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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-L1s bisulfite sequences. CU-L1s bisulfite sequenced methylated CpG dinucleotides and non-methylated CpGs of each clone are illustrated with closed and open circles, respectively. The 80-bp (methylated) and 98-bp (unmethylated) TasI-digested fragments are the 20th and 19th CpGs, respectively. Sample names and CU-L1 methylation levels are shown on the left.
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Figure 3: CU-L1s bisulfite sequences. CU-L1s bisulfite sequenced methylated CpG dinucleotides and non-methylated CpGs of each clone are illustrated with closed and open circles, respectively. The 80-bp (methylated) and 98-bp (unmethylated) TasI-digested fragments are the 20th and 19th CpGs, respectively. Sample names and CU-L1 methylation levels are shown on the left.

Mentions: To evaluate the relationship among all of the 5′ LINE-1 CpGs, CU-L1 amplicons were cloned and sequenced. Figure 3 demonstrates examples of CU-L1 sequences. Direct correlation of methylation levels between CU-L1 and bisulfite sequencing can be observed. Both CU-L1 and bisulfite sequences demonstrated low L1-LRP2 methylation levels in WSU-HN 6 and 22 cells and high methylation levels in WSU-HN 26 cells, compared with a sample of NOE. Therefore, CU-L1 methylation levels were applied to compare methylation levels between each DNA sample. The bisulfite sequences (Figure 3) demonstrated that even though they were directly correlated, the methylation statuses of the CpG dinucleotides from 5′ LINE-1 are not equally distributed. We found that the CpGs around TaqI and TasI COBRALINE-1 digested sites might be more prone to be demethylation than others (Figure 3).Figure 3.


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-L1s bisulfite sequences. CU-L1s bisulfite sequenced methylated CpG dinucleotides and non-methylated CpGs of each clone are illustrated with closed and open circles, respectively. The 80-bp (methylated) and 98-bp (unmethylated) TasI-digested fragments are the 20th and 19th CpGs, respectively. Sample names and CU-L1 methylation levels are shown on the left.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: CU-L1s bisulfite sequences. CU-L1s bisulfite sequenced methylated CpG dinucleotides and non-methylated CpGs of each clone are illustrated with closed and open circles, respectively. The 80-bp (methylated) and 98-bp (unmethylated) TasI-digested fragments are the 20th and 19th CpGs, respectively. Sample names and CU-L1 methylation levels are shown on the left.
Mentions: To evaluate the relationship among all of the 5′ LINE-1 CpGs, CU-L1 amplicons were cloned and sequenced. Figure 3 demonstrates examples of CU-L1 sequences. Direct correlation of methylation levels between CU-L1 and bisulfite sequencing can be observed. Both CU-L1 and bisulfite sequences demonstrated low L1-LRP2 methylation levels in WSU-HN 6 and 22 cells and high methylation levels in WSU-HN 26 cells, compared with a sample of NOE. Therefore, CU-L1 methylation levels were applied to compare methylation levels between each DNA sample. The bisulfite sequences (Figure 3) demonstrated that even though they were directly correlated, the methylation statuses of the CpG dinucleotides from 5′ LINE-1 are not equally distributed. We found that the CpGs around TaqI and TasI COBRALINE-1 digested sites might be more prone to be demethylation than others (Figure 3).Figure 3.

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