Special Topics: Genome Engineering | BIOL-UA 920

Syllabus & reading list


NYU Biology: Taught in-person and over Zoom Spring 2022 (4 units)

Course description

A discussion-based course on principles underlying current and future genetic engineering approaches, ranging from unicellular organisms to whole animals. Focuses on development and invention of technologies for engineering biological systems at the genomic level, including high-throughput functional genomic screens, gene editing therapies and ethical and social implications of new technologies.


Molecular & Cell Biology 2 (BIOL-UA 22)

Course organization

Lectures are organized into the following modules:
  1. Modern genome engineering
  2. Building on CRISPR
  3. Therapy and delivery

Class activities & readings

Class 1: Introductions & class overview.

Introduction to genome engineering. How to read a paper.


Module 1: Modern genome engineering


Class 2: Scissors that can cut DNA

Barrangou et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science.

Garneau et al. (2010). The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature.


Class 3: Breakthroughs in unexpected places — Yogurt to human editing

Jinek et al. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science.

Cong*, Ran* et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science.


Class 4: Programmability

Shalem*, Sanjana* et al. (2013). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science.

Behan*, Iorio*, Picco* et al. (2019). Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature.


Class 5: COVID-19 diagnostics & medicines

Daniloski*, Jordan* et al. (2020). Identification of required host factors for SARS-CoV-2 infection in human cells. Cell.

Joung et al. (2020). Detection of SARS-CoV-2 with SHERLOCK one-pot testing. New England Journal of Medicine.



Module 2: Building on CRISPR

Class 6: Building on CRISPR 1: Effectors

Tycko et al. (2020). High-throughput discovery and characterization of human transcriptional effectors. Cell.

Nuñez et al. (2021). Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell.


Class 7: Midterm: Genetic Disease Day

In-class presentations and write-up due.

Podcast: Hope Lies in Dreams – Ch. 9, Nature Biotechnology


Spring Break - no class


Class 8: Building on CRISPR 2: Base editing

Komor et al. (2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature.

Musunuru et al. (2021). In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates. Nature.


Class 9: Building on CRISPR 3: Prime editing

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

Durrant*, Fanton*, Tycko* et al. (2021). Large-scale discovery of recombinases for integrating DNA into the human genome. bioRxiv.



Module 3: Therapy and delivery

Class 10: Gene therapy 1.0

Beutler (2001). The Cline affair. Molecular Cell.

Blaese et al. (1995). T lymphocyte-directed gene therapy for ADAneg SCID: initial trial results after 4 years. Science.

Wilson (2009). Lessons learned from the gene therapy trial for ornithine transcarbamylase deficiency. Molecular Genetics and Metabolism.

Zimmer (2013). The fall and rise of gene therapy. WIRED.


Class 11: Delivery 1: AAV

Nelson et al. (2019). Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nature Medicine.

Chan et al. (2017). Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nature Neuroscience.


Class 12: Gene therapy 2.0

Canver*, Smith*, Sher*, Pinello*, Sanjana* et al. (2015). BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature.

Frangoul et al. (2021). CRISPR-Cas9 gene editing for sickle cell disease and β-thalassemia. New England Journal of Medicine.


Class 13: Delivery 2: LNPs & beyond

Segel et al. (2021). Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery. Science.

Da Silva Sanchez*, Paunovska* et al. (2020). Treating Cystic Fibrosis with mRNA and CRISPR. Human Gene Therapy.


Class 14: Future genome engineers

Recap & wrap-up. Final presentations and write-up due.


This syllabus is in no way a complete overview of genome engineering or applications of CRISPR (and my apologies to the many many great studies that I could not include) but I hope that making the reading list available will be useful to others designing & teaching similar seminar-style classes. It has been fun to put this together and teach this material. Please feel free to remix and reuse! ♻ 👍