Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix

Kyoko Kitagawa,Hiroshi Kimura,Anton Wutz,Kazuki Yamazawa,Masatoshi Kitagawa,Asuka Miura-Kamio,Chiharu Uchida,Saori Takahashi,Hiroyuki Niida,Tatsuya Ohhata,Hisato Kobayashi,Yuka Tamura,Ichiro Hiratani,Satoshi Sakai

doi:10.1016/j.celrep.2021.108912

Abstract

The fine-scale dynamics from euchromatin (EC) to facultative heterochromatin (fHC) has remained largely unclear. Here, we focus on Xist and its silencing initiator Tsix as a paradigm of transcription-mediated conversion from EC to fHC. In mouse epiblast stem cells, induction of Tsix recapitulates the conversion at the Xist promoter. Investigating the dynamics reveals that the conversion proceeds in a stepwise manner. Initially, a transient opened chromatin structure is observed. In the second step, gene silencing is initiated and dependent on Tsix, which is reversible and accompanied by simultaneous changes in multiple histone modifications. At the last step, maintenance of silencing becomes independent of Tsix and irreversible, which correlates with occupation of the -1 position of the transcription start site by a nucleosome and initiation of DNA methylation introduction. This study highlights the hierarchy of multiple chromatin events upon stepwise gene silencing establishment.

Highlights

Cells of multicellular organisms maintain distinct patterns of gene expression through division to facilitate their specific roles and functions
Maintenance of silencing becomes independent of Tsix and irreversible, which correlates with occupation of the À1 position of the transcription start site by a nucleosome and initiation of DNA methylation introduction
Generation and characterization of XDXistXTTGFP epiblast stem cells (EpiSCs) To examine the conversion from EC to facultative heterochromatin (fHC) at the Xist promoter, we established XDXistXTTGFP EpiSCs (Figure 1A) from XDXistXTTGFP embryonic stem cells (ESCs) (Figure S1A) as described previously

Summary

Introduction

Cells of multicellular organisms maintain distinct patterns of gene expression through division to facilitate their specific roles and functions. Gene expression patterns are inherited through distinct chromatin structures (Allis and Jenuwein, 2016). These chromatin structures are divided into euchromatin (EC) and heterochromatin (HC) that correlate with active and repressive transcriptional states, respectively. Constitutive heterochromatin (cHC) is mainly observed at pericentromeric and telomeric regions, which is stably maintained throughout the life cycle. Facultative heterochromatin (fHC) can interconvert between EC and HC during differentiation and development (Allis and Jenuwein, 2016; Trojer and Reinberg, 2007; Z_ ylicz and Heard, 2020). The fundamental question of how fHC is converted from EC remains largely unanswered

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