Effects of lncRNAs expression containing‐ Alu on human cancer cells

Abstract

In humans, 11% of the genome density is composed by Alu with an approximately of 1.3 million copies, approximately one- third of all genes contain Alu sequences, mainly in their flanking regions. There are reports suggesting that Alu sequences may influence gene expression, providing binding sites for transcription factors. To the extent long non-coding RNAs (lncRNA) may be in intergenic and intragenic regions, the presence of Alu may enhance its expression. LncRNA are involved in mechanisms such as chromatin reprogramming, cis regulation in enhancers and post-transcription regulation of mRNA. In 2015 a database of 7,256 RNA-seq was published, where they identified 58,648 lncRNA genes, of which 72% are ubicated in intergenic regions. Interestingly, in was observe that this lncRNA are expressed at lower levels than the genes encoding the protein. Taking together, this database and with the Alu coordinates obtained from the UCSC Genome Browser, we found that the Alu elements are present in 69% proteins-coding genes, 70% in lncRNAs and 54% in pseudogenes, with a higher Alu density at the beginning of the gene at the 5ʹ, also 3ʹ shows an increase in Alu density, but is lower than in the 5ʹ region. In relation to the genetic context, 93% of the Alus are present genes are found in the introns, as has previously been reported by several authors. The later, we focus on the expression of lncRNA because it is where there is the greatest abundance with respect to the total number of transcriptions, we analyze the tissue or cell line with primary tumors, with metastasis or tissues without tumors. We found that Alu position has effects of expression in the final region of the gene, mainly a higher expression in cancerous tissue, suggesting that Alu position in cancerous tissues may be recognized to activate the expression of lncRNAs.