First CRISPR Sickle Cell Patient
Collection of content from NPR

April 7^th | Phage-encoded CRISPR-Cas systems

Guest Speaker

Kim Seed, Assistant Professor at UC Berkeley

April 14^th | Base editing

Presenters	Eli McAmis, Student Leader for CRISPR Journal Club, and Sam Ghaffari-Kashani, club member
Paper	Base editing: precision chemistry on the genome and transcriptome of living cells Nature Reviews Genetics \| Rees & Liu \| October 2018

April 21^st | Ethics of non-human CRISPR applications

Guest Speaker

Lea Witkowsky, IGI Policy Analyst

April 28^th | Career panel

May 5^th | Game night (final meeting of the semester!)

Fall 2020

September 2^nd | CRISPR 101

Guest Speaker	Megan Hochstrasser, IGI Education Program Manager
Optional Review Paper	The Promise and Challenge of Therapeutic Genome Editing Nature \| Doudna \| February 2020

September 9^th | CRISPR-based genome editing in human cells

Paper

Multiplex Genome Engineering Using CRISPR/Cas Systems
Science | Cong et al. | February 2013

September 16^th | Student presentation: Agricultural applications

Paper

Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
Cell | Rodríguez-Leal et al. | October 2017

September 23^rd | CRISPR diversity

Guest Speaker

Luis Valentin-Alvarado, PhD student in Banfield and Savage labs at UC Berkeley

September 30^th | Student presentation: Treating sickle cell disease

Paper	Selection-Free Genome Editing of the Sickle Mutation in Human Adult Hematopoietic Stem/Progenitor Cells Science Translational Medicine \| DeWitt et al. \| October 2016
Press Release	IGI Makes Progress Toward Treating Sickle Cell Disease with CRISPR-Cas9 IGI \| October 2016

October 7^th | CRISPR toolbox: Directed evolution

Guest Speaker	Connor Tou (undergrad researcher) and Juan Hurtado (PhD student) in Dueber lab at UC Berkeley
Paper	CRISPR-Guided DNA Polymerases Enable Diversification of All Nucleotides in a Tunable Window Nature \| Halperin et al. \| August 2018
Press Release	CRISPR Diversifies: Cut, Paste, On, Off, and Now– Evolve! IGI \| August 2018

October 14^th | Student presentation: Editing crops for disease resistance

Paper

Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence
Plant Biotechnology Journal | Gomez & Lin et al. | June 2018

October 21^st | Delivery in plants

Guest Speaker	Gozde Demirer, former PhD student in Landry lab at UC Berkeley
Paper	High Aspect Ratio Nanomaterials Enable Delivery of Functional Genetic Material Without DNA Integration in Mature Plants Nature Nanotechnology \| Demirer et al. \| May 2019
Press Release	DNA Takes a Ride on a Nanotube: Next Stop, Genome-Edited Crops IGI \| February 2019

October 28^th | Student presentation: Identifying new Cas effectors

Paper

CRISPR-CasΦ from huge phages is a hypercompact genome editor
Science | Pausch & Al-Shayeb et al. | July 2020

November 4^th | Student presentation: CRISPR diagnostics

Review Paper

Nucleic Acid Detection Using CRISPR/Cas Biosensing Technologies
ACS Synthetic Biology | Aman et al. | March 2020

November 11^th | Veterans Day (no meeting)

November 18^th | Ethics & regulation

Guest Speaker

Michael Gomez, postdoc in Staskawicz lab at UC Berkeley

November 25^th | Thanksgiving (no meeting)

December 2^nd | Career panel (final meeting of the semester!)

Spring 2020

February 5^th | CRISPR overview

Paper	A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity Science \| Jinek et al. \| June 2012
Additional Content	Textbook chapter: CRISPR-Cas9: A New Tool for Genome Editing Guided paper: A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity The Explorer's Guide to Biology (XBio) \| 2019

February 12^th | Toward a CRISPR therapy for muscular dystrophy

Paper

Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy
Science | Amoasii et al. | October 2018

Additional Content

Guided paper: Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy

The Explorer's Guide to Biology (XBio) | 2019

Article: Can CRISPR Save Ben Dupree?

