Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

Francisco Rodriguez-Algarra,Amy F Danson,Harunori Yoshikawa,Selin Yildizoglu,Matthew Loose,Pui Pik Law,Madapura M Pradeepa,Ama Brew,Robert A E Seaborne,Michelle L Holland,Vardhman K Rakyan,Sarah J Marzi,Alan Hodgkinson,Mateus Ochôa,Zakaryya Ahmad,Victoria A Maudsley,Nadine Holmes

doi:10.1186/s13059-022-02617-x

Abstract

BackgroundRibosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed.ResultsUsing a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during aging only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with the total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, the rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are < 5%.ConclusionsOur work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.

Highlights

Ribosomal DNA displays substantial inter-individual genetic variation in human and mouse
Our work demonstrates that Ribosomal DNA (rDNA)-associated genetic variation has a considerable influence on rDNA epigenetic state and ribosomal RNA (rRNA) expression outcomes
It will be important to consider the impact of inter-individual rDNAgenetic variation on mammalian phenotypes and diseases

Summary

Introduction

Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. It has been shown that the protein composition of the ribosome can vary developmentally [1] and that the ribosomal RNA (rRNA) components display inter- and intra-individual genetic variation [2, 3] Such variation is thought to influence preferential translation of some mRNAs, i.e., the “ribosome filter hypothesis” [4]. Several smaller studies have noted inter-individual variation at the single-nucleotide level and copy number in mouse and human rDNA, and epigenetic variation in the context of whole organism stress responses [2, 5,6,7,8]. A systematic analysis of how human and/ or mouse rDNA-associated genetic variation influences associated epigenetic states, and rDNA transcriptional output, has far not been performed. We had three main aims in this study, to combine long- and short-read sequencing to establish: (i) how single-nucleotide genetic variation at the individual rDNA unit level influences epigenetic states and transcriptional outputs, (ii) whether rDNA copy number influences epigenetic states, (iii) if such genetic variation is relevant in examples of mammalian phenotypes

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Conclusion