Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

Abstract

Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.

Combined assessment of MHC binding and antigen abundance improves T cell epitope predictions

“…The background dataset was generated as follows: for each peptide in the Trolle set, ten peptides were randomly picked from the human proteome. As RNA expression data were not included in the Trolle study, we retrieved RNA-Seq data of HeLa cells from another previously published study (Cantarella et al, 2019) and used the provided UniProt identifiers of the ligand source proteins to annotate the corresponding expression level measured as transcripts per million (TPM). Next, we performed HLA class I binding predictions for each ligand and random background peptide using the NetMHCpan 4.1 algorithm (Jurtz et al, 2017).…”

“…As expression data was not included in the Trolle study, we retrieved expression data of HeLa cells from another previously published study (Cantarella et al, 2019). We downloaded raw read data from the Gene Expression Omnibus database under accession number GEO: GSM3899456 and used an in-house pipeline to process the raw RNA-Seq data and calculate gene expression as transcripts per million (TPM).…”

Coordination of transcription and processing of tRNA

“…A mature tRNA has 5 0 -P and 3 0 -OH end termini and after CCA addition (CCA) and aminoacylation (aa) leaves the nucleus to the cytoplasm by active transport through a nuclear pore complex (NPC). thousands of Alu elements, which belong to the short interspersed nuclear element (SINE) family of retrotransposons and count ~1.2 million copies covering approximately one tenth of the genome [57][58][59]. Pol III has seventeen protein subunits [60][61][62], three of which form a specific subcomplex, RPC3-RPC6-RPC7, implicated in promoter-dependent initiation and elongation [52,62,63,64,65,66,67].…”

Combined assessment of MHC binding and antigen expression improves T cell epitope predictions

“…As expression data was not included in the Trolle study, we retrieved expression data of HeLa cells from another previously published study 27 . We downloaded raw read data from the Gene Expression Omnibus database under accession number GSM3899456 and used an in-house pipeline to process the raw RNA-Seq data and calculate gene expression as transcripts per million (TPM).…”