Antonio Regalado | MIT Technology Review | October 2016

February 19^th | CRISPR's origin story: Bacterial immunity

Guest Speaker

Megan Hochstrasser, Science Communications Manager for IGI

Additional Content

Paper: Harnessing "A Billion Years of Experimentation’’: The Ongoing Exploration and Exploitation of CRISPR–Cas Immune Systems
The CRISPR Journal | Klompe & Sternberg | April 2018

Game: Phage Invaders (download the mobile app or play online!)

February 26^th | Clinical genome editing overview

Paper

The promise and challenge of therapeutic genome editing
Nature | Doudna | February 2020

March 4^th | Gene drives

Paper

A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes
Nature Biotechnology | Kyrou and Hammond et al. | November 2018

March 11^th | Clinical CRISPR therapies

Guest Speaker

Beeke Wienert, postdoc in Bruce Conklin's lab at the Gladstone Institutes

March 18^th | Cancelled due to COVID-19

March 25^th | Spring Break

April 1^st | Cancelled due to COVID-19

April 8^th | Cancelled due to COVID-19

April 15^th | Genome editing as a basic research tool — Butterfly wing patterning (via Zoom)

Guest Speaker

Aaron Pomerantz, grad student in Nipam Patel's lab at UC Berkeley

April 22^nd | Ethics (via Zoom)

Guest Speaker	Sharon O'Hara, postdoc with Jodi Halpern at the UC Berkeley School of Public Health
Paper	Annotated paper: Biomedical ethics 2.0: redefining the meaning of disease, patient and treatment Nature Reviews Molecular Cell Biology \| Frederick Grinnell \| April 2020

April 29^th | Genome editing as a basic research tool — Poison resistance in insects (via Zoom)

Guest Speaker

Marianna Karageorgi (postdoc) and Kirsten Vester (graduate student) in Noah Whiteman's lab at UC Berkeley

Fall 2019

September 11^th | CRISPR overview

Paper	Development and Applications of CRISPR-Cas9 for Genome Engineering Cell \| Hsu et al. \| June 2014
Additional Content	Radiolab's CRISPR Overview Podcast Radiolab \| 2015, updated 2017

September 18^th | The origins and future of genome editing

Guest Speaker

Dana Carroll – Founding researcher in the field of genome editing

Additional Content

Videos: Background on genome editing & Issues in CRISPR-Cas Editing

Podcast: The CRISPR Journal interview with Dr. Carroll, "Your Moment of ZFN"

September 25^th | Intro to genome editing with CRISPR

Paper

Multiplex Genome Engineering Using CRISPR/Cas Systems
Science | Cong et al. | January 2013

October 2^nd | Design your own CRISPR experiment

Paper	Genome engineering using the CRISPR-Cas9 system Nature Protocols \| Ran et al. \| October 2013
Additional Content	Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms – Paper & Video JOVE \| Farboud et al. \| May 2018

October 9^th | CANCELLED (⚡️ outage)

October 16^th | Genome editing in basic research: Editing butterflies!

Guest Speaker

Aaron Pomerantz – Graduate Student in Patel Lab

Additional Content

Paper: CRISPR/Cas9 as the Key to Unlocking the Secrets of Butterfly Wing Pattern Development and Its Evolution
Advances in Insect Physiology | December 2017

Video: Using Gene Editing To Repaint Butterfly Wings
PBS "It's Okay To Be Smart" | July 2019

October 23^rd | Hot off the press: Prime editing

Paper

Search-and-replace genome editing without double-strand breaks or donor DNA
Nature | Anzalone et al. | October 2019

October 30^th | Clinical trials and treating blindness

Paper	Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10 Nature \| Maeder et al. \| January 2019
Media Coverage	CRISPR enters its first human clinical trials ScienceNews \| Tina Hesman Saey \| August 2019

November 6^th | CRISPR challenges: Therapeutic delivery

Guest Speaker

Maroof Adil – Scientist at local biotech startup

November 13^th | Genome editing crops: CRISPR-edited tomatoes

Paper	Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing Cell \| Rodriguez-Leal et al. \| October 2017
Additional Reading	10 Unusual Applications of CRISPR Gene Editing Labiotech \| Clara Rodríguez Fernández \| April 2019

November 20^th | Student presentation: Toward a CRISPR therapy for cystic fibrosis

Paper

Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients
Cell Stem Cell | Schwank and Koo et al. | December 2013

