An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe

RNA Biol. 2019 Jun;16(6):742-753. doi: 10.1080/15476286.2019.1584026. Epub 2019 Mar 19.


In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. In this study, we have used an RNA aptamer that likely binds to the Swi6 hinge with high affinity, as a tool to perturb the natural interactions mediated by this domain. When the hinge is blocked by the aptamer RNA, Swi6 appears to become less restricted to the pericentromeres and is enriched at specific euchromatic loci. This suggests a role for the Swi6 hinge, along with the chromoshadow domain (previously shown) in controlling the spread of heterochromatin in S.pombe. The study also highlights the potential of using a synthetic aptamer RNA as a tool to perturb nucleic acid - protein interaction in vivo with the objective of understanding the functional relevance of such an interaction.

Keywords: Apatmer; SELEX; Swi6; heterochromatin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / metabolism*
  • Chromosomal Proteins, Non-Histone / antagonists & inhibitors*
  • Chromosomal Proteins, Non-Histone / chemistry
  • Chromosomal Proteins, Non-Histone / metabolism
  • Heterochromatin*
  • Nucleotide Motifs
  • Protein Domains
  • Schizosaccharomyces / metabolism
  • Schizosaccharomyces pombe Proteins / antagonists & inhibitors*
  • Schizosaccharomyces pombe Proteins / chemistry
  • Schizosaccharomyces pombe Proteins / metabolism


  • Aptamers, Nucleotide
  • Chromosomal Proteins, Non-Histone
  • Heterochromatin
  • Schizosaccharomyces pombe Proteins
  • Swi6 protein, S pombe

Grant support

This work was supported by grants from the Science and Engineering Research Board, Department of Science and Technology, Govt. of India [SB/YS/LS-149/2013]; and the Department of Biotechnology, Govt. of India [BT/PR12071/BRB/10/1321/2014] to A.S.