Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes.

Ruby J Roach,Carlos González,Vyacheslav V Filichev,Tracy K Hale,Geoffrey B Jameson,Miguel Garavís

doi:10.1093/nar/gkz1138

Ruby J Roach, Carlos González + Show 4 more

Open Access

https://doi.org/10.1093/nar/gkz1138

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Abstract

The eukaryotic genome is functionally organized into domains of transcriptionally active euchromatin and domains of highly compact transcriptionally silent heterochromatin. Heterochromatin is constitutively assembled at repetitive elements that include the telomeres and centromeres. The histone code model proposes that HP1α forms and maintains these domains of heterochromatin through the interaction of its chromodomain with trimethylated lysine 9 of histone 3, although this interaction is not the sole determinant. We show here that the unstructured hinge domain, necessary for the targeting of HP1α to constitutive heterochromatin, recognizes parallel G-quadruplex (G4) assemblies formed by the TElomeric Repeat-containing RNA (TERRA) transcribed from the telomere. This provides a mechanism by which TERRA can lead to the enrichment of HP1α at telomeres to maintain heterochromatin. Furthermore, we show that HP1α binds with a faster association rate to DNA G4s of parallel topology compared to antiparallel G4s that bind slowly or not at all. Such G4–DNAs are found in the regulatory regions of several oncogenes. This implicates specific non-canonical nucleic acid structures as determinants of HP1α function and thus RNA and DNA G4s need to be considered as contributors to chromatin domain organization and the epigenome.

Highlights

Within the confines of the nucleus, genomic DNA is packaged with histone proteins to create highly folded yet dynamic chromatin fibres
We show here that the unstructured hinge domain, necessary for the targeting of Heterochromatin Protein 1 (HP1)␣ to constitutive heterochromatin, recognizes parallel Gquadruplex (G4) assemblies formed by the TElomeric Repeat-containing RNA (TERRA) transcribed from the telomere
To determine the ability of HP1␣ to interact with telomeric repeat RNA, biolayer interferometry (BLI) was performed where purified his-tagged HP1␣ was immobilized on nickel sensor tips and the tips immersed in a K+ solution containing G-rich RNA of varying lengths: 96 nucleotides (TERRA96), 45 nucleotides (TERRA45) or 22 nucleotides (TERRA22) from the telomeric RNA UUAGGG repeat sequence

Summary

Introduction

Within the confines of the nucleus, genomic DNA is packaged with histone proteins to create highly folded yet dynamic chromatin fibres. Arrays of nucleosomes undergo further folding to form a more condensed fibre These chromatin fibres are further partitioned by architectural proteins into functionally distinct domains of transcriptionally active euchromatin and highly condensed transcriptionally silent heterochromatin, thereby ensuring appropriate patterns of gene expression and genomic stability [2,3]. HP1 consists of a conserved N-terminal chromodomain that binds histone H3 methylated on lysine 9 and a structurally related C-terminal chromoshadow domain that dimerizes and provides an interface for recruiting an array of proteins (Figure 1A). These domains are connected by a less conserved flexible hinge domain; present are short unstructured N- and C-terminal extensions [6]. The non-redundant functions of these highly conserved proteins that have emerged, and are reflected in their differing nuclear distributions, establish the need to identify the interactions that regulate and fine tune their individual functions within chromatin [7,8,9]

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