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Article
Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias
Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mut...
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Article
PROBER identifies proteins associated with programmable sequence-specific DNA in living cells
DNA–protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) in the identification and quant...
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Article
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes
A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into ‘co-essential’ p...
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Article
Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and variable sgRNA activity. Applying CERES to new genome-s...
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Article
Detecting DNA double-stranded breaks in mammalian genomes by linear amplification–mediated high-throughput genome-wide translocation sequencing
This protocol describes a genome-wide method to detect and to quantify DNA double-stranded breaks (DSBs). The approach is applicable to endogenous DSBs, but it can also be used to characterize the activity of ...
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Article
Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching
High-throughput genome-wide sequencing reveals why class switch recombination in the IgH locus, an essential step in the process of antibody generation, has a directional joining bias towards deletion rather t...
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Article
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
An unbiased genome-wide method reveals on- and off-target DNA cleavage by TALEN and Cas9 nucleases by detecting chromosome translocation events.
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Article
Microbial colonization influences early B-lineage development in the gut lamina propria
Primary B-cell development is thought to be restricted to the bone marrow; here it is shown to occur also in intestinal tissues of postnatal mice, that it peaks at the time of weaning and is increased upon col...