Benefits

• Performance optimized (h)MeDIP methods, rigorous QC process, and high mappable reads

• (hydroxy-)methylation analysis on both mRNA and lncRNA gene promoters

• Standard analysis package with advanced features

• Seamless integration with our lncRNA expression array profiling technology

The lncRNA transcription is tightly regulated in a cell type-, tissue-, or disease-specific manner, much more so than the transcription of protein coding genes. Understanding what is behind the lncRNA expression dysregulation and the upstream regulatory mechanisms is a key part of lncRNA research. Epigenetic study of transcriptional regulation on lncRNAs is an important avenue from the genomic perspective.

DNA methylation or hydroxymethylation in the promoter regions critical for transcription have the regulatory effects on gene expression. For example, the methyl group modification in the LncRNA-MEG3 promoter region is aberrantly changed in liver cancers and schizophrenia patients [1]. As biomarkers, the lncRNA promoter methylation signature has shown classifying power between tumor and non-tumor cells higher than mRNA promoters in esophageal cancers [2]. Dysregulation of lncRNA promoter methylation is common, present in up to 57% breast cancer specimens [3]. Not surprisingly, the levels of lncRNA promoter methylation and the lncRNA gene expression are significantly correlated.

Arraystar (h)MeDIP-seq service with lncRNA promoter analysis offers added benefits to obtain in depth data analyses and annotations of 5mC or 5hmC modifications on both mRNA and lncRNA gene promoters(Figure.1). Moreover, the analysis can be combined and integrated seamlessly with Arraystar LncRNA Array gene expression profiling of both lncRNA and mRNA, to systematically investigate the epigenetic regulation and gene expression in the biological system or disease.

Figure 1. The workflow of Arraystar MeDIP/hMeDIP-seq, which distinguishes itself with lncRNA promoter analysis along with mRNA promoters.

References
1.Thomson, J.P. et al.(2013) Nucleic Acids Res 41(11):5639-54 [PMID:23598998]
2.Wu, W. et al.(2013) Gastroenterology 144(5):956-966.e4 [PMID:23333711]
3.Li, Y. et al.(2015) Scientific Reports 5;5:8790 [PMID:25739977]

Differential methylation or hydroxymethylation in lncRNA promoter regions between samples or groups

The differential (hydroxy)methylation in the lncRNA promoter regions ( /- 2000 bp of TSS) is annotated with the reference genome (Fig. 1).

Figure 1. Differentially methylated regions in the lncRNA promoter regions are tabulated with the fold changes , p- and q-values for statistical significance, and genomic annotation.

Combined analysis of (h)MeDIP-seq of lncRNA promoters with lncRNA expression

The epigenetic modification data from (h)MeDIP-seq and the gene expression profiles are combined for integrative analysis. The 5mC, 5hmC or 6mA differentially modified genes and the differentially expressed genes are hierarchically clustered on the heatmaps, to allow correlation of the changes (Fig. 2).

Figure 2.  A combined analysis of hMeDIP-seq and LncRNA expression array profiling, as shown in the clustering heatmaps, to reveal the relationship of hydroxymethylation of lncRNA promoters with the lncRNA gene expression.

Visualization of LncRNA promoter (hydroxy)methylation

The (h)MeDIP-seq data are formatted as compatible WIG files for uploading to genome browsers such as UCSC Genome Browser. The (h)MeDIP signals can be visualized along with genomic features and a wealth of other gene expression, gene regulation, phenotypic tracks from many other sources.

Figure 3. Genome browser visualization of hydroxymethylation peaks from hMeDIP-seq data.

Your samples
Purified genomic DNA, or frozen tissues, or cell pellets

Please refer to Sample Submission for details in how to get your project started.

Arraystar (h)MeDIP-seq

1.  Genomic DNA isolation (Optional)

2.  Genomic DNA QC

3.  Immunoprecipitation by anti-5-methylcytosine, anti-5-hydroxyl-methylcytosine, or anti-6-methyladenine antibody

4. Sequencing library prep and library QC

5.  Sequencing by Illumina platform

6.  Data Extraction, Analysis and Summarization

TET3 is a positive regulator of mitochondrial respiration in Neuro2A cells. Leon Kropf V, et al, Plos one, 2023

MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy) methylation and gene expression to maintain a neoplastic phenotype in T-ALL. Poole C J, et al. Epigenetics & chromatin, 2019

Loss of Endometrial Plasticity in Recurrent Pregnancy Loss. Emma S. Lucas,et al. Stem cells, 2016.

Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis. Shivani N,et al. Clinical Epigenetics, 2016

Parp inhibition prevents ten eleven translocase enzyme activation and hyperglycemia induced DNA demethlation. Dhliwayo N, et al. Diabetes. 2014.

Heritable Transmission of Diabetic Metabolic Memory in Zebrafish Correlates With DNA Hypomethylation and Aberrant Gene Expression. Ansgar S. Olsen, et al. Diabetes. 2012.