Nuclear mRNA decay: regulatory networks that control gene expression

Rambout, Xavier; Maquat, Lynne E.

doi:10.1038/s41576-024-00712-2

Cited by 2 publications

(1 citation statement)

References 159 publications

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“…Using NMD as a model, CiBER-seq highlighted the known NMD factors and confirmed their dependence on ribosome elongation. This platform now opens opportunities to directly assess RNA-level phenotypes with CRISPR screens and paves the way to examine post-transcriptional processes that do not require translation, such as nuclear RNA decay or noncoding mRNA metabolism [37][38][39][40] .…”

Section: Discussionmentioning

confidence: 99%

Precise measurement of molecular phenotypes with barcode-based CRISPRi systems

Lobel,

Ingolia

2024

Preprint

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SummaryGenome-wide CRISPR-Cas9 screens have untangled regulatory networks and revealed the genetic underpinnings of diverse biological processes. Their success relies on experimental designs that interrogate specific molecular phenotypes and distinguish key regulators from background effects. Here, we realize these goals with a generalizable platform for CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) that dramatically improves the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely-matched control promoters, integrated together into the genome at single copy. To test our ability to capture post-transcriptional and post-translational regulation through sequencing, we screened for genes that affected nonsense-mediated mRNA decay and Doa10-mediated cytosolic protein decay. Our optimized CiBER-seq screens accurately capture the known components of well-studied RNA and protein quality control pathways with minimal background. These results demonstrate the precision and versatility of CiBER-seq for dissecting the genetic networks controlling cellular behaviors.

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Section: Discussionmentioning

confidence: 99%