Four RNA families with functional transient structures

RNA Biology
Jing Yun A Zhu, Irmtraud M Meyer

Abstract

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance mod...Continue Reading

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Citations

Jan 23, 2018·Frontiers in Microbiology·Chun Shen Lim, Chris M Brown
May 12, 2019·Nucleic Acids Research·Shungo KoboriYohei Yokobayashi
Dec 10, 2020·Viruses·Franziska HufskyVolker Thiel
Mar 24, 2021·Wiley Interdisciplinary Reviews. RNA·Elena Rivas

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Methods Mentioned

BETA
electrophoresis
X-ray
in vitro transcription

Software Mentioned

SAM
Mfold
Kinwalker
Infernal
chie
Infernal Taxonomy browser
USEARCH
VARNA
Rfam
Infernal Browser

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