The Mi-2 Homolog Mit1 Actively Positions Nucleosomes within Heterochromatin To Suppress Transcription

Abstract

Mit1 is the putative chromatin remodeling subunit of the fission yeast Snf2/histone deacetylase (HDAC) repressor complex (SHREC) and is known to repress transcription at regions of heterochromatin. However, how Mit1 modifies chromatin to silence transcription is largely unknown. Here we report that Mit1 mobilizes histone octamers in vitro and requires ATP hydrolysis and conserved chromatin tethering domains, including a previously unrecognized chromodomain, to remodel nucleosomes and silence transcription. Loss of Mit1 remodeling activity results in nucleosome depletion at specific DNA sequences that display low intrinsic affinity for the histone octamer, but its contribution to antagonizing RNA polymerase II (Pol II) access and transcription is not restricted to these sites. Genetic epistasis analyses demonstrate that SHREC subunits and the transcription-coupled Set2 histone methyltransferase, which is involved in suppression of cryptic transcription at actively transcribed regions, cooperate to silence heterochromatic transcripts. In addition, we have demonstrated that Mit1's remodeling activity contributes to SHREC function independently of Clr3's histone deacetylase activity on histone H3 K14. We propose that Mit1 is a chromatin remodeling factor that cooperates with the Clr3 histone deacetylase of SHREC and other chromatin modifiers to stabilize heterochromatin structure and to prevent access to the transcriptional machinery.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.01609-13.

ACKNOWLEDGMENTS

We thank M. Bedford, K. Gould, S. Forsburg, G. Thon, J. Nakayama, S. Jia, and S. Francesconi for plasmids and strains and Hartwell center staff (St. Jude Children's Research Hospital) for peptide synthesis, mass spectrometry, and tiling array services. We thank Marc Buhler for sharing updated genomic mapping data for the array analyses and Jon Obenauer for implementing the revisions. We thank Thomas Schalch, Paul Brindle, Nick Laribee, and Ben Alper for useful discussions.

This work was funded by NIA fellowship NRSA F31-AG038153 (to K.M.C.), NIH R01 GM084045 (to J.F.P.), NIH R01 GM070864 (to B.B.), Cancer Center support grant CCSG 2 P30 CA21765, and the American Lebanese Syrian Associated Charities of St. Jude Children's Research Hospital.