Histone H3K9 methylation and Heterochromatin Protein 1 do not limit DNA accessibility in living S. pombe cells

Abstract

Chromatin is intrinsically repressive, limiting access to DNA, implying a major regulatory role. Studies with nuclei support this model. However, we have shown previously that genomic DNA is completely accessible in living budding yeast and human cells, except for centromeric chromatin. The fission yeast, Schizosaccharomyces pombe, provides a tractable model for heterochromatin. As in mammalian cells, S. pombe heterochromatin is marked by histone H3K9 di- and tri-methylation (H3K9me2/3), introduced by the Clr4 histone methylase, and heterochromatin protein 1 (HP1/Swi6). Here, we developed a copper-inducible DNA methyltransferase system to measure heterochromatin accessibility in living S. pombe cells. We find that euchromatin and heterochromatin are similarly and generally accessible in vivo, indicating that S. pombe chromatin is globally dynamic. S. pombe centromeres are also fully accessible, unlike budding yeast and human centromeres. In contrast to living cells, S. pombe chromatin is mostly inaccessible in isolated nuclei, primarily due to tight nucleosome spacing with very little linker DNA. Loss of Clr4 or Swi6 has little effect on genome accessibility in live cells or nuclei, suggesting that the S. pombe H3K9me/HP1 system does not repress transcription by preventing access to DNA.