Transposable elements (TEs) make up approximately half of the human genome and can affect gene expression, chromatin accessibility, activate cell signalling pathways, RNA interference responses as well as trigger ageing and antiviral activities. Their study is challenging due to the high diversity in terms of sequences, loci and copy number in the genome. In this work we used RNA sequencing data to analyse the differential expression of TEs in children with COVID-19-associated inflammatory diseases before treatment, during flare, and at time of disease remission, after 6 months. The sample taken at remission was considered as control sample. The analysis was performed using the TEtranscripts bioinformatics tool and the GRCh38 and T2T-CHM13 reference genomes. The results of differential expression analysis performed by the tool showed 681 statistically significant differentially expressed TEs using GRCh38 and 738 using T2T-CHM13, with three TEs expressed using GRCh38 and two using T2T-CHM13 when filtering for |logFC| ≥ 2. All significant transposable elements with expression |logFC| ≥ 2 are expressed more in flare of disease than in the remission state, confirming the finding in literature that increased TE activity is characteristic of inflammatory state. The T2T-CHM13 reference genome as the first complete human genome provides a better reference for determining TE expression, however, the exact reasons for the differences with GRCh38 should be further investigated.
|
