H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis.

Andrey Poleshko,Karen G Wong,Cheryl L Smith,Jonathan A Epstein,Priya Sivaramakrishnan,Melike Lakadamyali,John Isaac Murray,Eric F Joyce,Son C Nguyen,Rajan Jain

doi:10.7554/elife.49278

Abstract

Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.

Highlights

In order for a dividing cell of a given lineage to maintain its identity, it must pass along to its progeny a complete copy of its genome, and the memory of its specific cellular identity (Buchwalter et al, 2019, Towbin et al, 2013, Amendola and van Steensel, 2014)
We show that the H3K9me2 modification of nuclear lamina-associated heterochromatin, revealed upon dephosphorylation of H3S10 at mitotic exit, provides a 3D spatial guidepost for genomic regions that are to be re-localized to the nuclear periphery following mitosis and that the nuclear lamina of daughter cells reassembles around the exposed H3K9me2 mark
We show that H3K9me2 marks chromatin domains that are positioned at the nuclear lamina during interphase

Summary

Introduction

In order for a dividing cell of a given lineage to maintain its identity, it must pass along to its progeny a complete copy of its genome, and the memory of its specific cellular identity (Buchwalter et al, 2019, Towbin et al, 2013, Amendola and van Steensel, 2014). Separation of transcriptionally active and inactive chromatin in three-dimensional space reinforces efficient regulation of gene expression and maintains silencing of heterochromatic loci (reviewed in (Andrey and Mundlos, 2017, Buchwalter et al, 2019, Amendola and van Steensel, 2014, Bickmore, 2013)). This is illustrated by examples of aberrant gene expression patterns that occur upon disruption of topological domains and, in extreme cases, are associated with oncogenic transformation (Andrey and Mundlos, 2017, Flavahan et al, 2016). Heterochromatin is segregated into spatially distinct subnuclear compartments including peripherally located lamina-associated domains (LADs)

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