Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response

Abstract

The field of non-coding RNA (ncRNA) has expanded over the last decade following the discoveries of several new classes of regulatory ncRNA. A growing amount of evidence now indicates that ncRNAs are involved even in the most fundamental of cellular processes. The heat shock response is no exception as ncRNAs are being identified as integral components of this process. Although this area of research is only in its infancy, this article focuses on several classes of regulatory ncRNA (i.e., miRNA, lncRNA, and circRNA), while summarizing their activities in mammalian heat shock. We also present an updated model integrating the traditional heat shock response with the activities of regulatory ncRNA. Our model expands on the mechanisms for efficient execution of the stress response, while offering a more comprehensive summary of the major regulators and responders in heat shock signaling. It is our hope that much of what is discussed herein may help researchers in integrating the fields of heat shock and ncRNA in mammals.

Fig. 1

HSF1 trimerization in response to heat shock requires lncRNA HSR1. In unstressed cells, HSF1 is predominantly monomeric. Upon heat shock, chaperone proteins dissociate from HSF1 freeing monomers to form functional homotrimers. HSR1 is an lncRNA ∼2 kb in length containing a long poly(A) tail. It is constitutively present in cells, but following heat shock HSR1 undergoes conformational changes and associates with protein eEF1A. Though typically involved in translational regulation, eEF1A acquires an apparent non-canonical function upon binding HSR1. Both eEF1A and HSR1 associate with HSF1 bringing about its trimerization. Within this mechanism, HSR1 behaves much like a molecular thermosensor that effectively regulates HSF1 mobilization

Fig. 2

Suppression of basal transcription following heat shock is mediated by lncRNA. a Under normal conditions, RNA polymerase II (Poll II) associates with gene promoters through the help of accessory factors such as TATA-binding protein (TBP) to drive basal transcription of house-keeping genes. Phosphorylation (P) of heptapeptide repeats at serine-5 within the carboxyl terminal domain (CTD) of Pol II is facilitated by TFIIH to signify transcription initiation. b LncRNAs B5 in mice (∼178 nts) or Alu in humans (∼300 nts) are upregulated in response to heat stress. Both RNA species function in trans as repressors of basal transcription by binding to the active site of Pol II, preventing proper association with DNA, and suppressing CTD phosphorylation. TFIIH does not appear to disassociate from the complex, rather its kinase activity is suppressed following lncRNA interaction with Pol II

Fig. 3

Transcription elongation of heat shock genes is regulated by lncRNA. RNA polymerase II (Pol II) pauses following transcription initiation at gene promoters. P-TEFb promotes transcription elongation by phosphorylating (P) heptapeptide repeats at serine-2 within the carboxyl terminal domain (CTD) of Pol II. 7SK is a nuclear lncRNA (∼331 nts) that interacts with a subpopulation of P-TEFb repressing its activity and sequestering its ability to interact with transcription complexes. Induction of the stress response (e.g., heat shock) causes P-TEFb to disassociate from 7SK allowing it to interact with Pol II and promote transcription elongation of susceptible genes including heat shock response factors. By this mechanism, 7SK functions in trans as a scaffold component of P-TEFb and regulator of gene transcription in response to stress signals

Fig. 4

Nucleolar sequestration of HSPA1A is facilitated by lncRNA. a Transcription of ribosomal DNA (rDNA) occurs in the nucleolus of mammalian cells. Between each ribosomal gene is a region of repetitive sequence long believed to be devoid of transcriptional activity referred to as the intergenic spacer (IGS). HSPA1A/HSP72 is a prototypical inducible protein activated in response to heat stress. b One hallmark of the heat shock response is nucleolar recruitment of HSPA1A/HSP72 in addition to its overexpression. Within the IGS region, heat stress activates transcription at specific loci located 16 kb (IGS₁₆) and 22 kb (IGS₂₂) downstream of the rRNA TSS. Other stress stimuli trigger transcription at different IGS loci. The resulting lncRNAs (∼300 nts) function in cis to capture a subfraction of HSPA1A/HSP72 at the sites of transcription forcing its sequestration in the nucleolus. RNA polymerase I (Pol I) is responsible for transcription within the IGS region; however, it is unclear if the lncRNAs remain tethered to chromatin as nascent transcripts (as shown) or bound by other factors

Fig. 5

ncRNAs function as integral components of the heat shock response in mammals. The heat shock response is typically characterized by the rapid trimerization/activation of HSF1 and subsequent transcriptional induction of heat shock proteins (e.g., HSPA1A, HSPA6, etc.). ncRNAs including lncRNAs and miRNAs are often overlooked regulators of the heat shock response pathway. This model illustrates the diverse functional roles that ncRNAs play or likely play in heat stress. Select examples of lncRNA (black boxes) and miRNA (white boxes) involved in the heat shock response are delineated by solid lines. Dashed lines define putative functional interactions of ncRNA not yet examined/reported