BAM files for long read alignments

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence, <i>Senescence Associated Long Non-coding RNA</i> (<i>SALNR</i>) was found to be down-regulated in different cellular models of senescence. Since its release in 2015, <i>SALNR</i> has not been annotated in any database or public repository, and no other experimental data have been published. The <i>SALNR</i> sequence is located on the long arm of chromosome 10, at band 10q23.33, and it overlaps the 3’ end of the <i>HELLS</i> gene. This investigation helped to unravel the mystery of the existence of <i>SALNR</i> by analyzing publicly available short- and long-read RNA sequencing data sets and RT-PCR analysis in human tissues and cell lines. Additionally, the expression of <i>HELLS</i> has been studied in cellular models of replicative senescence, both <i>in silico</i> and <i>in vitro</i>. Our findings, while not supporting the actual existence of <i>SALNR</i> as an independent transcript in the analyzed experimental models, demonstrate the expression of a predicted <i>HELLS</i> isoform entirely covering the <i>SALNR</i> genomic region. Furthermore, we observed a strong down-regulation of <i>HELLS</i> in senescent cells versus proliferating cells, supporting its role in the senescence and aging process.