The Lin28 cold-shock domain remodels pre-let-7 microRNA

Nucleic Acids Res. 2012 Aug;40(15):7492-506. doi: 10.1093/nar/gks355. Epub 2012 May 8.

Abstract

The RNA-binding protein Lin28 regulates the processing of a developmentally important group of microRNAs, the let-7 family. Lin28 blocks the biogenesis of let-7 in embryonic stem cells and thereby prevents differentiation. It was shown that both RNA-binding domains (RBDs) of this protein, the cold-shock domain (CSD) and the zinc-knuckle domain (ZKD) are indispensable for pri- or pre-let-7 binding and blocking its maturation. Here, we systematically examined the nucleic acid-binding preferences of the Lin28 RBDs and determined the crystal structure of the Lin28 CSD in the absence and presence of nucleic acids. Both RNA-binding domains bind to single-stranded nucleic acids with the ZKD mediating specific binding to a conserved GGAG motif and the CSD showing only limited sequence specificity. However, only the isolated Lin28 CSD, but not the ZKD, can bind with a reasonable affinity to pre-let-7 and thus is able to remodel the terminal loop of pre-let-7 including the Dicer cleavage site. Further mutagenesis studies reveal that the Lin28 CSD induces a conformational change in the terminal loop of pre-let-7 and thereby facilitates a subsequent specific binding of the Lin28 ZKD to the conserved GGAG motif.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Humans
  • MicroRNAs / chemistry*
  • MicroRNAs / metabolism
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleotides / metabolism
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA / chemistry
  • RNA / metabolism
  • RNA Precursors / chemistry*
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Xenopus

Substances

  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • LIN28B protein, human
  • MicroRNAs
  • Nucleotides
  • RNA Precursors
  • RNA-Binding Proteins
  • let-7 microRNA, Xenopus
  • RNA