Gene regulation under low oxygen: holding your breath for transcription Sonia Rocha College of Life Sciences, Division of Gene Regulation and Expression MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee, DD1 5EH, UK Oxygen is both an environmental and developmental signal that governs important cellular pathways. There- fore, hypoxia (or low oxygen tensions) is part of both physiological and pathological processes. To deal with hypoxic conditions, cells and organisms have evolved exquisite mechanisms for adaptation and survival. The cellular responses are reliant on controlled transcrip- tional and post-transcriptional events, where certain genes are positively regulated and others either remain inactive or are actively repressed. It has been known for some time that, during hypoxia, transcription is mainly regulated by the hypoxia inducible factor (HIF). However, recently it has been demonstrated that additional tran- scription factors are also activated and that non-HIF- dependent processes are involved in the hypoxic stress response. Therefore, gene expression following hypoxia is the result of combined effects on transcription, translation and adjustment mechanisms such as the induction of microRNAs and changes in chromatin. Dealing with low oxygen When faced with low oxygen supply, the cell orchestrates a coordinated response with the intent of restoring oxygen homeostasis. Alteration of gene expression is one of the most effective and fundamental methods by which a cell can respond to extracellular signals. Gene transcription is a complex cellular process that usually results from the interaction between transcription factors and their target consensus sequences within DNA. For the majority of extracellular stimuli, the signal must be transduced from outside the cell to the nucleus, resulting in the activation of specific transcription factors and their target genes. Relative to other stimuli, oxygen presents itself in a unique manner because it can diffuse easily into the cell and initiate cellular responses. Over the past decade, the identification of the putative oxygen sensors of the cell and the transcription factors responsible for the cellular response to hypoxia has been the subject of intense research. In addition, the identification of hypoxia as a component of many human diseases has made the field important in therapeutic terms [1]. In light of recent results showing that changes in translation effect replication and induction of microRNAs, I briefly review the hypoxia inducible factor (HIF)-dependent regulation of gene expression but focus primarily on the current understanding of how gene expression is regulated and achieved under low oxygen tensions by non-HIF-depend- ent processes. The HIF transcription factor family More than a decade ago, the Semenza group identified HIF as the key mediator of erythropoietin (EPO) expression following hypoxia [2]. HIF is a heterodimeric complex consisting of an a and a b subunit, which belong to a family characterized by the presence of basic helix–loop–helix Per/Arnt/Sim domains (bHLH-PAS) [3]. There are at least three identified a subunits (1, 2 and 3a)(Figure 1) and a b subunit (with several splice variants [4]). Of the three HIF-a-subunits, HIF-1a is the best studied and characterized to date. Nevertheless, the understand- ing of HIF-2a (also known as endothelial PAS domain protein 1, EPAS-1) function has increased dramatically, whereas the most recently identified and consequently less-well studied subunit is HIF-3a [5,6]. The past five years has helped established that HIF-1a and HIF-2a subunits possess non-redundant functions. Mouse knock- out studies have shown the vital importance of HIF-1a for development and survival, and that HIF-2a À/À mice have different phenotypes depending on their genetic back- ground, thus illustrating the importance of HIF-2a and the context-dependent nature of its activity [7–9]. In addition, a recent study has demonstrated that HIF-2a cannot functionally substitute for HIF-1a in embryonic stem cells [10]. HIF-b (also known as aryl hydrocarbon receptor nuclear translocator, ARNT) is not controlled by oxygen levels and is found constitutively expressed in all cell types. By con- trast, a-subunit levels are under tight control. In response to changing oxygen levels, the control of HIF-a subunit expression is achieved by regulating protein level, although other stimuli such as oncogene activation and cytokines can induce both transcription and protein synthesis increases of the a subunits [11]. The mechanism of HIF regulation in hypoxia The mechanism behind oxygen-dependent regulation of HIF-a was revealed with the identification of a novel class of prolyl hydroxylases (PHDs), of which four isoforms (PHD1, PHD2, PHD3 and PHD4) have been identified at this time [12,13]. In the presence of oxygen, PHDs catalyse hydroxylation of HIF-a. The hydroxylated HIF-a subunits are then polyubiquitylated and targeted for proteasome- mediated degradation (Figure 2), thus lowering the Review TRENDS in Biochemical Sciences Vol.32 No.8 Corresponding author: Rocha, S. (s.rocha@dundee.ac.uk). Available online 10 July 2007. www.sciencedirect.com 0968-0004/$ – see front matter ß 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.tibs.2007.06.005