title: Determination of in vivo RNA structure in low-abundance transcripts.
abstract: RNA structure plays important roles in diverse biological processes. However, the structures of all but the few most abundant RNAs are presently unknown in vivo. Here we introduce DMS/SHAPE-LMPCR to query the in vivo structures of low-abundance transcripts. DMS/SHAPE-LMPCR achieves attomole sensitivity, a 100,000-fold improvement over conventional methods. We probe the structure of low-abundance U12 small nuclear RNA (snRNA) in Arabidopsis thaliana and provide in vivo evidence supporting our derived phylogenetic structure. Interestingly, in contrast to mammalian U12 snRNAs, the loop of the SLIIb in U12 snRNA is variable among plant species, and DMS/SHAPE-LMPCR determines it to be unstructured. We reveal the effects of proteins on 25S rRNA, 5.8S rRNA and U12 snRNA structure, illustrating the critical importance of mapping RNA structure in vivo. Our universally applicable method opens the door to identifying and exploring the specific structure-function relationships of the multitude of low-abundance RNAs that prevail in living cells.
authors: 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: Chun Kit
authors: CK
authors: Kwok
authors: 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] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [4].
authors: Yiliang
authors: Y
authors: Ding
authors: 1] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors: Yin
authors: Y
authors: Tang
authors: 1] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of 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: Sarah M
authors: SM
authors: Assmann
authors: 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: Philip C
authors: PC
authors: Bevilacqua
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005821:Genetic Techniques; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry; D012340:RNA, Ribosomal, 5.8S / Q000737:chemistry; D012342:RNA, Small Nuclear / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D012340:RNA, Ribosomal, 5.8S; D012342:RNA, Small Nuclear; C096986:U12 small nuclear RNA; C065039:RNA, ribosomal, 25S