Detection of low-level gene induction using in vitro transcription heat shock genes

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.

Mapping of the mouse 86-kDa heat-shock protein expressed gene (Hsp86-1) on chromosome 12 and related genes on chromosomes 3, 4, 9, and 11

The HSP86 gene family in BALB/c, AKR/J, C58/J, and NFS/N inbred mice comprises an intron-containing expressed gene and, depending on the strain, two to four other HSP86-related members that are apparently processed pseudogenes. The expressed gene locus, Hsp86-1, was identified by its sequence identity with the mouse HSP86 cDNA coding region together with the presence of an intron at the same position as in the homologous human gene. Hsp86-1 was mapped 11.6 cM from the immunoglobulin heavy chain gene IgH on Chromosome 12 using an intersubspecies backcross. Two of the other loci that were common to all inbred strains tested, designated Hsp86-ps1 and Hsp86-ps2, were mapped to positions on Chromosomes 11 and 3, respectively. An HSP86-related locus specific to NFS/N and C58/J mice, designated Hsp86-ps3, was mapped on Chromosome 9. Also, an HSP86-related locus that was unique to NFS/N mice, designated Hsp86-ps4, was mapped to Chromosome 4.

On the mechanism of action of H2O2 in the cellular stress

We propose a hypothesis according to which the reactive and reduced species of oxygen could be the intracellular inducers of the stress (or "heat-shock") response. This hypothesis is based on the following observations on Drosophila cells: a) the return to normoxia after 24 h anaerobiosis is sufficient to induce the synthesis of the "heat shock" proteins without elevation of temperature together with a rapid increase of O2 consumption; b) hydrogen peroxide introduced in the culture medium induces the early transcriptional activation of the "heat shock" genes (maximal after 5 minutes); c) hydrogen peroxide added to cellular extracts in vitro (thus acting as an intracellular metabolite) activates instantaneously the binding capacity of a "heat shock" factor to a DNA "heat shock" regulatory element. Thus, hydrogen peroxide, and possibly other reactive reduced species of oxygen, could trigger the onset of the stress (or "heat shock") response.

Characterization of the mouse 84-kD heat shock protein gene family

The nucleotide sequence of a 6-kb region containing the gene for mouse 84-kD heat shock protein, HSP84, was determined. The hsp84 gene codes for a 5,500-base transcript and consists of 11 exons and 10 introns, ranging in length from 94 to 357 bp and 85 to 1,271 bp, respectively. One of the exons codes for a stretch of highly charged amino acids with two known phosphorylation sites. The presence of numerous introns in the hsp84 gene suggests that synthesis of the HSP84 protein would be precluded during severe heat shock, since such conditions interfere with splicing. The first intron, which is the largest, is located at the exact boundary between the 5'-untranslated region and the coding region and contains a sequence homologous to the heat shock element (HSE), an enhancer that is a characteristic feature of heat-inducible genes. A 71% homology was found between a 569-bp stretch within the first intron of the hsp84 gene, which includes the HSE-like sequence, and a portion of the first intron of the previously reported sequence of the human hsp89 beta gene. The promoter region of the hsp84 gene contained G + C-rich upstream sequences, potential binding sites for transcription factor Sp1, and a canonical TATA box. The hsp84 gene family includes at least six different hsp84-related pseudogenes, which arose about 2-3 million years ago.

Hydrogen peroxide activates immediate binding of a Drosophila factor to DNA heat-shock regulatory element in vivo and in vitro

The synthesis of heat-shock proteins via activation of heat-shock genes occurs in response to heat and various physical or chemical stressing agents. Transcriptional activation of heat-shock genes requires a heat-shock regulatory element in their promoter, to which a heat-shock specific transcription factor binds. In Drosophila cells, the heat-shock factor already exists in unstressed cells in an inactive form and acquires the capacity to bind to the heat-shock element following stress. The mechanism of this activation is not known: neither is it known whether the different stressing agents induce the heat-shock response through a common mechanism. We previously proposed that many agents known to induce the heat-shock response (substances interfering with respiratory metabolism, agents reacting with sulphydryl groups, metals, recovery from anaerobiosis and ischemia) might act via accumulation of reactive oxygen species, i.e. superoxide ion or H2O2. We show here that H2O2, introduced either in Drosophila cell cultures or in cell extracts, was able to activate heat-shock-element binding. Activation was rapid and H2O2 concentration dependent, with a threshold of 1 microM. These results were confirmed with mouse fibroblast cells. This very rapid activation, in vivo or in vitro, suggests a direct effect of H2O2 either on the heat-shock factor itself or on its activator.

