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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

CU-L1 methylation levels. (A) NOE and WBC, (B) NOE and epithelial cell lines, (C) NOE and HNSCC. Each dot represents means ± SD each CU-L1 methylation level. Dashed and solid lines connect the measurements from the same samples.
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Figure 4: CU-L1 methylation levels. (A) NOE and WBC, (B) NOE and epithelial cell lines, (C) NOE and HNSCC. Each dot represents means ± SD each CU-L1 methylation level. Dashed and solid lines connect the measurements from the same samples.

Mentions: A general concern with the COBRA method is the misinterpretation of cases of a mutation or polymorphism at a restriction site. For COBRALINE-1, this type of error is irrelevant because of the vast number of targeted LINE-1 sequences in the genome (4). For CU-L1, we were able to check for the possibility of a mutation error. If there is a mutation at the TaqI restriction site, for example TCGA to TTGA, then the homozygous or heterozygous polymorphic sample will result in a false positive as completely unmethylated for two or one alleles, respectively. Therefore, CU-L1 methylation levels should dramatically deviate from the linear correlation of the linked CpGs. However, striking deviation was rare when methylation levels between CpGs were compared (Figure 2A). Nevertheless, because CU-L1 contains several methylated and unmethylated fragments, alternative sites could be selected if the density of the representative sites deviated strikingly from the group (Figure 2A). Moreover, in normal cells, particularly WBCs, CU-L1s of most loci usually demonstrated methylation levels in a limited range without a striking deviation (Figure 4A). In conclusion, mutations or polymorphisms of these CU-L1 restriction sites are rare and several informative amplicons help prevent interpretation errors.Figure 4.


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)

CU-L1 methylation levels. (A) NOE and WBC, (B) NOE and epithelial cell lines, (C) NOE and HNSCC. Each dot represents means ± SD each CU-L1 methylation level. Dashed and solid lines connect the measurements from the same samples.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: CU-L1 methylation levels. (A) NOE and WBC, (B) NOE and epithelial cell lines, (C) NOE and HNSCC. Each dot represents means ± SD each CU-L1 methylation level. Dashed and solid lines connect the measurements from the same samples.
Mentions: A general concern with the COBRA method is the misinterpretation of cases of a mutation or polymorphism at a restriction site. For COBRALINE-1, this type of error is irrelevant because of the vast number of targeted LINE-1 sequences in the genome (4). For CU-L1, we were able to check for the possibility of a mutation error. If there is a mutation at the TaqI restriction site, for example TCGA to TTGA, then the homozygous or heterozygous polymorphic sample will result in a false positive as completely unmethylated for two or one alleles, respectively. Therefore, CU-L1 methylation levels should dramatically deviate from the linear correlation of the linked CpGs. However, striking deviation was rare when methylation levels between CpGs were compared (Figure 2A). Nevertheless, because CU-L1 contains several methylated and unmethylated fragments, alternative sites could be selected if the density of the representative sites deviated strikingly from the group (Figure 2A). Moreover, in normal cells, particularly WBCs, CU-L1s of most loci usually demonstrated methylation levels in a limited range without a striking deviation (Figure 4A). In conclusion, mutations or polymorphisms of these CU-L1 restriction sites are rare and several informative amplicons help prevent interpretation errors.Figure 4.

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