miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction

Nat Chem Biol. 2015 Feb;11(2):107-14. doi: 10.1038/nchembio.1713. Epub 2014 Dec 22.


Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 immunopurification followed by streptavidin affinity purification of probe-linked RNAs provided selectivity in the capture of targets, which were identified by deep sequencing. miR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. miR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long noncoding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation, levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a 'sponge' for these miRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Biotin / metabolism
  • Cell Culture Techniques
  • Cell Differentiation / genetics*
  • Computational Biology / methods
  • Ficusin / metabolism
  • HeLa Cells
  • Humans
  • Immunoprecipitation
  • MicroRNAs* / genetics
  • MicroRNAs* / metabolism
  • Molecular Sequence Data
  • Muscle Cells / cytology
  • Muscle Cells / metabolism
  • Myoblasts / cytology
  • Myoblasts / metabolism
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / metabolism
  • RNA, Messenger / genetics
  • Real-Time Polymerase Chain Reaction
  • Transcriptome*


  • H19 long non-coding RNA
  • MIRN106 microRNA, human
  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Messenger
  • Biotin
  • Ficusin

Associated data

  • GEO/GSE62681