In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size

Abstract

Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between −2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.

Targeted demethylation of the CDO1 promoter based on CRISPR system inhibits the malignant potential of breast cancer cells

“…To validate these findings, a MassARRAY mass spectrometry methylation sequencing analysis was performed. MethPrimer predicted the presence of two CGIs (CGI1 and CGI2) within the CDO1 promoter 34,35 . Considering that CGI1 (+78 to −354) encompasses the transcription start site and contains more CpG sites, we focused on analysing the methylation status of the region within CGI1 (+18 to −332) (Figure 2A, top).…”

“…MethPrimer predicted the presence of two CGIs (CGI1 and CGI2) within the CDO1 promoter. 34 , 35 Considering that CGI1 (+78 to −354) encompasses the transcription start site and contains more CpG sites, we focused on analysing the methylation status of the region within CGI1 (+18 to −332) (Figure 2A , top). Fourteen BC tissues and seventeen unpaired NATs were subjected to MassARRAY mass spectrometry methylation sequencing to evaluate the methylation status of this region (Figure 2A , bottom).…”

Molecular Mechanisms and the Significance of Synonymous Mutations

“…In cancer cells, mutations that decrease the number of CpGs in oncogene promoter regions and mutations that create CpGs in tumor suppressor gene promoter regions have been observed [13]. In another study, mutations that lead to the removal or creation of CpGs in promoter regions of various genes involved in cancer, coronary artery disease, and diabetes mellitus were identified [14].…”

DNA Tandem Repeats as Iterable Objects to Count Cell Divisions: A Computational Model

“…SatDNA is actively methylated [21] and plays an important role in epigenetics [22] [23] [24]; epigenetic tools comprise specialized enzymes [25] able to recognize the particular 3D structure of their target sequences: "writers" [26] catalyze biochemical modifications (e.g. DNA methyltransferases: methylation on the 5th position of the pyrimidine ring of cytosine, C ↠ 5mC), "readers" [27] recognize and interpret the significance of such modifications and recruit a set of methyl CpG-binding proteins and "erasers" [28] remove methylations [29] [30] [31]. Hypomethylated TR arrays have been found in different human diseases, cancer, and psychiatric disorders [32].…”