Effects of folic acid in late gestation on the neural methylome and the ZFP57 transcription factor

Abstract

DNA methylation plays an essential role in many biological processes, including development, growth and disease, through regulation of various gene classes susceptible to alterations through environmental exposures. Maternal diet can directly affect the methylome of the developing child, which can later affect its development and disease susceptibility. Folic acid supplementation during first trimester of pregnancy represents a unique maternal dietary supplement benefiting the child in the form of prevention of neural tube defects. Folic acid provides the universal methyl donor S-adenosyl methionine, contributing to the DNA methylation cycle. In this thesis, we looked at the role of folic acid supplementation in the second and third trimester of pregnancy on the methylome of the child in a randomised control trial, the EpiFASSTT study. In the first study we used genome-wide methylation analysis and identified the imprinted gene regulator ZFP57 as the top hit and using cell line models
confirmed that its transcription is affected by methylation, now published as Irwin et al., Clinical Epigenetics, 2019. In the second study, more general patterns of methylation change in the same cohort were examined using Gene Ontology and bioinformatic tools such as DAVID: this showed enrichment for neural genes. This study showed two groups of higher-function brain-specific genes, distinguished by their methylation distribution, that are affected by folate supplementation. Such targets for methylation alteration fit well with previously observed psychological benefits in children born to folic acid supplemented mothers.

Even though the DNA methylation patterns are established during early embryonal development, the epigenetic reprogramming process erases these marks, with the exception of some gene families, including the imprinted genes. This group of genes is expressed in a parent- of origin determined manner and is directly controlled by DNA methylation, being protected from erasure during reprogramming. DNA methylation of these genes is maintained by the KRAB-ZF protein ZFP57- mediated silencing complex. In this thesis, in the third study we discuss the evolution of imprinted genes and their relationship with the retrotransposons, specifically the role of the KRAB-ZFs in these processes, published as Ondičova et al., PLoS Genetics, 2020. ZFP57 is a key imprinted gene regulator in mice, and in human is known to bind transposable elements and the imprinted genes, moreover its mutation is linked with the imprinted disorder transient neonatal diabetes mellitus. In the fourth study we looked more closely at the role of DNA methylation in the regulation of the gene. We establish that various transcripts originated within the methylation- susceptible DMR that controls the expression of the gene. We also show that DNA methylation of human ZFP57 seems to be controlled by our newly identified mQTL variant. Here we also present evidence that the region within the promoter bound by the transcription factor CTCF has insulator-like properties. In this thesis, we therefore show that the major imprint regulator ZFP57 is both controlled by DNA methylation and susceptible to environmental changes. This thesis also presents new insights into the role of late folic acid supplementation on the neural methylome of the child.

Date of Award	Sept 2021
Original language	English
Supervisor	Rachelle Irwin (Supervisor) & Colum Walsh (Supervisor)