Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle

Abstract

Background More than half of human protein-coding genes have an alternative transcription start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute-stress-induced transcriptome response in human tissue (skeletal muscle) using the cap analysis of gene expression approach. TSSs were examined at baseline and during recovery after acute stress (a cycling exercise). Results We identified 44,680 CAGE TSS clusters (including 3764 first defined) belonging to 12,268 genes and annotated for the first time 290 TSSs belonging to 163 genes. The transcriptome dynamically changes during the first hours after acute stress; the change in the expression of 10% of genes was associated with the activation of alternative TSSs, indicating differential TSSs usage. The majority of the alternative TSSs do not increase proteome complexity suggesting that the function of thousands of alternative TSSs is associated with the fine regulation of mRNA isoform expression from a gene due to the transcription factor-specific activation of various alternative TSSs. We identified individual muscle promoter regions for each TSS using muscle open chromatin data (ATAC-seq and DNase-seq). Then, using the positional weight matrix approach we predicted time course activation of “classic” transcription factors involved in response of skeletal muscle to contractile activity, as well as diversity of less/un-investigated factors. Conclusions Transcriptome response induced by acute stress related to activation of the alternative TSSs indicates that differential TSSs usage is an essential mechanism of fine regulation of gene response to stress stimulus. A comprehensive resource of accurate TSSs and individual promoter regions for each TSS in muscle was created. This resource together with the positional weight matrix approach can be used to accurate prediction of TFs in any gene(s) of interest involved in the response to various stimuli, interventions or pathological conditions in human skeletal muscle.

SARS-CoV-2 shifts transcription of host gene to increase Spike acylation and boost infectivity

“…Alternative promoters are not unusual and have been found for about half of human genes (10,11). The usage of alternative TSSs, recently described as a conserved stress-response mechanism, however seems to be aimed at fine-tuning mRNA expression without altering the proteome (12), in contrast to what we observed here. Noteworthy, genomic analyses predict the possible synthesis of N-terminally extended versions of ZDHHC20, similar to the one induced by SARS-CoV-2 infection of human cells, in a wide range of animal species, including many mammals, fishes, amphibians and the fruit fly (Fig.…”

“…Given the proposed association between alternative transcription and stress (12), and the fact that ZDHHC20 Long is expressed physiologically in the upper intestinal tract, we wondered whether the expression of ZDHHC20 Long could be triggered in the colon in response to stress. Mice were treated orally with dextran sodium sulfate (DSS), a well-established chemically induced colitis model (18), for 7 days and then allowed 3 days of recovery, after which we assessed zdhhc20 expression.…”

Age‐related changes in human skeletal muscle transcriptome and proteome are more affected by chronic inflammation and physical inactivity than primary aging

“…org/ index. php/ Search_ for_ enric hed_ TFBSs_ (tracks)_(analysis)) using the PWM database TRANSFAC v2022.2, as described elsewhere (Makhnovskii et al, 2022). Briefly, the maximum fold enrichment (FE adj , statistically corrected odds ratios with a confidence interval of 99%) was determined for each PWM (site frequency ≤1 per 2000 bp) relative to that in 5000 random individual promoters showing no differential expression in any of the experimental groups (DESeq2 method, p adj > 0.4).…”

Age-related changes in human skeletal muscle transcriptome and proteome are more affected by chronic inflammation and physical inactivity than primary aging

“…To predict transcription factors associated with primary aging genes, the individual promoter regions identified for human skeletal muscle were investigated by gene-specific positions of the transcription start site and open chromatin (Makhnovskii et al, 2022). Enrichment of the transcription factor binding sites (and corresponding transcription factors) in individual promoter regions of genes associated with primary aging was performed by the GeneXplain platform (the "Search for enriched TFBSs (tracks)" function http://wiki.biouml.org/index.php/Search_for_enriched_TFBSs_(tracks)_(analysis)) using the PWM database TRANSFAC v2022.2, as described elsewhere (Makhnovskii et al, 2022). Briefly, if a transcription factor has several PWM, the most enriched PWM was used.…”