Additional Content

Video: What is Cystic Fibrosis? Explained 60 Seconds

Let There Be | February 2018

Video: How Gene Editing Could Be Used for CF

Cystic Fibrosis Foundation | November 2016

November 27^th | Thanksgiving Break — No Meeting

December 4^th | The diverse CRISPR toolbox — Molecular recording

Paper	CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria Nature \| Shipman et al. \| July 2017
Additional Content	Video: Movie Replayed From Living Cells' DNA Debuts "Molecular Recorder" NIMH \| July 2017

Spring 2019

CRISPR-Cas9 basics

Paper

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Science | Jinek et al. | June 28, 2012

CRISPR-Cas9 editing in animal models

Paper

Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes
Nature Biotechnology | Staahl et al. | February 13, 2017

CRISPR screens

Paper	Identification and characterization of essential genes in the human genome Science \| Wang et al. \| November 27, 2015
Additional Reading	The indispensable genome – General public Science \| November 27, 2015
Videos	Introduction to dCas9 – Seminar (51 min) Luke Gilbert \| 2017 CRISPR Workshop Repurposing CRISPR an RNA-guided DNA binding platform – Seminar (1 hr 33 min) Luke Gilbert \| 2017 CRISPR Workshop Expanding the CRISPR toolbox – Animation (4 min) Nature Methods \| October 31, 2017

Evolution and developmental biology

Paper	CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution Cell \| Martin et al. \| December 10, 2015
Video	Homeotic (Hox) Genes and Evolution of Crustacean Body Plan – General Audience iBiology \| Nipam Patel \| September 18, 2018

Sickle cell genome editing clinical trial

Paper	High-level correction of the sickle mutation amplified in vivo during erythroid differentiation bioRxiv \| Magis et al. \| January 8, 2019
Additional Readings	Clinical applications of CRISPR‐based genome editing and diagnostics – Review Transfusion \| Foss et al. \| January 2, 2019 Prioritizing Sickle Cell Patients: A Chance to Mend Broken Ties – General Audience IGI blog post \| Shakir Cannon \| September 28, 2017

CRISPR gene drives

Paper	A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes Nature Biotechnology \| Kyrou et al. \| September 24, 2018
Additional Reading	CRISPR/Cas9-mediated gene knockout of Anopheles gambiae FREP1 suppresses malaria parasite infection – Paper PLOS Pathogens \| Dong et al. \| March 8, 2018 Gene Drives, White-Footed Mice, and Black Sheep: An Interview with Kevin Esvelt – Interview The CRISPR Journal \| Kevin Davies & Kevin Esvelt \| November 5, 2018

CRISPR-induced chromosomal truncations

Paper	CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations Nature Communications \| Cullot et al. \| March 8, 2018
Additional Reading	What happens at the break of a Cas9 edit? IGI Perspectives \| July 18, 2018

Barcoding

Paper

Developmental barcoding of whole mouse via homing CRISPR
Science | Kalhor et al. | August 31, 2018

Ethics

Paper	#CRISPRbabies: Notes on a Scandal The CRISPR Journal \| Sean Ryder \| November 6, 2018
Videos	Ethical and Societal Issues – Seminar (58 min) Hank Greely \| 2017 CRISPR Workshop

Beyond genome editing – Programmable chromosomal looping

Paper

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping
Nature Communications | Morgan et al. | July 13, 2017

Circular Permutation of Cas9

Paper	CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification Cell \| Oakes et al. \| January 10, 2019
Additional Reading	CRISPR, Reprogrammed: A New Sidekick for the Human Immune System? – Press release IGI \| Hope Henderson \| January 10, 2019

Fall 2018

CRISPR-Cas9 basics

Paper

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Science | Jinek et al. | June 28, 2012

CRISPR-Cas9 editing in human cells

Paper	Multiplex Genome Engineering Using CRISPR/Cas Systems Science \| Cong et al. \| January 3, 2013
Additional Reading	RNA-Guided Human Genome Engineering via Cas9 – Paper Science \| Mali et al. \| January 3, 2013