Early activation of heat shock genes in H2O2-treated Drosophila cells

Drosophila cells of a diploid clone derived from line Kc were treated with 1 mM H2O2 for 1 to 20 minutes. Dot blot and Northern blot analysis of RNAs extracted from control and treated cells showed that the transcriptional activation of the 6 heat-shock genes tested was early, and maximal within 5 minutes of H2O2 treatment. Analysis of the kinetics of induction of the heat-shock proteins (hsps) after an exposure to H2O2 of 2 or 5 minutes, followed by removal, suggests that this brief treatment was sufficient to trigger the synthesis of all the hsps, which was maximal 1.5 to 3h after this short H2O2 treatment.

DNA damage does not appear to be a trigger for thermotolerance in mammalian cells

The hypothesis that DNA damage is the trigger for thermotolerance in mammalian cells was tested in Chinese hamster ovary cells by looking for evidence of thermotolerance after ionizing radiation or ultraviolet light exposure. As previous studies have demonstrated that relatively non-toxic radiation exposures do not induce thermotolerance in mammalian cells (Li et al. 1976), higher doses, comparable to those used in yeast to induce thermotolerance (Mitchel and Morrison 1984), were tested in this study. Doses of this magnitude are lethal to mammalian cells, thereby precluding the use of clonogenic survival as an endpoint. We therefore used three alternative assays which are indicators of the subsequent development of thermotolerance. These were; (a) heat-induced inhibition of total protein synthesis, (b) heat-induced uptake of dansyl lysine, and (c) synthesis of heat shock proteins. Only total protein synthesis revealed evidence of a small degree of thermotolerance which occurred immediately after ionizing radiation exposure. By 4 h postirradiation the tolerance, as measured by this assay, was no longer evident. No evidence of thermotolerance was seen following UV exposure. In addition, when a large radiation dose was given either immediately before or after a heat treatment used to induce thermotolerance, there was no alteration in the level of heat-induced tolerance, despite the extensive number of DNA stand breaks caused by the radiation. Our data therefore suggest that, in mammalian cells, the type of DNA damage caused by ionizing radiation is not the trigger for the induction of thermotolerance.

Phenobarbital induction of cytochrome P-450 b,e genes is dependent on protein synthesis

Phenobarbital induces liver cytochrome P-450 b,e proteins mainly by increasing the rate of transcription of these genes. The mechanism responsible for the phenobarbital increment in the rate of transcription of cytochrome P-450 b,e genes is unknown. The objective of this study was to assess whether active protein synthesis was needed for phenobarbital to induce the liver cytochrome P-450 b,e genes. Cycloheximide (2 mg per kg, i.p.) was administered 90 min prior to a single inductive dose of phenobarbital (80 mg per kg, i.p.) and mRNAS measured at 3, 6 and 12 hr by dot-blot hybridization. While phenobarbital increased cytochrome P-450 b,e mRNAs about 12-fold at 3 hr, this induction was abolished by cycloheximide. To define whether the absence of protein synthesis in hepatocytes inhibited the phenobarbital induction of cytochrome P-450 at the transcriptional level, in vitro transcription rates using isolated nuclei were measured. After phenobarbital administration, there was about a 20-fold increment in transcriptional rate of cytochrome P-450 b,e genes. This increment was abolished by prior injection of cycloheximide. It is proposed that either preexisting regulatory proteins or transacting factors dependent on active protein synthesis participate in the regulation of liver cytochrome P-450 b,e gene transcription after phenobarbital.

Hydrogen peroxide (H2O2) induces actin and some heat-shock proteins in Drosophila cells

Drosophila cells of a clone derived from line Kc were treated with various concentrations of hydrogen peroxide (H2O2). The concentration of 10 mM was lethal, whereas concentrations of 1-100 microM did not affect cell viability, rate of multiplication or protein synthesis. The intermediate concentration of 1 mM H2O2 was used to study the response of the cells to an oxidative stress. We observed a transitory decrease of the global protein synthesis, which was accompanied by changes in the polypeptide pattern. There was a 2.5-fold increase of the synthesis of the heat-shock proteins 70-68 and 23. The most prominent response was a 6.5-fold increase of actin synthesis 3 h after a 1 mM H2O2 treatment. When aminotriazole (an inhibitor of catalase) was added in association with H2O2, the increase of actin synthesis became 8.5-fold. Experiments in which catalase was added at various times after H2O2 showed that a 10-min treatment with H2O2 was sufficient to induce actin and heat-shock protein synthesis 3 h later. H2O2 was shown to induce the transcriptional activation of an actin gene and of the heat-shock protein genes 70 and 23 within minutes. These results are coherent with the hypothesis that the byproducts of O2 reduction (the superoxide ion and hydrogen peroxide) could be inducers of the heat-shock response. Whether the increase of actin synthesis is a stress-related response, and the mode of action of H2O2 are discussed.