Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells

Jianquan Xu,Hongqiang Ma,Jingyi Jin,Shikhar Uttam,Rao Fu,Yi Huang,Yang Liu

doi:10.1016/j.celrep.2018.06.085

Abstract

SUMMARYHistone modifications influence higher-order chromatin structures at individual epigenomic states and chromatin environments to regulate gene expression. However, genome-wide higher-order chromatin structures shaped by different histone modifications remain poorly characterized. With stochastic optical reconstruction microscopy (STORM), we characterized the higher-order chromatin structures at their epigenomic states, categorized into three major types in interphase: histone acetylation marks form spatially segregated nanoclusters, active histone methylation marks form spatially dispersed larger nanodomains, and repressive histone methylation marks form condensed large aggregates. These distinct structural characteristics are also observed in mitotic chromosomes. Furthermore, active histone marks coincide with less compact chromatin and exhibit a higher degree of co-localization with other active marks and RNA polymerase II (RNAP II), while repressive marks coincide with densely packed chromatin and spatially distant from repressive marks and active RNAP II. Taken together, super-resolution imaging reveals three distinct chromatin structures at various epigenomic states, which may be spatially coordinated to impact transcription.

Highlights

Eukaryotic cells package genomic DNA up to 2 m long into a nucleus with a diameter of several microns through a hierarchical scheme of compaction into DNA-protein assemblies
We focus on a comprehensive in situ characterization of genome-wide higher-order chromatin structures defined by histone acetylation and methylation marks and their spatial proximity that collectively form the chromatin environment in single mammalian cell nuclei via stochastic optical reconstruction microscopy (STORM)
The super-resolution images clearly show the presence of highly condensed mega-sized and even super-sized clumps enriched at the periphery of the nucleus, nucleolus, and nucleoplasm, consistent with our conventional view of heterochromatin observed under electron microscopy (Heitz, 1928; van Steensel, 2011)

Summary

Introduction

Eukaryotic cells package genomic DNA up to 2 m long into a nucleus with a diameter of several microns through a hierarchical scheme of compaction into DNA-protein assemblies. The first level is nucleosome, consisting of 147 bp of DNA wrapped around an octamer of four core histone (H2A, H2B, H3, and H4) proteins. This basic repeating unit of nucleosomes is organized into $10-nm ‘‘beads-on-string’’ chromatin fiber, which is further compacted into a higher-order chromatin structure, to fit into the micron-sized nucleus. Histone modifications regulate the packaging of nucleosomes into a higher-order chromatin structure to influence the accessibility of genomic DNA to the transcription machinery proteins. Chromatin compaction at different epigenomic states controls their gene expression (Strahl and Allis, 2000; Turner, 2000) and imposes a significant effect on many cellular processes, such as DNA replication, cell division, DNA damage, and DNA repair

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Conclusion