Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends

Abstract

Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.

5’ extended protein-codingINO80Etranscript regulates expression of two head-to-head overlapping genes:INO80EandHIRIP3

“…Similarly, a positive expression correlation was found when data was divided according to the tumor type and the organ system (Supplementary materials, Figure S1A and S1B). These results confirm our previous report, demonstrating a positive correlation of expression of 5’ overlapping genes (Rosikiewicz et al 2021).…”

“…One possible consequence is that TI may cause a decrease in the level of gene expression, however, there are studies that do not confirm such a pattern (C. H. Chen, Pan, and Lin 2019; Ning et al 2017; Zhou and Blumberg 2003). Our previous analyses have shown that expression of genes utilizing an TSS which is overlapping at the 5’ end with gene on the opposite DNA strand, is on average higher than when the same genes use only none overlapping TSSs (Rosikiewicz et al 2021).…”

“…Our previous studies, however, did not demonstrate any negative effects due to gene overlap. In contrast, genes utilizing overlapping TSSs had, on average, higher expression levels than the same genes utilizing only non-overlapping TSSs (Rosikiewicz et al 2021). Therefore, the head-to-head overlap of INO80E and HIRIP3 genes raises important questions on how their expression is regulated and what is the role of overlapping transcripts.…”

“…There are also genes that use multiple TSSs for transcription - proximal and more distal. When they use the distal TSS/TSSs, there is an overlap with the gene on the other strand of the DNA, however, when they use only proximal TSS/TSSs, the overlap does not occur (Rosikiewicz et al 2021). This dynamically changes under the influence of various intra- and extra-cellular conditions (Makhnovskii et al 2022; Rosikiewicz et al 2021; Tatip et al 2020).…”

“…When they use the distal TSS/TSSs, there is an overlap with the gene on the other strand of the DNA, however, when they use only proximal TSS/TSSs, the overlap does not occur (Rosikiewicz et al 2021). This dynamically changes under the influence of various intra- and extra-cellular conditions (Makhnovskii et al 2022; Rosikiewicz et al 2021; Tatip et al 2020). It has been described that changes in the TSSs used by certain genes have a translation regulatory function, e.g., in cancers, such as squamous cell carcinomas (Weber et al 2022) and during cerebellar development (P. Zhang et al 2017).…”