Changes in transcription start sites of Zap1‐regulated genes during zinc deficiency: Implications for HNT1 gene regulation

Abstract

Changes in RNA are often poor predictors of protein accumulation. One factor disrupting this relationship are changes in transcription start sites (TSSs). Therefore, we explored how alterations in TSS affected expression of genes regulated by the Zap1 transcriptional activator of Saccharomyces cerevisiae. Zap1 controls their response to zinc deficiency. Among over 80 known Zap1-regulated genes, several produced long leader transcripts (LLTs) in one zinc status condition and short leader transcripts (SLTs) in the other. Fusing LLT and SLT transcript leaders to green fluorescent protein indicated that for five genes, the start site shift likely has little effect on protein synthesis.For four genes, however, the different transcript leaders greatly affected translation.We focused on the HNT1 gene. Zap1 caused a shift from SLT HNT1 RNA in zinc-replete cells to LLT HNT1 RNA in deficient cells. This shift correlated with decreased protein production despite increased RNA. The LLT RNA contains multiple upstream open reading frames that can inhibit translation. Expression of the LLT HNT1 RNA was dependent on Zap1. However, expression of the long transcript was not required to decrease SLT HNT1 mRNA. Our results suggest that the Zap1-activated LLT RNA is a "fail-safe" mechanism to ensure decreased Hnt1 protein in zinc deficiency. K E Y W O R D Spromoter regions, regulation, RNA, Saccharomyces cerevisiae, transcription factors, transcription start site, zinc

Identification and Functional Characterization of the RcFAH12 Promoter from Castor Bean in Arabidopsis thaliana

“…Therefore, this difference may be caused by different sampling periods of male flowers in the early study. Each promoter deletion fragment has at least one TSS, and the GUS staining results show that different promoter deletion fragments can drive the expression of the GUS gene in Arabidopsis thaliana, indicating that this result may be related to the selected TSS [36,37]. The RcFAH12 promoter deletions could drive GUS gene expression in anthers except for FP1611.…”

Swi/Snf Chromatin Remodeling Regulates Transcriptional Interference and Gene Repression

“…Case studies have revealed that diverse gene targets are subject to LUTI-based repression, including the genes encoding the kinetochore subunit Ndc80 (J. Chen et al, 2017;Chia et al, 2017), the superoxide dismutase enzyme Sod1 (Vander Wende et al, 2023), the transcription factor Swi4 (Su et al, 2023), and the purine hydrolase enzyme Hnt1 (Van Dalfsen et al, 2018;Tatip et al, 2020). Importantly, the observation that the human protooncogene MDM2 is subject to LUTI-based interference has revealed this form of gene repression is broadly conserved (Hollerer et al, 2019).…”

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

“…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).…”