Vertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5' T to 5' A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5' Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5' T and 5' A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation. CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.
AT Rich Sequence ; Animals ; CpG Islands ; genetics ; DNA Methylation ; GC Rich Sequence ; Gene Frequency ; Genome ; Genomics ; methods ; Humans ; Invertebrates ; genetics ; Isochores ; genetics ; Mutation ; Vertebrates ; genetics

OBJECTIVETo identify whether GC-box (-348 to -338) in human insulin gene promoter is a key cis-acting element.

METHODSHuman insulin gene promoter was sub-cloned into secreted alkaline phosphatase (SEAP) reporter plasmid. The deletion and mutation of GC-box in insulin gene promoter was performed. The activity of human insulin gene promoter was determined by evaluating the activity of SEAP in the supernatant of cell culture after the reporter plasmids were transfected in beta cell line betaTC3.

RESULTDeletion and mutation of GC box in human insulin gene promoter did not result in significant changes of the activity of the promoter in betaTC3.

CONCLUSIONThe GC-box is not a key cis-acting element in human insulin gene promoter.

Alkaline Phosphatase ; genetics ; metabolism ; Base Sequence ; Cell Line ; Enhancer Elements, Genetic ; GC Rich Sequence ; Gene Expression Regulation ; Humans ; Insulin ; genetics ; Promoter Regions, Genetic ; Recombinant Fusion Proteins ; genetics ; metabolism ; Sequence Deletion ; Transcription, Genetic ; Transfection

No abstract available.
CpG Islands* ; Methylation*

In forensic science practice, age is an important individual information, and one of the indicators to be considered first to depict features of the suspect. Recently, DNA methylation has become a research hotspot in age estimation because of its hig accuracy and stability. New progress has been made in specificity of DNA methylation sites, age estimation in multiple tissues, DNA methylation age estimation of minors, sensitivity of age estimation, forensic practical applications, etc. At the same time, several studies also established more accurate statistical modeling methods, eliminated differences between different detection platforms, found appropriate number of sites in models and analyzed the influence of environment and diseases. This review summarizes these to provide references.
CpG Islands ; DNA Methylation ; Forensic Genetics ; Humans

Colorectal cancer (CRC) has been assumed for many years to be a homogenous condition with the vast majority developing within preexisting-adenomas. However, over the last two-decades, it has become clear that CRC evolves through multiple pathways at the genetic and the epigenetic level. Each of these processes is associated with a unique genetic or epigenetic signature identifiable in the tumor cells. The pathway may be defined on the basis of three molecular features: 1) chromosomal instability (CIN), 2) microsatellite instability (MSI), and 3) CpG island methylator phenotype (CIMP). Those molecular pathways are determined at an early evolutionary stage and are fully established within early cancer. Recently, five subgroups were outlined by using morphological findings and associated molecular changes: type 1 (CIN-stable/ MSI-H/CIMP-H), type 2 (CIN-stable/MSI-L or MSS/ CIMP-H), type 3 (CIN-unstable/MSI-L or MSS/CIMP-L), type 4 (CIN-instable/MSS/CIMP-neg), and type 5 (CIN- stable/MSI-H/CIMP-neg). This approach to the classification of CRC should accelerate understanding of causation and will have an impact on clinical management in the areas of both prevention and treatment.
Chromosomal Instability ; Colorectal Neoplasms ; CpG Islands ; Epigenomics ; Microsatellite Instability ; Phenotype

Sinonasal mucosal melanoma (SMM) is an aggressive and rare type of melanoma. Although the classic RAS-RAF-MEK pathway is thought to be the main pathway involved in melanoma pathogenesis, genetic alterations in the phosphatidylinositol 3-kinase-AKT pathway, including PTEN-regulated signaling, are also thought to contribute. So far, data regarding altered PTEN expression and epigenetic mechanism of PTEN silencing in development of SMM is extremely limited. Herein we report on a case of SMM with liver and bone metastases with an epigenetic alteration of PTEN. Results of mutation analysis for BRAF, NRAS, HRAS, KRAS, PIK3CA, c-Kit, and PTEN were negative; however, methylation of PTEN CpG islands was observed. Our case not only supports PTEN as a major tumor suppressor involved in melanoma tumorigenesis, but also a potential epigenetic mechanism of PTEN silencing in development of SMM.
Carcinogenesis ; CpG Islands ; Epigenomics ; Liver ; Melanoma* ; Methylation* ; Neoplasm Metastasis ; Phosphatidylinositols

