Universität zu Köln

Boileau, Etienne, Altmueller, Janine, Naarmann-de Vries, Isabel S. and Dieterich, Christoph (2021). A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover. Brief. Bioinform., 22 (6). OXFORD: OXFORD UNIV PRESS. ISSN 1477-4054

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Abstract

Metabolic labeling of newly transcribed RNAs coupled with RNA-seq is being increasingly used for genome-wide analysis of RNA dynamics. Methods including standard biochemical enrichment and recent nucleotide conversion protocols each require special experimental and computational treatment. Despite their immediate relevance, these technologies have not yet been assessed and benchmarked, and no data are currently available to advance reproducible research and the development of better inference tools. Here, we present a systematic evaluation and comparison of four RNA labeling protocols: 4sU-tagging biochemical enrichment, including spike-in RNA controls, SLAM-seq, TimeLapse-seq and TUC-seq. All protocols are evaluated based on practical considerations, conversion efficiency and wet lab requirements to handle hazardous substances. We also compute decay rate estimates and confidence intervals for each protocol using two alternative statistical frameworks, pulseR and GRAND-SLAM, for over 11 600 human genes and evaluate the underlying computational workflows for their robustness and ease of use. Overall, we demonstrate a high inter-method reliability across eight use case scenarios. Our results and data will facilitate reproducible research and serve as a resource contributing to a fuller understanding of RNA biology.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Boileau, Etienne UNSPECIFIED UNSPECIFIED UNSPECIFIED Altmueller, Janine UNSPECIFIED UNSPECIFIED UNSPECIFIED Naarmann-de Vries, Isabel S. UNSPECIFIED UNSPECIFIED UNSPECIFIED Dieterich, Christoph UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-593378
DOI:	10.1093/bib/bbab219
Journal or Publication Title:	Brief. Bioinform.
Volume:	22
Number:	6
Date:	2021
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1477-4054
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MICROARRAY ANALYSIS; READ ALIGNMENT; DEGRADATION; INITIATION; EFFICIENT; MAPS; KEY Multiple languages Biochemical Research Methods; Mathematical & Computational Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/59337