title: In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.
abstract: RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.
authors.affiliation: 1] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [4].
authors.forename: Yiliang
authors.initials: Y
authors.lastname: Ding
authors.affiliation: 1] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA [4].
authors.forename: Yin
authors.initials: Y
authors.lastname: Tang
authors.affiliation: 1] Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3].
authors.forename: Chun Kit
authors.initials: CK
authors.lastname: Kwok
authors.affiliation: 1] Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Statistics, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 1] Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Plant Biology Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Philip C
authors.initials: PC
authors.lastname: Bevilacqua
authors.affiliation: 1] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA [4] Plant Biology Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Assmann
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D018387:Codon, Initiator / Q000235:genetics; D019295:Computational Biology; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D026723:Polyadenylation / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000032:analysis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012337:RNA, Ribosomal, 18S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D013329:Structure-Activity Relationship
chemical_list: D018387:Codon, Initiator; D022821:RNA Splice Sites; D012333:RNA, Messenger; D018749:RNA, Plant; D012337:RNA, Ribosomal, 18S; D038621:Regulatory Sequences, Ribonucleic Acid