Toward a next-generation atlas of RNA secondary structure.
RNA structure plays a crucial role in gene maturation, regulation and function. Determining the form and frequency of RNA folds is essential for a better understanding of how RNA exerts its functions. Low-throughput studies have focused on RNA primary sequences and expression levels, but with an emphasis on relatively small numbers of transcripts. However, with the recent advent of high-throughput technologies, it is realistic to begin analyzing RNA secondary structures on a genome-wide scale. Here, we review genome-wide RNA secondary structure profiles as well as advances in computational structure predictions. We further discuss the novel characteristics of RNA secondary structure across messenger RNAs. Probing RNA secondary structure by high-throughput sequencing will enable us to build atlases of RNA secondary structures, an important step in helping us to understand the versatility of RNA functions in diverse cellular processes.
Youhuang
Y
Bai
Xiaozhuan
X
Dai
Andrew
A
Harrison
Caroline
C
Johnston
Ming
M
Chen
D000465:Algorithms; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D044127:Epigenesis, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data; D006801:Humans; D000069550:Machine Learning; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000706:statistics & numerical data; D013269:Stochastic Processes; D013816:Thermodynamics
D012333:RNA, Messenger; D012313:RNA
RNA secondary structure; RNA structure–function relationships; computational prediction; high-throughput sequencing