NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

Priscillia Lhoumaud,Richard Bonneau,Theodore Sakellaropoulos,Macintosh Cornwell,Javier Rodriguez-Hernaez,Sana Badri,Ferhat Ay,Sourya Bhattacharyya,Aristotelis Tsirigos,Andreas Kloetgen,Gunjan Sethia,Jane A Skok

doi:10.1038/s41467-019-12811-4

Abstract

CTCF and cohesin play a key role in organizing chromatin into topologically associating domain (TAD) structures. Disruption of a single CTCF binding site is sufficient to change chromosomal interactions leading to alterations in chromatin modifications and gene regulation. However, the extent to which alterations in chromatin modifications can disrupt 3D chromosome organization leading to transcriptional changes is unknown. In multiple myeloma, a 4;14 translocation induces overexpression of the histone methyltransferase, NSD2, resulting in expansion of H3K36me2 and shrinkage of antagonistic H3K27me3 domains. Using isogenic cell lines producing high and low levels of NSD2, here we find oncogene activation is linked to alterations in H3K27ac and CTCF within H3K36me2 enriched chromatin. A logistic regression model reveals that differentially expressed genes are significantly enriched within the same insulated domain as altered H3K27ac and CTCF peaks. These results identify a bidirectional relationship between 2D chromatin and 3D genome organization in gene regulation.

Highlights

CTCF and cohesin play a key role in organizing chromatin into topologically associating domain (TAD) structures
Using RNA-seq we observed that NSD2 High expression leads to the deregulation of many genes (1650 up and 303 downregulated genes) (Fig. 1b, Supplementary Data 1) and principal component analysis (PCA) revealed that NSD2 High and Low replicates separated into distinct clusters (Supplementary Fig. 1a)[23,25], consistent with previous studies[23,25]
The activation of oncogenic transcriptional pathways in this context has been shown to rely on the histone methyl transferase activity of NSD2 and deposition of H3K36me[231]

Summary

Introduction

CTCF and cohesin play a key role in organizing chromatin into topologically associating domain (TAD) structures. A logistic regression model reveals that differentially expressed genes are significantly enriched within the same insulated domain as altered H3K27ac and CTCF peaks These results identify a bidirectional relationship between 2D chromatin and 3D genome organization in gene regulation. A number of labs have demonstrated that disruption of a single CTCF-binding site is sufficient to alter chromosomal interactions leading to the spreading of active chromatin and altered gene regulation[14,18,19,20] It is not known if the reverse is true, and whether alterations in chromatin modifications themselves can impact chromosome organization at the level of A and B compartments, TAD structure, CTCF binding and enhancer–promoter contacts in a manner that corresponds to changes in gene regulation. Given the poor prognosis of patients suffering from these cancers, it is important to better understand the mechanisms underlying changes in gene expression in diseases with an H3K36me[2] versus H3K27me[3] imbalance

Methods

Results

Conclusion