Choline nutrition programs brain development via DNA and histone methylation

Abstract

Choline is an essential nutrient for humans. Metabolically choline is used for the synthesis of membrane phospholipids (e.g. phosphatidylcholine), as a precursor of the neurotransmitter acetylcholine, and, following oxidation to betaine, choline functions as a methyl group donor in a pathway that produces S-adenosylmethionine. As a methyl donor choline influences DNA and histone methylation--two central epigenomic processes that regulate gene expression. Because the fetus and neonate have high demands for choline, its dietary intake during pregnancy and lactation is particularly important for normal development of the offspring. Studies in rodents have shown that high choline intake during gestation improves cognitive function in adulthood and prevents memory decline associated with old age. These behavioral changes are accompanied by electrophysiological, neuroanatomical, and neurochemical changes and by altered patterns of expression of multiple cortical and hippocampal genes including those encoding key proteins that contribute to the biochemical mechanisms of learning and memory. These actions of choline are observed long after the exposure to the nutrient ended (months) and correlate with fetal hepatic and cerebral cortical choline-evoked changes in global- and gene-specific DNA cytosine methylation and with dramatic changes of the methylation pattern of lysine residues 4, 9 and 27 of histone H3. Moreover, gestational choline modulates the expression of DNA (Dnmt1, Dnmt3a) and histone (G9a/Ehmt2/Kmt1c, Suv39h1/Kmt1a) methyltransferases. In addition to the central role of DNA and histone methylation in brain development, these processes are highly dynamic in adult brain, modulate the expression of genes critical for synaptic plasticity, and are involved in mechanisms of learning and memory. A recent study documented that in a cohort of normal elderly people, verbal and visual memory function correlated positively with the amount of dietary choline consumption. It will be important to determine if these actions of choline on human cognition are mediated by epigenomic mechanisms or by its influence on acetylcholine or phospholipid synthesis.

Figure 1

Choline and methyl group metabolism and its relation to DNA methylation and influence on regulation of gene expression: a simplified diagram. Choline is used as a precursor of phosphatidylcholine, acetylcholine [in a reaction catalyzed by choline acetyltransferase (CHAT)], or betaine [in a reaction catalyzed by choline dehydrogenase (CHDH)]. The methyl groups of betaine are used by betaine:homocysteine S-methyltransferase (BHMT) to regenerate methionine from homocysteine. In an alternative pathway, catalyzed by vit. B12-requiring 5-methyltetrahydrofolate-homocysteine S-methyltransferase (MTR), methyltetrahydrofolate (CH₃THF) is used as a methyl donor. Methionine is used as a precursor of S-adenosylmethionine (AdoMet) in a reaction catalyzed by methionine adenosyltransferase(s) (MAT1A, MAT2A or MAT2B). AdoMet is used by multiple methylating enzymes including DNA methyltransferases (DNMT1, DNMT3A, DNMT3B) that use AdoMet as a donor of methyl groups to methylate DNA at the 5-position of cytosine residues within the CpG sequences. The DNA methylation state and pattern exerts a modulatory influence on expression of multiple genes (see text). The second product of this, and all other AdoMet-requiring methylation reactions, S-adenosylhomocysteine (AdoHcy) is hydrolyzed to free homocysteine by AdoHcy hydrolase (AHCY). The metabolic pathway linking choline to DNA methylation is indicated by thick arrows.

Figure 2

Methylation of DNA and histone H3 modifies chromatin state and regulates transcription. DNA is wrapped around nucleosomes that are composed of a histone octamer containing two molecules of H3. On the left cytosines within CpGs of DNA are unmethylated (white lollipops) and lysine 4 of the H3 N-terminal tail (thick line above the nucleosomes) is methylated (H3K4me3). Under these conditions transcription tends to be active (thick arrow). On the right, DNA has become more methylated (black lollipops) – initially due to the de novo process catalyzed by the DNMT3 enzymes and subsequently maintained in the cell lineage by DNMT1, and H3 is methylated on lysine 9 (H3K9me3). Under these conditions transcription is attenuated (thin arrow). Additional processes, including histone deacetylation, attachment of methylated DNA binding proteins (e.g. MECP2) also contribute to this transcriptional repression and chromatin compaction (illustrated on the right by closer packing of the nucleosomes). The two states are reversible.

Figure 3

Developmental pattern of expression of selected choline- and methylation-related genes (see Figure 1) in rat frontal cortex. Cortical RNA was analyzed using Affymetrix RG_U34A microarrays as described [73]. Left panel: Chdh, choline dehydrogenase; Mtr, 5-methyltetrahydrofolate-homocysteine S-methyltransferase; Mat2a, methionine adenosyltransferase 2a; Dnmt1, DNA methyltransferase 1; Ahcy, S-adenosylhomocysteine hydrolase. Right panel: Kdm3a/Jmjd1a, lysine (K)-specific demethylase 3A; Prmt3, protein arginine N-methyltransferase 3; G9a/Ehmt2/Kmt1c, euchromatic histone-lysine N-methyltransferase 2; Prmt1, protein arginine N-methyltransferase 1. X axis on the graph corresponds to days post-conception. The day of birth is indicated by an arrow. Postnatal days 1, 8, 15, 18, 22, and 34 are conceptual ages 23, 30, 37, 40, 44, and 56, respectively.