Pubfacts - Scientific Publication Data
  • Categories
  • |
  • Journals
  • |
  • Authors
  • Login
  • Categories
  • Journals

Search Our Scientific Publications & Authors

Publications
  • Publications
  • Authors
find publications by category +
Translate page:

Optimization of AsCas12a for combinatorial genetic screens in human cells.

Authors:
Peter C DeWeirdt Kendall R Sanson Annabel K Sangree Mudra Hegde Ruth E Hanna Marissa N Feeley Audrey L Griffith Teng Teng Samantha M Borys Christine Strand J Keith Joung Benjamin P Kleinstiver Xuewen Pan Alan Huang John G Doench

Nat Biotechnol 2021 01 13;39(1):94-104. Epub 2020 Jul 13.

Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Cas12a RNA-guided endonucleases are promising tools for multiplexed genetic perturbations because they can process multiple guide RNAs expressed as a single transcript, and subsequently cleave target DNA. However, their widespread adoption has lagged behind Cas9-based strategies due to low activity and the lack of a well-validated pooled screening toolkit. In the present study, we describe the optimization of enhanced Cas12a from Acidaminococcus (enAsCas12a) for pooled, combinatorial genetic screens in human cells. By assaying the activity of thousands of guides, we refine on-target design rules and develop a comprehensive set of off-target rules to predict and exclude promiscuous guides. We also identify 38 direct repeat variants that can substitute for the wild-type sequence. We validate our optimized AsCas12a toolkit by screening for synthetic lethalities in OVCAR8 and A375 cancer cells, discovering an interaction between MARCH5 and WSB2. Finally, we show that enAsCas12a delivers similar performance to Cas9 in genome-wide dropout screens but at greatly reduced library size, which will facilitate screens in challenging models.

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41587-020-0600-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854777PMC
January 2021

Publication Analysis

Top Keywords

screens human
8
human cells
8
combinatorial genetic
8
genetic screens
8
screening toolkit
4
optimization enhanced
4
promiscuous guides
4
pooled screening
4
toolkit screening
4
exclude promiscuous
4
cancer cells
4
describe optimization
4
enascas12a delivers
4
well-validated pooled
4
toolkit study
4
study describe
4
delivers performance
4
performance cas9
4
strategies low
4
cas9-based strategies
4

Keyword Occurance

Similar Publications

Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach.

Authors:
Oriana Genolet Anna A Monaco Ilona Dunkel Michael Boettcher Edda G Schulz

Genome Biol 2021 Apr 16;22(1):110. Epub 2021 Apr 16.

Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.

Background: X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signaling pathway, and delaying differentiation.

Results: To identify the genetic basis of these sex differences, we use a two-step CRISPR screening approach to comprehensively identify X-linked genes that cause the female pluripotency phenotype in murine embryonic stem cells. Read More

View Article and Full-Text PDF
April 2021
Similar Publications

Intestinal immunoregulation: lessons from human mendelian diseases.

Authors:
Fabienne Charbit-Henrion Marianna Parlato Georgia Malamut Frank Ruemmele Nadine Cerf-Bensussan

Mucosal Immunol 2021 Apr 15. Epub 2021 Apr 15.

Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France.

The mechanisms that maintain intestinal homeostasis despite constant exposure of the gut surface to multiple environmental antigens and to billions of microbes have been scrutinized over the past 20 years with the goals to gain basic knowledge, but also to elucidate the pathogenesis of inflammatory bowel diseases (IBD) and to identify therapeutic targets for these severe diseases. Considerable insight has been obtained from studies based on gene inactivation in mice as well as from genome wide screens for genetic variants predisposing to human IBD. These studies are, however, not sufficient to delineate which pathways play key nonredundant role in the human intestinal barrier and to hierarchize their respective contribution. Read More

View Article and Full-Text PDF
April 2021
Similar Publications

Flexible wearable sensors - an update in view of touch-sensing.

Authors:
Chi Cuong Vu Sang Jin Kim Jooyong Kim

Sci Technol Adv Mater 2021 Mar 31;22(1):26-36. Epub 2021 Mar 31.

Department of Organic Materials and Fibers Engineering, Soongsil University, Seoul, Republic of Korea.

Nowadays, much of user interface is based on touch and the touch sensors have been common for displays, Internet of things (IoT) projects, or robotics. They can be found in lamps, touch screens of smartphones, or other wide arrays of applications as well. However, the conventional touch sensors, fabricated from rigid materials, are bulky, inflexible, hard, and hard-to-wear devices. Read More

View Article and Full-Text PDF
March 2021
Similar Publications

Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition.

Authors:
Daichi Inoue Jacob T Polaski Justin Taylor Pau Castel Sisi Chen Susumu Kobayashi Simon J Hogg Yasutaka Hayashi Jose Mario Bello Pineda Ettaib El Marabti Caroline Erickson Katherine Knorr Miki Fukumoto Hiromi Yamazaki Atsushi Tanaka Chie Fukui Sydney X Lu Benjamin H Durham Bo Liu Eric Wang Sanjoy Mehta Daniel Zakheim Ralph Garippa Alex Penson Guo-Liang Chew Frank McCormick Robert K Bradley Omar Abdel-Wahab

Nat Genet 2021 Apr 12. Epub 2021 Apr 12.

Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA.

Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles of the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections among minor introns, hematopoiesis and cancers are unclear. Read More

View Article and Full-Text PDF
April 2021
Similar Publications

Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate.

Authors:
Ryan J Weiss Philipp N Spahn Austin W T Chiang Qing Liu Jing Li Kristina M Hamill Sandra Rother Thomas M Clausen Marten A Hoeksema Bryce M Timm Kamil Godula Christopher K Glass Yitzhak Tor Philip L S M Gordts Nathan E Lewis Jeffrey D Esko

Nat Chem Biol 2021 Apr 12. Epub 2021 Apr 12.

Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Read More

View Article and Full-Text PDF
April 2021
Similar Publications
© 2021 PubFacts.
  • About PubFacts
  • Privacy Policy
  • Sitemap