RNA structure probing uncovers RNA structure-dependent biological functions

Wang, Xiwen; Liu, Chu-Xiao; Chen, Lingling; Zhang, Qiangfeng Cliff

doi:10.1038/s41589-021-00805-7

Cited by 81 publications

(55 citation statements)

References 100 publications

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“…DMS modifications on RNA are decoded through RT mutation in our optimized DMS-MaPseq method, instead of RT stop in Structure-seq. DMS-MaPseq increases RNA structure information content in sequencing data and reduces false-positive signals from unwanted RNA decay ( Wang et al, 2021 ). However, RT mutation-based DMS-MaPseq method requires a greater sequencing depth to generate accurate RNA structurome ( Zubradt et al, 2017 ; Wang et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Probing in vivo RNA Structure With Optimized DMS-MaPseq in Rice

Jin

Zhang

et al. 2022

Front. Plant Sci.

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RNA transcripts form various secondary and tertiary structures that have a wide range of regulatory functions. Several methods have been developed to profile in vivo RNA secondary structure in prokaryotes and eukaryotes. These methods, such as dimethyl sulfate (DMS) mutational profiling with high-throughput sequencing (DMS-MaPseq), couple small chemical-mediated RNA modifications with next-generation sequencing. DMS-MaPseq, a powerful method for genome-wide and target-specific RNA secondary structure profiling, has been applied in yeast, mammals, Drosophila, and Arabidopsis thaliana, but not in crops. Here, we used DMS-MaPseq to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). The DMS treatment conditions were optimized for rice leaf and root tissues. To increase the sequencing depth and coverage of low-abundance transcripts in genome-wide DMS-MaPseq, we used streptavidin-biotin depletion to reduce the abundance of highly expressed chloroplast transcripts during library construction. The resulting target-specific and genome-wide rice DMS-MaPseq data were of high quality and reproducibility. Furthermore, we used DMS-MaPseq to profile the in vivo RNA secondary structure of an OsmiR399 target region located at 5′UTR of OsPHO2, which participates in rice phosphate homeostasis. An unfolded RNA structure downstream of miRNA target site was observed in predicted in vivo RNA secondary structure, reminiscence of the TAM (Target Adjacent nucleotide Motif) involved in mRNA structure-mediated regulation in miRNA cleavage. Our study optimized DMS-MaPseq for probing in vivo RNA secondary structure in rice, facilitating the study of RNA structure-mediated regulations in crops.

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Section: Discussionmentioning

confidence: 99%

Probing in vivo RNA Structure With Optimized DMS-MaPseq in Rice

Jin

Zhang

et al. 2022

Front. Plant Sci.

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“…As with proteins, RNA molecules form complex higher-order structures that are indispensable regulators of many biological processes [ 61 ]. For instance, ribosomal RNA depends on scaffolding RNA as a key assembly platform to fold into well-defined secondary and tertiary structures for regulating protein translation [ 62 ].…”

Section: Pas Rna Structure In Gene Regulationmentioning

confidence: 99%

Promoter antisense RNAs: beyond transcription by-products of active promoters

Yang

2022

RNA Biology

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Omics-based technologies, which have developed rapidly over the last few decades, have generated increasing evidence demonstrating pervasive divergent transcription from RNA polymerase II (Pol II) promoters of eukaryotic genome, and indeed have raised considerable discussion as to their potential physiopathological function. Unlike many other long non-coding RNAs (lncRNAs), promoter antisense RNAs (PAS RNAs) were initially considered to be merely passive transcription by-products of active promoters. However, recent studies have begun to reveal their critical importance in a broad spectrum of biological processes. In this Review, I summarize recent technological advances that enable accurate detection of PAS RNA and discuss the mechanisms of PAS RNA biogenesis emphasizing the functional importance of its structure enabling the diverse functions of PAS RNA in transcription and chromatin regulation.

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“…The millions of reads generated by deep-sequencing make the SHAPE-Seq a more sensitive technique than hSHAPE. Furthermore, this method can be adapted to get transcriptome-wide structural information or by using sequence-specific reverse transcription primers to focus on the structure of an RNA of interest [12,139]. However, particular attention must be paid to the construction of the library because biases can be introduced at this level, especially during the ligation of adapters and/or during the PCR amplification step (Figure 3).…”

Section: A New Era For Enzymatic and Chemical Probing 41 The Deep-sequencing Leapsmentioning

confidence: 99%

“…Finally, we will also discuss how hSHAPE paved the way for the development of sophisticated RNA structural techniques that provide more detailed structural information. However, the crosslinking-based structural methods, which have also been developed recently and are complementary to the RNA probing methods, are not reviewed here (for recent reviews of these techniques, see [10][11][12]).…”

Section: Introductionmentioning

confidence: 99%

Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

Gilmer

Quignon

Jousset

et al. 2021

Viruses

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RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.

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RNA structure probing uncovers RNA structure-dependent biological functions

Cited by 81 publications

References 100 publications

Probing in vivo RNA Structure With Optimized DMS-MaPseq in Rice

Probing in vivo RNA Structure With Optimized DMS-MaPseq in Rice

Promoter antisense RNAs: beyond transcription by-products of active promoters

Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

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