Expression of L1 Retrotransposon-Initiated Fusion Transcripts (L1 RIFTs) in Human Embryonic Stem Cells
Open AccessIn the past 15 years, scientists have learned much about the contribution of the L1 retrotransposon to genomic variation and human evolution. However, the contribution of L1 to transcriptional variation is still unclear. L1 has been reported to cause transcriptional attenuation, premature polyadenylation, alternate splice isoforms, chromatin remodeling, and transcription initiations. These mechanisms by which L1 can create transcriptional variation have been observed in a few instances so far and are not comprehensive. Considering that there are over 500,000 L1 elements in the human genome out of which 3,657 are full-length, we do not have a clear understanding of the extent to which these mechanisms occur throughout the genome. The goal of this project was to identify transcripts initiated from specific L1 retrotransposons in the genome. In this dissertation, two different approaches were used identify retrotransposon expression. Aim 1 attempted to determine whether L1 is expressed in rat aortic smooth muscle cells by using techniques such as microarray, Northern blotting, and Western blotting. In Aim 2, L1-containing cDNA inserts from the UC06 human embryonic stem cell cDNA library were PCR amplified, subcloned, sequenced, and characterized. The results revealed the presence of previously unidentified L1 retrotransposon-initiated fusion transcripts (L1 RIFTs) derived from L1 antisense promoter activity. These transcripts may represent alternate transcriptional start sites or possible substrates for RNA silencing via antisense sequence homology. Other L1 RIFTs were also identified based on 3' downstream flanking sequences. Additionally, expression of these L1 RIFTs is decreased in differentiated Caco-2 cells. Several L1 RIFTs also exhibit decreased expression in metastatic SW620 colon cancer cells as compared to non-metastatic SW480 cells. This observation suggests that L1 RIFT expression is not only associated with the cancer phenotype alone, but it may also be inversely associated with cancer invasion potential.
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