Association of dietary folate and vitamin B-12 intake with genome-wide DNA methylation in blood: a large-scale epigenome-wide association analysis in 5841 individuals

Pooja R Mandaviya, Roby Joehanes, Jennifer Brody, Juan E Castillo-Fernandez, Koen F Dekkers, Anh N Do, Mariaelisa Graff, Ismo K Hänninen, Toshiko Tanaka, Ester A L de Jonge, Jessica C Kiefte-de Jong, Devin M Absher, Stella Aslibekyan, Yolanda B de Rijke, Myriam Fornage, Dena G Hernandez, Mikko A Hurme, M Arfan Ikram, Paul F Jacques, Anne E JusticeDouglas P Kiel, Rozenn N Lemaitre, Michael M Mendelson, Vera Mikkilä, Ann Z Moore, Tess Pallister, Olli T Raitakari, Casper G Schalkwijk, Jin Sha, Eline P E Slagboom, Caren E Smith, Coen D A Stehouwer, Pei-Chien Tsai, André G Uitterlinden, Carla J H van der Kallen, Diana van Heemst, Donna K Arnett, Stefania Bandinelli, Jordana T Bell, Bastiaan T Heijmans, Terho Lehtimäki, Daniel Levy, Kari E North, Nona Sotoodehnia, Marleen M J van Greevenbroek, Joyce B J van Meurs, Sandra G Heil*, BIOS Consortium, CHARGE Consortium Epigenetics Working Group, CHARGE Consortium Nutrition Working Group

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


BACKGROUND: Folate and vitamin B-12 are essential micronutrients involved in the donation of methyl groups in cellular metabolism. However, associations between intake of these nutrients and genome-wide DNA methylation levels have not been studied comprehensively in humans.

OBJECTIVE: The aim of this study was to assess whether folate and/or vitamin B-12 intake are asssociated with genome-wide changes in DNA methylation in leukocytes.

METHODS: A large-scale epigenome-wide association study of folate and vitamin B-12 intake was performed on DNA from 5841 participants from 10 cohorts using Illumina 450k arrays. Folate and vitamin B-12 intakes were calculated from food-frequency questionnaires (FFQs). Continuous and categorical (low compared with high intake) linear regression mixed models were applied per cohort, controlling for confounders. A meta-analysis was performed to identify significant differentially methylated positions (DMPs) and regions (DMRs), and a pathway analysis was performed on the DMR annotated genes.

RESULTS: The categorical model resulted in 6 DMPs, which are all negatively associated with folate intake, annotated to FAM64A, WRAP73, FRMD8, CUX1, and LCN8 genes, which have a role in cellular processes including centrosome localization, cell proliferation, and tumorigenesis. Regional analysis showed 74 folate-associated DMRs, of which 73 were negatively associated with folate intake. The most significant folate-associated DMR was a 400-base pair (bp) spanning region annotated to the LGALS3BP gene. In the categorical model, vitamin B-12 intake was associated with 29 DMRs annotated to 48 genes, of which the most significant was a 1100-bp spanning region annotated to the calcium-binding tyrosine phosphorylation-regulated gene (CABYR). Vitamin B-12 intake was not associated with DMPs.

CONCLUSIONS: We identified novel epigenetic loci that are associated with folate and vitamin B-12 intake. Interestingly, we found a negative association between folate and DNA methylation. Replication of these methylation loci is necessary in future studies.

Original languageEnglish
Article number15
Pages (from-to)437-450
Number of pages14
JournalAmerican Journal of Clinical Nutrition
Issue number2
Early online date5 Jun 2019
Publication statusPublished - Aug 2019


  • CALM
  • DNA methylation
  • Epigenome-wide Association Study
  • FFQ
  • diet
  • epigenetics
  • folate
  • genome-wide
  • vitamin B-12

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