High-throughput determination of RNA structure by proximity ligation

Details

• Alternative Title:
  Nat Biotechnol
• Personal Author:
  Ramani, Vijay ; Qiu, Ruolan ; Shendure, Jay
• Description:
  We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.
• Subjects:
  Article Base Sequence Computer Simulation High-Throughput Nucleotide Sequencing Models, Chemical Models, Genetic Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Real-Time Polymerase Chain Reaction RNA Sequence Alignment Sequence Analysis, RNA

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• Source:
  Nat Biotechnol. 33(9):980-984.
• Pubmed ID:
  26237516
• Pubmed Central ID:
  PMC4564351
• Document Type:
  Journal Article
• Funding:
  DP1 HG007811/HG/NHGRI NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; 1DP1HG007811/DP/NCCDPHP CDC HHS/United States ; 5T32HG000035/HG/NHGRI NIH HHS/United States
• Volume:
  33
• Issue:
  9
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:df1370da1ed40d7bb1f7cd7282be31baf5ec36d6f72ac62a2225f2905a01a7b5
• Download URL:
  https://stacks.cdc.gov/view/cdc/36190/cdc_36190_DS1.pdf
• File Type:
  [PDF - 1.39 MB ]