Undergraduate CRISPR Journal Club

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

Guest Speakers	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

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

Overview

Details

Helpful Resources

Spring 2020

February 5th | CRISPR overview

February 12th | Toward a CRISPR therapy for muscular dystrophy

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

February 26th | Clinical genome editing overview

March 4th | Gene drives

March 11th | Clinical CRISPR therapies

March 18th | Cancelled due to COVID-19

March 25th | Spring Break

April 1st | Cancelled due to COVID-19

April 8th | Cancelled due to COVID-19

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

April 22nd | Ethics (via Zoom)

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

Archived Materials

Fall 2019

September 11th | CRISPR overview

September 18th | The origins and future of genome editing

September 25th | Intro to genome editing with CRISPR

October 2nd | Design your own CRISPR experiment

October 9th | CANCELLED (⚡️ outage)

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

October 23rd | Hot off the press: Prime editing

October 30th | Clinical trials and treating blindness

November 6th | CRISPR challenges: Therapeutic delivery

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

November 20th | Student presentation: Toward a CRISPR Therapy for Cystic Fibrosis

November 27th | Thanksgiving Break — No Meeting

December 4th | The diverse CRISPR toolbox — Molecular recording

Spring 2019

CRISPR-Cas9 basics

CRISPR-Cas9 editing in animal models

CRISPR screens

Evolution and developmental biology

Sickle cell genome editing clinical trial

CRISPR gene drives

CRISPR-induced chromosomal truncations

Barcoding

Ethics

Beyond genome editing – Programmable chromosomal looping

Circular Permutation of Cas9

Fall 2018

CRISPR-Cas9 basics

CRISPR-Cas9 editing in human cells

CRISPR screens

Anti-CRISPRs

Base editing

Cas9 protein engineering

Discovering new CRISPR systems

Nucleic acid detection with CRISPR enzymes

Delivery

Ethics

Treating muscular dystrophy

Domestication of crops using CRISPR

Human immune reaction to CRISPR treatments

Novel Coronavirus Updates

February 5^th | CRISPR overview

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

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

February 26^th | Clinical genome editing overview

March 4^th | Gene drives

March 11^th | Clinical CRISPR therapies

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)

April 22^nd | Ethics (via Zoom)

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

September 11^th | CRISPR overview

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

September 25^th | Intro to genome editing with CRISPR

October 2^nd | Design your own CRISPR experiment

October 9^th | CANCELLED (⚡️ outage)

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

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

October 30^th | Clinical trials and treating blindness

November 6^th | CRISPR challenges: Therapeutic delivery

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

November 20^th | Student presentation: Toward a CRISPR Therapy for Cystic Fibrosis

November 27^th | Thanksgiving Break — No Meeting

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