Integration of epigenomic and transcriptome analyses of neural tube defects reveals methylation driver lncRNAs and mRNAs

Abstract

Abstract Background Abnormal genome-wide methylation during embryogenesis is associated with neural tube defects (NTDs) at birth. Long noncoding RNAs (lncRNAs) may be promising biomarkers for nervous system-related diseases. Therefore, we aimed to investigate the role of lncRNAs with aberrant methylation in the pathogenesis of NTDs. Methods Pregnant mice were given retinoic acid (dissolved in corn oil, 50 mg/kg) to build the NTDs model by gavage. After collecting brain tissues, reduced representation bisulfite sequencing (RRBS) and lncRNAs sequencing were conducted. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEGs) between NTDs and control group were screened, and then integrated with RRBS data to obtain genes with aberrant methylation, followed by functional enrichment analysis. Subsequently, protein-protein interaction (PPI) network and lncRNA-miRNA-mRNA network were constructed. Finally, qRT-PCR was applied to determine the expression levels of identified hub lncRNAs. Results A total of 8 DElncRNAs as well as 213 DEGs with aberrant methylation between NTD group and normal group were screened. By bioinformatics analysis, several hub lncRNAs including Gm15521, Gm4681, Gm13974 and Gm40638, were identified. Function analysis showed these genes were mainly enriched in axon guidance pathway. The qRT-PCR assay revealed that the expression level of Gm15521, Gm4681 and Gm13974 in the NTDs group was significantly lower than those in the control group. Conclusion The study screened DElncRNAs with aberrant methylation in the NTDs and the identified genes could be potential biomarkers for prenatal diagnosis of NTDs. These findings will provide a reference for further study on the regulatory mechanism of non-coding RNAs in the NTDs.