Sinonasal mucosal melanoma (SMM) is an aggressive and rare type of melanoma. Although the classic RAS-RAF-MEK pathway is thought to be the main pathway involved in melanoma pathogenesis, genetic alterations in the phosphatidylinositol 3-kinase-AKT pathway, including PTEN-regulated signaling, are also thought to contribute. So far, data regarding altered PTEN expression and epigenetic mechanism of PTEN silencing in development of SMM is extremely limited. Herein we report on a case of SMM with liver and bone metastases with an epigenetic alteration of PTEN. Results of mutation analysis for BRAF, NRAS, HRAS, KRAS, PIK3CA, c-Kit, and PTEN were negative; however, methylation of PTEN CpG islands was observed. Our case not only supports PTEN as a major tumor suppressor involved in melanoma tumorigenesis, but also a potential epigenetic mechanism of PTEN silencing in development of SMM.
Carcinogenesis ; CpG Islands ; Epigenomics ; Liver ; Melanoma* ; Methylation* ; Neoplasm Metastasis ; Phosphatidylinositols

CpG is the pair of nucleotides C and G, appearing successively, in this order, along one DNA strand. It is known that due to biochemical considerations CpG is relatively rare in most DNA sequences. However, in particular subsequences, which are a few hundred to a few thousand nucleotides long, the couple CpG is more frequent. These subsequences, called CpG islands, are known to appear in biologically more significant parts of the genome. The ability to identify CpG islands along a chromosome will therefore help us spot its more significant regions of interest, such as the promoters or 'start' regions of many genes. In this respect, I developed the CpG islands search tool, CpG Islands Detector, which was implemented in JAVA to be run on any platform. The window-based graphical user interface of CpG Islands Detector may facilitate the end user to employ this tool to pinpoint CpG islands in a genomic DNA sequence. In addition, this tool can be used to highlight potential genes in genomic sequences since CpG islands are very often found in the 5' regions of vertebrate genes.
Base Sequence ; CpG Islands ; DNA ; Genome ; Indonesia ; Nucleotides ; Vertebrates

With the improvement of DNA methylation detection techniques, studies on age-related methylation sites have found more age-specific ones across tissues, which improves the sensitivity and accuracy of age estimation. In addition, the establishment of various statistical models also provides a new direction for the age estimation of tissues from different sources. This review summarizes the related studies of age estimation based on DNA methylation from the aspects of detection technology, age-related cytosine phosphate guanine site and model selection in recent years.
DNA Methylation ; Forensic Genetics/methods* ; CpG Islands ; Forensic Medicine

PURPOSE: DNA methylation is a major epigenetic mechanism for modification of genetic expression without a change in the DNA sequence. MBD2 (methyl-CpG-binding domain 2 protein) belongs to a family of enzymes concerning of DNA demethylation and suppresses the hypermethylation of the CpG island and DNA transcription. In this study, we investigated the change of MBD2 expression in the blood and tissue of colorectal cancer patients and compared the two expression levels. METHODS: The 68 patients included in this study were patients with colorectal cancer who had undergone surgery at our hospital, and 50 other patients with no malignant disease were recruited from normal populations. Total RNA samples were isolated from whole blood samples and cancer tissues of specimens using a TRI REAGENT BD kit. MBD 2 expression was measured by real-time quantitative reverse transcription-polymerase chain reaction assays. RESULTS: The mean age was older in the case group than in the control group. The mean expression level of MBD2 in blood was not different between the two groups. In the case group, the tissue MBD2 expression was lower than the blood MBD2 expression under all conditions, and that difference was statistically significant (P<0.01). The expression of MBD2 in cancer tissue showed a negative correlation with that in the blood of cancer patients, correlation coefficient of R=0.073, but that result was not statistically significant (P=0.611). CONCLUSIONS: The blood MBD2 expression was statistically the same in the cancer and the control groups. In the cancer group, blood MBD2 expression was significantly higher than tissue MBD2 expression. The reverse correlation between blood MBD2 expression and tissue MBD2 expression in cancer patients suggests that MBD2 may affect the mechanism of carcinogenesis.
Base Sequence ; Colorectal Neoplasms ; CpG Islands ; DNA ; DNA Methylation ; Epigenomics ; Humans ; RNA