On the optimal design of metabolic RNA labeling experiments

PLoS Computational Biology
Alexey UvarovskiiChristoph Dieterich

Abstract

Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the key aspects of experimental design: For example, which protocol should be used (biochemical separation vs. nucleotide conversion) and what is the optimal labeling time? In this work, we provide approximate answers to these questions using the asymptotic theory of optimal design. Specifically, we investigate, how the variance of degradation rate estimates depends on the time and derive the optimal time for any given degradation rate. Subsequently, we show that an increase in sample numbers should be preferred over an increase in sequencing depth. Lastly, we provide some guidance on use cases when laborious biochemical separation outcompetes recent nucleotide conversion based methods (such as SLAMseq) and show, how inefficient conversion influences the precision of estimates. Code and documentation can be found at https://github.com/dieterich-lab/DesignMetabolicRNAlabeling.

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Citations

Mar 17, 2020·Frontiers in Cell and Developmental Biology·Adriano Biasini, Ana Claudia Marques
Dec 22, 2020·Briefings in Bioinformatics·Mattia FurlanMattia Pelizzola
Feb 19, 2020·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Emma DesgrangesDavid Lalaouna

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Methods Mentioned

BETA
RNA-seq
in vitro transcription
electrophoresis
dot blot
RNAseq

Software Mentioned

EnsEMBL
pulseR
QuantSeq
StringTie
STAR
bowtie2
flexbar
SLAMseq
DESeq

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