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Undergraduate CRISPR Journal Club

Crazy for CRISPR? Join the club!

 

Overview

Our club will be entirely virtual this fall. If you'd like to join, please contact igi-education@berkeley.edu with your name and what year you're in at Berkeley to be added to our email list and receive a Zoom invitation.

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Our undergraduate journal club covers 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 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, figures, 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, September 2 – December 2, 2020.

Time: 6 – 7 pm (sharp, not Berkeley time)

Location: Virtual!

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 2020 Schedule

September 2nd | 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 9th | CRISPR-based genome editing in human cells

Paper

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

 

September 16th | Agricultural applications

Paper TBD

 

September 23rd | CRISPR Diversity

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

 

September 30th | 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

 

October 7th | CRISPR toolbox: Directed evolution

Guest Speaker

TBD
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 8th | CRISPR toolbox: Diagnostics

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

 

October 14th | TBD

 

October 21st | Delivery in plants

Guest Speaker

Gozde Demirer, postdoc 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 28th | TBD

 

November 4th | Design your own genome-editing experiment!

 

November 11th | Veterans Day (no meeting)

 

April 22nd | Ethics & regulation

Guest Speaker

TBD

 

November 25th | Thanksgiving (no meeting)

 

December 2nd | Final meeting, activity TBD!

 

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!

Spring 2020

February 5th | 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 12th | 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 19th | 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 26th | Clinical genome editing overview

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

 

March 4th | 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 11th | Clinical CRISPR therapies

Guest Speaker

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

 

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)

Guest Speaker

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

 

April 22nd | Ethics (via Zoom)

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

 

April 29th | 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 11th | 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 18th | 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 25th | Intro to genome editing with CRISPR

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

 

October 2nd | 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 9th | CANCELLED (⚡️ outage)

 

October 16th | 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 23rd | 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 30th | 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 6th | CRISPR challenges: Therapeutic delivery

Guest Speaker Maroof Adil – Scientist at local biotech startup

 

November 13th | 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 20th | 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 27th | Thanksgiving Break — No Meeting

 

December 4th | 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

 

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

 

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-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

 

Anti-CRISPRs

Paper Disabling Cas9 by an anti-CRISPR DNA mimic
Science Advances | Shin et al. | July 12, 2017
Additional Readings

 

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

 

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
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

 

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

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.