Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence

Eriko Oya,Ronit Weisman,Mickaël Durand-Dubief,Benoit Arcangioli,Karl Ekwall,Jun-Ichi Nakayama,Catherine Schurra,Adiel Cohen,Vladimir Maksimov

doi:10.1186/s13072-019-0292-7

Abstract

BackgroundCellular quiescence is a reversible differentiation state during which cells modify their gene expression program to inhibit metabolic functions and adapt to a new cellular environment. The epigenetic changes accompanying these alterations are not well understood. We used fission yeast cells as a model to study the regulation of quiescence. When these cells are starved for nitrogen, the cell cycle is arrested in G1, and the cells enter quiescence (G0). A gene regulatory program is initiated, including downregulation of thousands of genes—for example, those related to cell proliferation—and upregulation of specific genes—for example, autophagy genes—needed to adapt to the physiological challenge. These changes in gene expression are accompanied by a marked alteration of nuclear organization and chromatin structure.ResultsHere, we investigated the role of Leo1, a subunit of the conserved RNA polymerase-associated factor 1 (Paf1) complex, in the quiescence process using fission yeast as the model organism. Heterochromatic regions became very dynamic in fission yeast in G0 during nitrogen starvation. The reduction of heterochromatin in early G0 was correlated with reduced target of rapamycin complex 2 (TORC2) signaling. We demonstrated that cells lacking Leo1 show reduced survival in G0. In these cells, heterochromatic regions, including subtelomeres, were stabilized, and the expression of many genes, including membrane transport genes, was abrogated. TOR inhibition mimics the effect of nitrogen starvation, leading to the expression of subtelomeric genes, and this effect was suppressed by genetic deletion of leo1.ConclusionsWe identified a protein, Leo1, necessary for survival during quiescence. Leo1 is part of a conserved protein complex, Paf1C, linked to RNA polymerase II. We showed that Leo1, acting downstream of TOR, is crucial for the dynamic reorganization of chromosomes and the regulation of gene expression during cellular quiescence. Genes encoding membrane transporters are not expressed in quiescent leo1 mutant cells, and cells die after 2 weeks of nitrogen starvation. Taken together, our results suggest that Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence.

Highlights

Cellular quiescence is a reversible differentiation state during which cells modify their gene expression program to inhibit metabolic functions and adapt to a new cellular environment
Leo1 is required for survival during long‐term quiescence To identify additional factors involved in chromatin regulation during cellular quiescence, we applied a small-scale genetic screen using a selection of mutants affecting chromatin dynamics (Additional file 1: Fig. S1a)
The activity of the target of rapamycin complex 2 (TORC2)/Gad8 pathway is modulated during quiescence To investigate the means by which Leo1 regulates heterochromatin during quiescence, we focused on target of rapamycin (TOR) complex 2 (TORC2)

Summary

Introduction

Cellular quiescence is a reversible differentiation state during which cells modify their gene expression program to inhibit metabolic functions and adapt to a new cellular environment. We used fission yeast cells as a model to study the regulation of quiescence When these cells are starved for nitrogen, the cell cycle is arrested in G1, and the cells enter quiescence (G0). A gene regulatory program is initiated, including downregulation of thousands of genes—for example, those related to cell proliferation—and upregulation of specific genes—for example, autophagy genes—needed to adapt to the physiological challenge. These changes in gene expression are accompanied by a marked alteration of nuclear organization and chromatin structure. The transcriptional profile of quiescent S. pombe cells is dramatically reprogrammed to allow survival under low-nitrogen conditions [4] This change is accompanied by a marked alteration of nuclear organization. The results of these studies clearly show that dynamic regulation of heterochromatin is essential during quiescence in fission yeast

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