CRISPR screens

Paper	Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression Cell \| Qi et al. \| February 28, 2013
Additional Reading	CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes Cell \| Gilbert et al. \| July 18, 2013
Videos	Introduction to dCas9 – Seminar (51 min) Luke Gilbert \| 2017 CRISPR Workshop Repurposing CRISPR an RNA-guided DNA binding platform – Seminar (1 hr 33 min) Luke Gilbert \| 2017 CRISPR Workshop Expanding the CRISPR toolbox – Animation (4 min) Nature Methods \| October 31, 2017

Anti-CRISPRs

Paper	Disabling Cas9 by an anti-CRISPR DNA mimic Science Advances \| Shin et al. \| July 12, 2017
Additional Readings	Anti-CRISPR Proteins Decrease Off-Target Effects of Cas9 – General public Berkeley News \| July 12, 2017 The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs – Review Annual Review of Virology \| Borges et al \| July 27, 2017 A Broad-Spectrum Inhibitor of CRISPR-Cas9 – Paper Cell \| Harrington et al. \| August 24, 2017

Base editing

Paper	Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage Nature \| Komor et al. \| April 20, 2016
Additional Readings	CRISPR 2.0 Is Here and It's Way More Precise – General public MIT Technology Review \| Emily Mullin \| October 25, 2017 Genome editor CRISPR's latest trick? Offering a sharper snapshot of activity inside the cell – General public Science \| Jon Cohen \| February 15, 2018 With embryo base editing, China gets another CRISPR first – General public WIRED \| Megan Molteni \| August 21, 2018

Cas9 protein engineering

Paper	Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch Nature Biotechnology \| Oakes et al. \| May 2, 2016
Additional Reading	Engineered CRISPR-Cas9 nuclease with expanded targeting space – Paper Science \| Nishimasu et al. \| August 30, 2018

Discovering new CRISPR systems

Paper	Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems Molecular Cell \| Shmakov et al. \| October 22, 2015
Additional Reading	Compact CRISPR systems found in some of world's smallest microbes – General public Berkeley News \| Robert Sanders \| December 22, 2016

Nucleic acid detection with CRISPR enzymes

Paper	CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity Science \| Chen et al. \| February 15, 2018
Additional Reading	Nucleic acid detection with CRISPR-Cas13a/C2c2 – Paper Science \| Gootenberg et al. \| April 13, 2017

Delivery

Paper	Nanoparticle delivery of CRISPR into the brain rescues a mouse model of fragile X syndrome from exaggerated repetitive behaviours Nature Biomedical Engineering \| Lee et al. \| June 25, 2018
Additional Readings	Emerging Strategies for Genome Editing in the Brain – "Spotlight" putting the paper in the context of the field Trends in Molecular Medicine \| Foss et al. \| October 24, 2018 It’s gold! Nanoparticles delivery of CRISPR in mouse brain – Lay-friendly overview PLoS Blog \| Kostas Vavitsas \| September 18, 2018
Videos	Delivery Methods – Seminar (45 min) Dana Carroll \| 2017 CRISPR Workshop

Ethics

Paper	Gene modification therapies: views of parents of people with Down syndrome Genetics in Medicine \| Michie & Allyse \| June 21, 2018
Additional Reading	Translating dosage compensation to trisomy 21 – Paper Nature \| Jiang et al. \| August 15, 2018
Videos	Ethical and Societal Issues – Seminar (58 min) Hank Greely \| 2017 CRISPR Workshop

Treating muscular dystrophy

Paper	Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy Science \| Amoasii et al. \| August 30, 2018
Additional Readings	A CRISPR cure for Duchenne muscular dystrophy is closer after a trial in dogs – General public MIT Technology Review \| Antonio Regalado \| August 24, 2018

Domestication of crops using CRISPR

Paper	Rapid improvement of domestication traits in an orphan crop by genome editing Nature Plants \| Lemmon et al. \| October 1, 2018
Additional Readings	Taming the Groundcherry: With Crispr, a Fussy Fruit Inches Toward the Supermarket – Generalp public New York Times \| Veronique Greenwood \| October 5, 2018 Fixing the tomato: CRISPR edits correct plant-breeding snafu – General public Nature \| Heidi Ledford \| May 18, 2018

Human immune reaction to CRISPR treatments

Paper	High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population Nature Medicine \| Wagner et al. \| October 29, 2018
Additional Reading	You May Already Be Immune to CRISPR – General public The Atlantic \| Sarah Zhang \| January 9, 2018