Abstract
Long interspersed elements (LINEs or L1 s) are an abundant class of autonomous retrotransposons in the human genome. Full-length L1 elements have two transcriptional regulatory regions: an internal sense promoter and an antisense promoter (ASP). The ASP of L1 elements can generate chimeric RNAs via direct transcription of adjacent genomic sequences. Chimeric transcripts derived from the L1ASP are highly represented, but the extent to which this occurs is largely unknown. Using a genome-wide L1 chimera display (LCD) technique, we have isolated 4 L1 chimeric transcripts (LCTs) in the lung cancer genome. Then, we analyzed the structural characteristics of the 4 LCTs using bioinformatics tool. Expression patterns of the 4 LCTs were analyzed by reverse transcription polymerase chain reaction using normal and lung cancer tissues. LCT24 and LCT25 showed higher expression in lung cancer tissue than in normal tissue. These results suggest that the genome-wide LCD technique could be of great use for further study to find cancer markers via cancer-associated LCTs and to understand cancer biology.
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Acknowledgments
The biospecimens for this study were provided by the Pusan National University Hospital, a member of the National Biobank of Korea, which is supported by the Ministry of Health, Welfare and Family Affairs. All samples derived from the National Biobank of Korea were obtained with informed consent under institutional review board-approved protocols. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012R1A1A4A01001616).
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13258_2014_220_MOESM1_ESM.pptx
Figure S1. Scheme of the L1 chimera display (LCD) technique. (A) Schematic representation of the LCD technique. First, cDNA was synthesized from total RNA in normal lung and lung cancer tissues. Second, the cDNA was digested with a restriction enzyme that does not cut in the L1 antisense promoter (ASP) region, and complementary adapters were ligated with the digested cDNA. Last, nested PCR was carried out using L1-specific primers and linker primers. (B) Visualization of LCD products from lung normal and tumor tissues. GAPDH (120 bp) indicates the positive control. M indicates the size marker. (PPTX 124 kb)
13258_2014_220_MOESM2_ESM.ppt
Figure S2. Hairpin structure analysis of the MER20 element in LCT 24. (A) Palindromic MER20 secondary structure was predicted using the RNAfold program. The minimum free energy (mfe) was -58.60 kcal/mol, and the sequence size was 226 bp. (B) The precursor form of MER20-derived miRNA is presented, and the mature form is indicated by the line. (PPT 233 kb)
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Lee, JR., Jung, YD., Kim, YJ. et al. Identification of L1ASP-derived chimeric transcripts in lung cancer. Genes Genom 36, 853–859 (2014). https://doi.org/10.1007/s13258-014-0220-y
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DOI: https://doi.org/10.1007/s13258-014-0220-y