We are analyzing https://link.springer.com/article/10.1186/s13059-014-0491-2.

Title:
Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome | Genome Biology
Description:
Background The understanding of RNA structure is a key feature toward the comprehension of RNA functions and mechanisms of action. In particular, non-coding RNAs are thought to exert their functions by specific secondary structures, but an efficient annotation on a large scale of these structures is still missing. Results By using a novel high-throughput method, named chemical inference of RNA structures, CIRS-seq, that uses dimethyl sulfate, and N-cyclohexyl- N
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Keywords {🔍}

rna, pubmed, article, google, scholar, structure, structures, cirsseq, reactivity, secondary, analysis, data, central, rnas, structural, figure, average, folding, regions, file, mouse, transcripts, biol, coding, additional, nucleotides, cell, noncoding, lina, binding, human, chemical, mrnas, region, protein, cells, methods, utr, method, native, ncrnas, probing, dms, mol, conformation, vivo, test, authors, higher, escs,

Topics {✒️}

cirs-seq-guided folding outperformed cirs-seq-derived data compared superimposed dms/shape-reactive positions perform transcriptome-wide probing cirs-seq methodology represents cirs-seq constrained structures cirs-seq data correlated cirs-seq data improves de novo prediction full size image cirs-seq-derived structures superimposed dms/cmct-reactive positions cirs-seq data revealed superimposed shape-reactive positions vivo genome-wide profiling obtain genome-wide information integrates single-nucleotide variants internal loop il2/il2′ n-cyclohexyl-n'-beta rna-seq library preparation article download pdf carbodiimide metho-p-toluenesulfonate canonical rna-seq data g-rich dna flap protein-facilitated rna folding genome-wide profiling embryonic stem cells stem-loop structure located single-stranded rna residues mouse protein-coding transcripts secondary structure inferred related subjects u5 tri-snrnp particles yeast spliceosomal u4/u6 low-abundance u12 snrna probe protein-coding rnas protein-coding rnas revealed sample secondary structures modification-induced reverse transcription low-abundance u12 snrnas cirs-seq data genome-wide measurement genome-wide probing full access rna-seq data recently published variant pomeranz krummel da teulade-fichou m shape data files dms/cmct treatment induced

Schema {🗺️}

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         headline:Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
         description:The understanding of RNA structure is a key feature toward the comprehension of RNA functions and mechanisms of action. In particular, non-coding RNAs are thought to exert their functions by specific secondary structures, but an efficient annotation on a large scale of these structures is still missing. By using a novel high-throughput method, named chemical inference of RNA structures, CIRS-seq, that uses dimethyl sulfate, and N-cyclohexyl- N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate to modify RNA residues in single-stranded conformation within native deproteinized RNA secondary structures, we investigate the structural features of mouse embryonic stem cell transcripts. Our analysis reveals an unexpected higher structuring of the 5′ and 3′ untranslated regions compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observe that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we find that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation. This work defines for the first time the complete RNA structurome of mouse embryonic stem cells, revealing an extremely distinct RNA structural landscape. These results demonstrate that CIRS-seq constitutes an important tool for the identification of native deproteinized RNA structures.
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            Kozak Sequence
            Normalize Read Count
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            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
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         Mouse Embryonic Stem Cell
         Mouse ESCs
         Kozak Sequence
         Normalize Read Count
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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