Defective folate metabolism causes germline epigenetic instability and distinguishes Hira as a phenotype inheritance biomarker

Georgina E T Blake,Anne C Ferguson-Smith,Erica D Watson,Hong Wa Yung,Xiaohui Zhao,Graham J Burton,Russell S Hamilton

doi:10.1038/s41467-021-24036-5

Georgina E T Blake, Anne C Ferguson-Smith + Show 5 more

Open Access

https://doi.org/10.1038/s41467-021-24036-5

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Abstract

The mechanism behind transgenerational epigenetic inheritance is unclear, particularly through the maternal grandparental line. We previously showed that disruption of folate metabolism in mice by the Mtrr hypomorphic mutation results in transgenerational epigenetic inheritance of congenital malformations. Either maternal grandparent can initiate this phenomenon, which persists for at least four wildtype generations. Here, we use genome-wide approaches to reveal genetic stability in the Mtrr model and genome-wide differential DNA methylation in the germline of Mtrr mutant maternal grandfathers. We observe that, while epigenetic reprogramming occurs, wildtype grandprogeny and great grandprogeny exhibit transcriptional changes that correlate with germline methylation defects. One region encompasses the Hira gene, which is misexpressed in embryos for at least three wildtype generations in a manner that distinguishes Hira transcript expression as a biomarker of maternal phenotypic inheritance.

Highlights

The mechanism behind transgenerational epigenetic inheritance is unclear, through the maternal grandparental line
As one-carbon metabolism is directly linked to DNA synthesis[15], we first addressed whether the Mtrrgt allele influences genetic stability
The sequenced genomes were compared to the C57Bl/6 J reference genome to identify structural variants (SVs) and single-nucleotide polymorphisms (SNPs)

Summary

Introduction

The mechanism behind transgenerational epigenetic inheritance is unclear, through the maternal grandparental line. We previously reported the Mtrrgt mouse line, a rare model of maternal grandparental TEI in which congenital malformations are transgenerationally inherited for at least four wildtype generations[3] (see below, Supplementary Fig. 1a, d–e). Similar to mutations in the human MTRR gene[13,20,21,22] or dietary folate deficiency in humans[23], Mtrrgt/gt mice display hyperhomocysteinemia[3,12] and macrocytic anaemia[24] in adulthood, as well as altered DNA methylation patterns associated with gene misexpression[3] and a broad range of incompletely penetrant developmental phenotypes at midgestation (e.g., growth defects and/or congenital malformations including heart, placenta, and neural tube closure defects)[3]. Through highly controlled genetic pedigrees (Supplementary Fig. 1a, d–e), we demonstrated that an Mtrr+/gt heterozygous male or female mouse (i.e., the F0 generation) can initiate TEI of developmental phenotypes at embryonic day (E) 10.5 in the wildtype (Mtrr+/+) descendants until the F4 generation[3]. F1 wildtype mice derived from F0 Mtrr+/gt males display indicators of direct epigenetic inheritance including locus-specific epigenetic dysregulation in placentas at E10.5 associated with gene misexpression in the absence of gross phenotype[3], a hematopoietic phenotype later in life[24], and the ability of F1 wildtype females to perpetuate epigenetically inherited phenotypes to their offspring in a manner similar to those derived from an F0 Mtrr+/gt female (Supplementary fig. 1d–e)[3]

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