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Luzak, V.* ; Osses, E.* ; Danese, A. ; Odendaal, C.* ; Cosentino, R.O.* ; Stricker, S.H. ; Haanstra, J.R.* ; Erhard, F.* ; Siegel, T.N.*

SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.

Nucleic Acids Res., DOI: 10.1093/nar/gkae1203 (2024)
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Gene expression is a multi-step process that converts DNA-encoded information into proteins, involving RNA transcription, maturation, degradation, and translation. While transcriptional control is a major regulator of protein levels, the role of post-transcriptional processes such as RNA processing and degradation is less well understood due to the challenge of measuring their contributions individually. To address this challenge, we investigated the control of gene expression in Trypanosoma brucei, a unicellular parasite assumed to lack transcriptional control. Instead, mRNA levels in T. brucei are controlled by post-transcriptional processes, which enabled us to disentangle the contribution of both processes to total mRNA levels. In this study, we developed an efficient metabolic RNA labeling approach and combined ultra-short metabolic labeling with transient transcriptome sequencing (TT-seq) to confirm the long-standing assumption that RNA polymerase II transcription is unregulated in T. brucei. In addition, we established thiol (SH)-linked alkylation for metabolic sequencing of RNA (SLAM-seq) to globally quantify RNA processing rates and half-lives. Our data, combined with scRNA-seq data, indicate that RNA processing and stability independently affect total mRNA levels and contribute to the variability seen between individual cells in African trypanosomes.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Genome-wide Analysis; Blood-stream Forms; Messenger-rna; Brucei; Polyadenylation; Life; Identification; Translation; Degradation; Systems
Language english
Publication Year 2024
HGF-reported in Year 2024
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Journal Nucleic Acids Research
Publisher Oxford University Press
Publishing Place Great Clarendon St, Oxford Ox2 6dp, England
Reviewing status Peer reviewed
Institute(s) Institute of Stem Cell Research (ISF)
POF-Topic(s) 30204 - Cell Programming and Repair
Research field(s) Stem Cell and Neuroscience
PSP Element(s) G-500800-001
Grants German Academic Scholarship Foundation
Center for Integrative Protein Science
DOI 10.1093/nar/gkae1203
WOS ID 001377190700001
PubMed ID 39673807
Erfassungsdatum 2024-12-17
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