Transcriptional lockdown during acute proteotoxic stress

Abstract

Cells experiencing proteotoxic stress downregulate the expression of thousands of active genes and upregulate a few stress-response genes. The strategy of downregulating gene expression has conceptual parallels with general lockdown in the global response to the coronavirus disease 2019 (COVID-19) pandemic. The mechanistic details of global transcriptional downregulation of genes, termed stress-induced transcriptional attenuation (SITA), are only beginning to emerge. The reduction in RNA and protein production during stress may spare proteostasis capacity, allowing cells to divert resources to control stress-induced damage. Given the relevance of translational downregulation in a broad variety of diseases, the role of SITA in diseases caused by proteotoxicity should be investigated in future, paving the way for potential novel therapeutics.

Keywords: NELF; RNA polymerase II; heat shock; proteostasis; transcription.

Figure 1

Global transcriptional changes caused by heat shock in metazoan. (A,B) Autoradiographs of drosophila salivary polytene chromosomes after exposure to normal (A) or heat-shock (B) temperatures. The chromosomes were treated to perform in situ hybridization with H³-labeled mRNA. The red box indicates the position of the 'heat-shock puff' representing chaperone HSP70 induction. The blue boxes indicate arms of chromosomes with transcription under normal conditions that is downregulated during heat shock. Panels (A) and (B) reproduced, with permission, from Spradling et al. [14]. (C) A summary histogram showing the number of upregulated and downregulated genes in heat-shocked cells in four independent studies. Cell type used in the study, stress regimes, and techniques used to assay nascent transcription in each study are indicated in the table below the histogram. Abbreviations: PRO-seq, precision run-on sequencing. See also [1,15., 16., 17.].

Figure 2

Molecular mechanisms underlying stress-induced transcriptional attenuation. (A) A schematic illustration showing various steps during mRNA transcription by Pol II that are subject to potential regulation by stress. The steps are numbered in the schematic as follows: initiation and RNA Pol II complex assembly (1), promoter-proximal Pol II subject to transition to elongation (2) or release from chromatin (3), elongating Pol II subject to regulation of speed (4) and premature termination (5), and termination of Pol II after full mRNA transcription (6). (B) The current understanding of the likely regulation of Pol II at stress-induced transcriptional attenuation (SITA) target genes under unstressed and stressed conditions. The black stars denote phosphorylation mediated by positive transcription elongator factor b (P-TEFb). Stress leads to a decrease in the active P-TEFb pool. (C) Additional regulatory layers of transcription in the context of chromatin that may be affected by stress. Abbreviations: NELF, negative elongation factor; DSIF, DRB-sensitivity-inducing factor.

Figure 3

Stress-induced signaling and dynamic compartmentalization in the nucleus and the cytosol. (A) A schematic illustration showing our current understanding of stress signaling leading to stress-induced transcriptional attenuation (SITA). Nascent polypeptides on the ribosome are subject to polyubiquitination, activating p38 kinase and its translocation to the promoters of downregulated genes. Polyubiquitin denotes a chain of ubiquitin proteins added to the nascent polypeptide. (B,C) Confocal images showing nuclear negative elongation factor (NELF) condensates (B) and cytosolic stress granules (C) formed as a result of heat shock in HeLa cells. Markers of the nuclear and cytosolic granules are indicated. Abbreviation: DAPI, 4′,6-diamidino-2-phenylindole. (B) Reproduced, with permission, from Rawat et al. [40] and (C) reproduced, with permission, from Cirillo et al. [53].