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Only about 2% of the DNA sequences in the human genome are ultimately encoded to produce proteins, and most of the rest of the region is transcribed to form long-chain non-coding RNA. With the discovery of the biological function of lncRNA, the status of these eferenceseq studies, which were originally considered to be "junk DNA", rose to "dark matter." The transcription of lncRNA is tightly regulated, and its expression profile is cell-specific and tissue-specific even higher than that of protein-coding genes. To find and discover the causes of LncRNA expression changes during disease, and to understand the upstream regulation mechanism of lncRNA is an important part of lncRNA research, and epigenetics is an important field to study RNA transcription regulation from the genomic level. 
Figure 3. Visual analysis
Technical advantages:
â— Focus on non-coding RNA field, perfect lncRNA promoter analysis process
â— Can be combined with lncRNA expression profiling chip to achieve seamless docking between platforms
â— Visual data display, providing paper-level results chart
â— Optimized IP test method, reliable detection platform and data results
Introduction :
Methylation of DNA in the promoter region inhibits RNA transcription. The study found that the genomic region of LncRNA MEG3 transcribed in liver cancer and schizophrenic patients has abnormal changes in the degree of DNA methylation; esophageal cancer has a characteristic lncRNA promoter DNA methyl map that distinguishes between cancer and adjacent tissues. The effect is better than the mRNA promoter; up to 57.18% of lncRNA in breast cancer undergoes a change in promoter DNA methylation level, and the degree of methylation of the lncRNA promoter is significantly correlated with the expression level of lncRNA.
Kang Cheng Bio adds the DNA methylation analysis of the lncRNA promoter to the MeDIP-seq data. The client can simultaneously obtain DNA methylation data of lncRNA and mRNA, which can be combined with the Arraystar lncRNA chip to achieve seamless docking between the two platforms. The lncRNA promoter assay is also applicable to the hMeDIP-seq platform, which allows rapid and easy determination of the distribution of DNA methylation modifications in the lncRNA promoter region.
Figure 1. Methylation/hydroxymethylation sequencing lncRNA promoter analysis process
Important data results show:
1. Differential (hydroxy) methylation analysis of lncRNA promoters in two groups/sample
Kang Cheng Bio uses the latest software to analyze the differential (hydroxy) methylation region between the two groups/samples. Compared with the traditional method of combining the first readings, calculating the difference enrichment area, or calculating the difference enrichment area separately, the method is more robust and can better utilize the variation in the repeated data to obtain better. Statistical results. Based on genomic coordinates, the differential (hydroxy) methylation region located in the lncRNA promoter region (TSS - 2000 bp to TSS + 2000 bp) was annotated using the UCSC RefSeq database.
Table 1: List of differential methylation regions of the lncRNA promoter
2. Joint analysis with lncRNA expression profiling chip
Methylation sequencing/hydroxymethylation sequencing data and lncRNA expression profile data were combined to analyze the clustering heat map of differential (hydroxy) methylation.
Figure 2. DNA methylation sequencing and LncRNA expression profiling combined analysis clustering
3. Visualization analysis of lncRNA promoter methylation/hydroxymethylation
The wig file in the methylation sequencing/hydroxymethylation sequencing results can be uploaded to the UCSC genome browser for visualization of the lncRNA promoter region signal.
references
1. Anamaria Necsulea. et al. (2014) Nature 505 (7485): 635-40 [PMID]
2. John P. Thomson. et al. (2013) Nucleic Acids Res 41(11): 5639-54 [PMID]
3. Wenjing Wu. et al. (2013) Gastroenterology 144(5): 956-966.e4 [PMID]
4. Yongsheng Li. et al. (2015) Scientific Reports 5; 5:8790 [PMID]