Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination

Nucleic Acids Res. 2014 Oct 29;42(19):11952-64. doi: 10.1093/nar/gku874. Epub 2014 Sep 30.


Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Survival
  • Chromatin Assembly Factor-1 / metabolism
  • Chromatin Assembly Factor-1 / physiology*
  • DNA, Protozoan / metabolism*
  • Epigenesis, Genetic*
  • Histones / metabolism
  • Macronucleus / metabolism
  • Paramecium tetraurelia / genetics
  • Paramecium tetraurelia / growth & development
  • Paramecium tetraurelia / metabolism
  • Protozoan Proteins / metabolism
  • Protozoan Proteins / physiology*
  • RNA, Protozoan / metabolism*
  • RNA, Small Untranslated / metabolism*
  • Reproduction


  • Chromatin Assembly Factor-1
  • DNA, Protozoan
  • Histones
  • Protozoan Proteins
  • RNA, Protozoan
  • RNA, Small Untranslated

Associated data

  • PDB/ERR372001
  • PDB/ERR372239
  • PDB/ERR372240
  • PDB/ERR372241
  • PDB/ERR372242
  • PDB/ERR372243
  • PDB/ERR372244
  • PDB/ERR372245
  • PDB/ERR372246
  • PDB/ERR372247
  • PDB/ERR372248
  • PDB/ERR372249
  • PDB/ERR372250
  • PDB/PRJEB4978
  • PDB/SRR907874
  • PDB/SRR907875
  • PDB/XM001427355
  • PDB/XM001457471
  • PDB/XM001461420