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LINE-1 methylation patterns of different loci in normal and cancerous cells.

Phokaew C, Kowudtitham S, Subbalekha K, Shuangshoti S, Mutirangura A - Nucleic Acids Res. (2008)

Bottom Line: Therefore, the loss of genome-wide methylation in cancerous cells occurs as a generalized process.However, different LINE-1 loci showed different incidences of HNSCC hypomethylation, which is a lower methylation level than NOE.In conclusion, even though the global hypomethylation process that occurs in cancerous cells can generally deplete LINE-1 methylation levels, LINE-1 methylation can be influenced differentially depending on where the particular sequences are located in the genome.

View Article: PubMed Central - PubMed

Affiliation: Inter-Department Program of BioMedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.

ABSTRACT
This study evaluated methylation patterns of long interspersed nuclear element-1 (LINE-1) sequences from 17 loci in several cell types, including squamous cell cancer cell lines, normal oral epithelium (NOE), white blood cells and head and neck squamous cell cancers (HNSCC). Although sequences of each LINE-1 are homologous, LINE-1 methylation levels at each locus are different. Moreover, some loci demonstrate the different methylation levels between normal tissue types. Interestingly, in some chromosomal regions, wider ranges of LINE-1 methylation levels were observed. In cancerous cells, the methylation levels of most LINE-1 loci demonstrated a positive correlation with each other and with the genome-wide levels. Therefore, the loss of genome-wide methylation in cancerous cells occurs as a generalized process. However, different LINE-1 loci showed different incidences of HNSCC hypomethylation, which is a lower methylation level than NOE. Additionally, we report a closer direct association between two LINE-1s in different EPHA3 introns. Finally, hypermethylation of some LINE-1s can be found sporadically in cancer. In conclusion, even though the global hypomethylation process that occurs in cancerous cells can generally deplete LINE-1 methylation levels, LINE-1 methylation can be influenced differentially depending on where the particular sequences are located in the genome.

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Related in: MedlinePlus

Correlation between the bands of CU-L1. Pixel counts of CU-L1 fluorescent intensities from 19 cell lines, 12 WBCs and 12 NOEs are shown. Examples of two LINE-1 loci are shown. (A and B) Comparison between methylated bands. (C and D) Comparison between unmethylated bands. (A and C) The L1-EPHA3-IVS5 locus. (B and D) The L1-MGC4217 locus. Each band was named according to the restriction enzymes and sizes of the digested fragment. Most samples demonstrate a linear correlation. The arrow indicates a striking deviation of the 151-bp TaqI band from the same sample.
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Figure 2: Correlation between the bands of CU-L1. Pixel counts of CU-L1 fluorescent intensities from 19 cell lines, 12 WBCs and 12 NOEs are shown. Examples of two LINE-1 loci are shown. (A and B) Comparison between methylated bands. (C and D) Comparison between unmethylated bands. (A and C) The L1-EPHA3-IVS5 locus. (B and D) The L1-MGC4217 locus. Each band was named according to the restriction enzymes and sizes of the digested fragment. Most samples demonstrate a linear correlation. The arrow indicates a striking deviation of the 151-bp TaqI band from the same sample.

Mentions: We designed the CU-L1 PCR to constitute several digested fragments, including methylated, unmethylated and control, which are without candidate CpG restriction sequences, so that we could check for multiple CpG dinucleotides containing TaqI sites and an unmethylated CpG containing TasI site. Therefore, the intensities of each methylated and unmethylated band could be measured to compare the methylation status among several CpG nucleotides. Figure 2A and B provides examples of the positive linear correlation between methylated fragments from the CU-L1 locations. Direct correlations between unmethylated fragments were also demonstrated (Figure 2C and D). Therefore, the methylation levels of the representative COBRALINE-1 TaqI and TasI sites represent methylation levels of each LINE-1 in a positive correlated fashion.Figure 2.


