Effect of Folate Deficiency on the Changes of Histone H3 Lysine 4 Monomethylation-Marked Enhancers and Its Molecular Exploration in Low Folate-Induced Neural Tube Defects.
10.3881/j.issn.1000-503X.16323
- Author:
Qiu XIE
1
;
Jin HU
1
;
Jian-Ting LI
2
;
Ting ZHANG
2
Author Information
1. Department of Medical Research Center,PUMC Hospital,CAMS and PUMC,Beijing 100730,China.
2. Beijing Municipal Key Laboratory of Child Development and Nutriomics,Capital Institute of Pediatrics,Beijing 100020,China.
- Publication Type:Journal Article
- Keywords:
chromatin immunoprecipitation;
embryonic stem cells;
folate;
histone;
neural tube defects
- MeSH:
Neural Tube Defects/genetics*;
Animals;
Mice;
Folic Acid Deficiency/complications*;
Histones/metabolism*;
Folic Acid/metabolism*;
Methylation;
Mouse Embryonic Stem Cells/metabolism*;
Wnt Signaling Pathway;
Lysine/metabolism*;
Chromatin Immunoprecipitation Sequencing
- From:
Acta Academiae Medicinae Sinicae
2025;47(5):782-791
- CountryChina
- Language:English
-
Abstract:
Objective To investigate the effects of folate deficiency on changes in histone H3 lysine 4 (H3K4) mono-methylation (me1)-marked enhancers and the molecular mechanism underpinning the folate deficiency-induced neural tube defects (NTD). Methods Mouse embryonic stem cells (mESCs) were cultured in the folate-free DMEM medium (folate-deficient group) and the DMEM medium containing 4 mg/L folate (normal control group),respectively.Chromatin immunoprecipitation sequencing (ChIP-seq) was performed for H3K4me1. The mouse model of folate-induced NTD was established,and transcriptome sequencing (RNA-seq) was performed for the brain tissue of fetal mice to reveal the differential expression profiles.The results were validated through real-time quantitative polymerase chain reaction (RT-qPCR).The activity of the differential peak regions of H3K4me1 was verified through the luciferase reporter assay. Results The folate content in the mESCs cultured in the folate-free medium reduced compared with that in the normal control group (P=0.008).The H3K4me1-maked enhancers in the mESCs cultured in the folate-free medium induced significant changes in intronic regions,and these changes were concentrated in metabolic and energy metabolism processes (q=9.56×10-48,P=1.28×10-47).The differentially expressed genes harboring H3K4me1-marked enhancers in mESCs were mainly enriched in the Wnt signaling pathway (q=0.004,P=0.004 7).ChIP-qPCR results confirmed that H3K4me1 binding decreased in the differential peak regions of the Ldlrap1 gene (P=0.008),Camta1 gene (P=0.002),and Apc2 gene (P=0.012).The H3K4 demethylase inhibitor T-448 effectively reversed the H3K4me1 binding in the differential peak regions of the aforementioned genes (P=0.01).The results of RNA-seq for the brain tissue of NTD fetal mice showed significant enrichment of the differentially expressed genes in the Wnt signaling pathway (P=1.52×10-5).The enrichment of differential peak regions of H3K4me1-marked enhancers in Apc2,Ldlrap1,and Camta1 genes in the brain tissue also showed significant changes.The differential peak region in Apc2 exhibited transcription factor activity (P=0.020). Conclusion Folate deficiency may affect changes in H3K4me1-marked enhancers to participate in the regulation of neural tube closure genes,thereby inducing the occurrence of NTD.
