Class 2 CRISPR/Cas: an expanding biotechnology toolbox for and beyond genome editing

Y Tang, Y Fu - Cell & bioscience, 2018 - Springer
Artificial nuclease-dependent DNA cleavage systems (zinc-finger nuclease, ZFN;
transcription activator like effectors, TALENs) and exogenous nucleic acid defense systems …

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

KR Sanson, RE Hanna, M Hegde, KF Donovan… - Nature …, 2018 - nature.com
The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference
(CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene …

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects

JM Dempster, I Boyle, F Vazquez, DE Root, JS Boehm… - Genome biology, 2021 - Springer
CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a
number of biases and artifacts that can confound the results. Here, we introduce Chronos …

Integrated cross-study datasets of genetic dependencies in cancer

C Pacini, JM Dempster, I Boyle, E Gonçalves… - Nature …, 2021 - nature.com
CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across
large panels of cell lines to identify new therapeutic targets for precision cancer therapy …

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

J Joung, S Konermann, JS Gootenberg… - Nature protocols, 2017 - nature.com
Forward genetic screens are powerful tools for the unbiased discovery and functional
characterization of specific genetic elements associated with a phenotype of interest …

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

MA Horlbeck, LA Gilbert, JE Villalta, B Adamson… - elife, 2016 - elifesciences.org
We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA. Here,
we build on this observation with a comprehensive algorithm that incorporates chromatin …

Challenges and strategies in ascribing functions to long noncoding RNAs

Y Zhao, H Teng, F Yao, S Yap, Y Sun, L Ma - Cancers, 2020 - mdpi.com
Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological
processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs …

TP53-dependent toxicity of CRISPR/Cas9 cuts is differential across genomic loci and can confound genetic screening

MM Álvarez, J Biayna, F Supek - Nature communications, 2022 - nature.com
CRISPR/Cas9 gene editing can inactivate genes in a precise manner. This process involves
DNA double-strand breaks (DSB), which may incur a loss of cell fitness. We hypothesize that …

Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS

X Shi, B Reinstadler, H Shah, TL To, K Byrne… - Nature …, 2022 - nature.com
The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors
across mitochondrial membranes. The family is highly redundant and their transport …

BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors

X Wang, S Wang, EC Troisi, TP Howard… - Nature …, 2019 - nature.com
Abstract Bromodomain-containing protein 9 (BRD9) is a recently identified subunit of
SWI/SNF (BAF) chromatin remodeling complexes, yet its function is poorly understood. Here …