LINE-1 methylation patterns of different loci in normal and cancerous cells.

Phokaew C, Kowudtitham S, Subbalekha K, Shuangshoti S, Mutirangura A - Nucleic Acids Res. (2008)

Correlation between the bands of CU-L1. Pixel counts of CU-L1 fluorescent intensities from 19 cell lines, 12 WBCs and 12 NOEs are shown. Examples of two LINE-1 loci are shown. (A and B) Comparison between methylated bands. (C and D) Comparison between unmethylated bands. (A and C) The L1-EPHA3-IVS5 locus. (B and D) The L1-MGC4217 locus. Each band was named according to the restriction enzymes and sizes of the digested fragment. Most samples demonstrate a linear correlation. The arrow indicates a striking deviation of the 151-bp TaqI band from the same sample.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553567&req=5

Figure 2: Correlation between the bands of CU-L1. Pixel counts of CU-L1 fluorescent intensities from 19 cell lines, 12 WBCs and 12 NOEs are shown. Examples of two LINE-1 loci are shown. (A and B) Comparison between methylated bands. (C and D) Comparison between unmethylated bands. (A and C) The L1-EPHA3-IVS5 locus. (B and D) The L1-MGC4217 locus. Each band was named according to the restriction enzymes and sizes of the digested fragment. Most samples demonstrate a linear correlation. The arrow indicates a striking deviation of the 151-bp TaqI band from the same sample.
Mentions: We designed the CU-L1 PCR to constitute several digested fragments, including methylated, unmethylated and control, which are without candidate CpG restriction sequences, so that we could check for multiple CpG dinucleotides containing TaqI sites and an unmethylated CpG containing TasI site. Therefore, the intensities of each methylated and unmethylated band could be measured to compare the methylation status among several CpG nucleotides. Figure 2A and B provides examples of the positive linear correlation between methylated fragments from the CU-L1 locations. Direct correlations between unmethylated fragments were also demonstrated (Figure 2C and D). Therefore, the methylation levels of the representative COBRALINE-1 TaqI and TasI sites represent methylation levels of each LINE-1 in a positive correlated fashion.Figure 2.

Bottom Line: Therefore, the loss of genome-wide methylation in cancerous cells occurs as a generalized process.However, different LINE-1 loci showed different incidences of HNSCC hypomethylation, which is a lower methylation level than NOE.In conclusion, even though the global hypomethylation process that occurs in cancerous cells can generally deplete LINE-1 methylation levels, LINE-1 methylation can be influenced differentially depending on where the particular sequences are located in the genome.

View Article: PubMed Central - PubMed

Affiliation: Inter-Department Program of BioMedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.

ABSTRACT
This study evaluated methylation patterns of long interspersed nuclear element-1 (LINE-1) sequences from 17 loci in several cell types, including squamous cell cancer cell lines, normal oral epithelium (NOE), white blood cells and head and neck squamous cell cancers (HNSCC). Although sequences of each LINE-1 are homologous, LINE-1 methylation levels at each locus are different. Moreover, some loci demonstrate the different methylation levels between normal tissue types. Interestingly, in some chromosomal regions, wider ranges of LINE-1 methylation levels were observed. In cancerous cells, the methylation levels of most LINE-1 loci demonstrated a positive correlation with each other and with the genome-wide levels. Therefore, the loss of genome-wide methylation in cancerous cells occurs as a generalized process. However, different LINE-1 loci showed different incidences of HNSCC hypomethylation, which is a lower methylation level than NOE. Additionally, we report a closer direct association between two LINE-1s in different EPHA3 introns. Finally, hypermethylation of some LINE-1s can be found sporadically in cancer. In conclusion, even though the global hypomethylation process that occurs in cancerous cells can generally deplete LINE-1 methylation levels, LINE-1 methylation can be influenced differentially depending on where the particular sequences are located in the genome.

Show MeSH
Related in: MedlinePlus