CRISPR Journal Club - Innovative Genomics Institute (IGI)

Innovative
Genomics
Institute

CRISPR Journal Club

Crazy for CRISPR? Join the club!

Overview

This semester, we'll be covering CRISPR genome-editing technology, basic research uses, and real-world applications. The seminal papers we'll discuss reveal core concepts and key experiments, touching on a range of topics, from the foundational development of CRISPR to its use in treating genetic diseases and engineering agriculture.

We'll also bring in guest speakers and run interactive activities to break up the material and encourage more interactive learning.

Reading and critically analyzing primary scientific literature is an important skill for any scientist. Working through these papers will expose you to new vocabulary, graphs, and protocols common in the CRISPR field. After reading and dissecting these papers, you'll be able to understand the science and effectively dissect scientific literature in the future.

Details

Date: Every Wednesday (from September 11^thto December 4^th)

Time: 6 – 7 pm

Location: Energy Biosciences Building, Room 115

Food: Food and drinks will be provided!

Note: The front doors of EBB are locked after 5 pm, but someone should be there to let you in. The seminar room is on the first floor with windows facing the front door of the building. If you are unable to enter, please grab the attention of someone in the room to let you in.

Helpful Resources

The IGI's illustrated glossary defines a lot of words that commonly appear in CRISPR and genome editing papers! View Glossary >

Visit our Multimedia Library for articles, animations, and graphics to dive deeper into a range of CRISPR topics.

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

Archived Materials

Check out the papers, multimedia resources, and activities used during previous semesters. Follow the outlined schedules or pick and choose your own content!

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

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

We strive to make our events accessible and inclusive. The Innovative Genomics Institute Building is ADA accessible, and has a lactation room that visitors can use. For disability accommodation information and requests and/or access to the lactation room, please contact Kristy Nordahl at knordahl@berkeley.edu or 510-664-7110.