In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum.

Yanwei Qi,Guixing Zheng,Bingxia Chen,Yuhong Zhang,Jun Huang,Mengxin Zhang,Xinhua Wang,Tao Peng,Jian Li

doi:10.3389/fcimb.2021.673966

Abstract

It is widely accepted that the structure of RNA plays important roles in a number of biological processes, such as polyadenylation, splicing, and catalytic functions. Dynamic changes in RNA structure are able to regulate the gene expression programme and can be used as a highly specific and subtle mechanism for governing cellular processes. However, the nature of most RNA secondary structures in Plasmodium falciparum has not been determined. To investigate the genome-wide RNA secondary structural features at single-nucleotide resolution in P. falciparum, we applied a novel high-throughput method utilizing the chemical modification of RNA structures to characterize these structures. Structural data from parasites are in close agreement with the known 18S ribosomal RNA secondary structures of P. falciparum and can help to predict the in vivo RNA secondary structure of a total of 3,396 transcripts in the ring-stage and trophozoite-stage developmental cycles. By parallel analysis of RNA structures in vivo and in vitro during the Plasmodium parasite ring-stage and trophozoite-stage intraerythrocytic developmental cycles, we identified some key regulatory features. Recent studies have established that the RNA structure is a ubiquitous and fundamental regulator of gene expression. Our study indicate that there is a critical connection between RNA secondary structure and mRNA abundance during the complex biological programme of P. falciparum. This work presents a useful framework and important results, which may facilitate further research investigating the interactions between RNA secondary structure and the complex biological programme in P. falciparum. The RNA secondary structure characterized in this study has potential applications and important implications regarding the identification of RNA structural elements, which are important for parasite infection and elucidating host-parasite interactions and parasites in the environment.

Highlights

RNA, a multitasking biomolecule, plays important roles in many aspects of cellular and physiological processes, such as the regulation of transcription, RNA processing and stability including splicing events, and translation (Wan et al, 2011; Mortimer et al, 2014)
IcSHAPE in vivo libraries were subsequently prepared using RNA from pellets treated with 100 mM NAI-N3 for 15 min, and control pellets not treated with NAI-N3 but with DMSO solution
We investigated whether a correlation is shared between intrinsic mRNA secondary structure propensity around the translation start/stop site and whether the efficiency of protein translation correlates with mRNA abundance

Summary

Introduction

RNA, a multitasking biomolecule, plays important roles in many aspects of cellular and physiological processes, such as the regulation of transcription, RNA processing and stability including splicing events, and translation (Wan et al, 2011; Mortimer et al, 2014). As the carrier of genetic information for translation into proteins, RNA molecules can fold into a wide array of complicated and exquisite secondary and tertiary structures via complex patterns of intramolecular base pairing formed by Watson-Crick-base pairing (Vandivier et al, 2016) These complex secondary and tertiary structures of RNAs play important roles in regulating such processes as catalytic and ligand sensing, the regulation of mRNA maturation, translation and turnover, alternative polyadenylation and alternative splicing (Ding et al, 2014). Due to the multiple functions of RNA structural elements changed by base pairing and folding, they can be considered another layer of the genetic code that is only beginning to be understood (Bevilacqua et al, 2016) Characterizing these complex global RNA structures, especially in vivo, is essential to achieve a mechanistic understanding of the function and regulation of RNA transcripts. These studies may help to identify additional temperature sensors (RNA thermometers), enzymes (ribozymes), ligandbinding sensors (riboswitches) or other environmentally responsive structural elements in various organisms, not in Plasmodium parasites

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Results

Conclusion