Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells.

Yiqin Ma,Daniel J Mckay,Laura Buttitta,Hilary A Coller

doi:10.1371/journal.pbio.3000378

Abstract

During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals. Entry into G0 is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM). However, when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here, we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators Cyclin E (cycE), E2F transcription factor 1 (e2f1), and string (stg). This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle reactivation, and the regions that close contain known binding sites for effectors of mitogenic signaling pathways such as Yorkie and Notch. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains unaffected, and the closing of distal enhancers at cycE, e2f1, and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle–independent timer to limit the response to mitogenic signaling and aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross talk between cell cycle exit and terminal differentiation during metamorphosis.

Highlights

The majority of cells in mature multicellular organisms spend most of their existence in nonproliferating states, often referred to as cellular quiescence or the G0 phase [1]
Chromatin accessibility and gene expression are temporally dynamic during wing metamorphosis During metamorphosis, wings undergo morphogenetic changes coordinated with cell cycle alterations, loss of regeneration capacity, and activation of a wing terminal differentiation program [28,29,30]
To identify the global landscape of potential regulatory elements driving these gene expression changes, we carried out formaldehyde-assisted isolation of regulatory elements (FAIRE)-seq in parallel with RNA sequencing (RNA-seq) in a time course of wild-type Drosophila wings from the late wandering third instar stage when wing cells are Chromatin accessibility and robust cell cycle exit proliferating to 44 h after puparium formation (APF), when wing cells are postmitotic and begin to deposit adult cuticle

Summary

Introduction

The majority of cells in mature multicellular organisms spend most of their existence in nonproliferating states, often referred to as cellular quiescence or the G0 phase [1]. Substantial progress has been made on understanding how developmental signaling pathways interface with the cell cycle machinery to control tissue growth and proliferation [2,3]. We understand very little about why some cell types can enter a more flexible G0 state and retain the ability to reenter the cell cycle in response to mitogens, whereas others become permanently postmitotic and refractory to mitogenic signaling. The molecular details of how this silencing is initiated and maintained in maturing tissues remain unresolved. This impacts a wide range of biological questions, as the proper control of G0 is critical during development and tissue regeneration but becomes disrupted in cancer

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