Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

BMC Genomics
Chao ZengMichiaki Hamada

Abstract

Although the number of discovered long non-coding RNAs (lncRNAs) has increased dramatically, their biological roles have not been established. Many recent studies have used ribosome profiling data to assess the protein-coding capacity of lncRNAs. However, very little work has been done to identify ribosome-associated lncRNAs, here defined as lncRNAs interacting with ribosomes related to protein synthesis as well as other unclear biological functions. On average, 39.17% of expressed lncRNAs were observed to interact with ribosomes in human and 48.16% in mouse. We developed the ribosomal association index (RAI), which quantifies the evidence for ribosomal associability of lncRNAs over various tissues and cell types, to catalog 691 and 409 lncRNAs that are robustly associated with ribosomes in human and mouse, respectively. Moreover, we identified 78 and 42 lncRNAs with a high probability of coding peptides in human and mouse, respectively. Compared with ribosome-free lncRNAs, ribosome-associated lncRNAs were observed to be more likely to be located in the cytoplasm and more sensitive to nonsense-mediated decay. Our results suggest that RAI can be used as an integrative and evidence-based tool for distinguishing between ribosome-a...Continue Reading

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Citations

May 29, 2020·Proceedings of the National Academy of Sciences of the United States of America·Yazhou ChenSaskia A Hogenhout
Oct 1, 2019·RNA Biology·Jade HebrasJérôme Cavaillé
Jan 2, 2019·BMC Genomics·Chao Zeng, Michiaki Hamada
Jan 13, 2019·Nature Communications·Caihuan TianYuling Jiao
Mar 30, 2020·The Journal of Infectious Diseases·Antón Vila-SanjurjoMariana Leguia
Nov 5, 2019·Frontiers in Oncology·Alina-Andreea ZimtaIoana Berindan-Neagoe
Oct 11, 2020·Cancers·Alexander V GopanenkoVyacheslav S Kosorukov
Feb 18, 2021·ELife·Luca MinatiMassimiliano Clamer
Mar 12, 2021·Wiley Interdisciplinary Reviews. RNA·J J David HoPhilip A Marsden
Jun 2, 2021·NPJ Breast Cancer·Zhenbo TuAntoine E Karnoub
Sep 28, 2021·Nucleic Acids Research·Igor FesenkoEugene V Koonin

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Methods Mentioned

BETA
Ribo-seq
RNA-seq

Software Mentioned

phyloP
custom Python scripts
RRS
Bowtie2
Framescore
RAI
FLOSS
Cutadapt
spec
Bowtie

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