Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability

• Published in: The New phytologist Vol. 190; no. 2; pp. 442 - 456
• Main Authors: Licausi, Francesco, Weits, Daan A., Pant, Bikram Datt, Scheible, Wolf-Rüdiger, Geigenberger, Peter, van Dongen, Joost T.
• Format: Journal Article
• Language: English
• Published: Oxford, UK John Wiley & Sons 01.04.2011; Blackwell Publishing Ltd; Wiley Subscription Services, Inc
• Subjects: anaerobic conditions; Anoxia; Anoxic conditions; Arabidopsis; Arabidopsis - cytology; Arabidopsis - drug effects; Arabidopsis - genetics; Arabidopsis Proteins; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Availability; Base Sequence; Binding sites; biosynthesis; Cell Hypoxia; Cell Hypoxia - drug effects; Cell Hypoxia - genetics; cytology; Deoxyribonucleic acid; Development; DNA; DNA, Plant; DNA, Plant - metabolism; drug effects; Flooding; Gene expression; Gene Expression Profiling; Gene expression regulation; Gene Expression Regulation, Plant; Gene Expression Regulation, Plant - drug effects; Gene regulation; Genes; Genes, Plant; Genes, Plant - genetics; genetics; growth and development; Hypoxia; Indoleacetic Acids; Indoleacetic Acids - metabolism; metabolism; MicroRNA; microRNA (miRNA); MicroRNAs; MicroRNAs - biosynthesis; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Molecular Sequence Data; Nucleotide sequence; Oxygen; Oxygen - pharmacology; PCR; pharmacology; Plant physiology; Plants; polymerase chain reaction; Promoter Regions, Genetic; Promoter Regions, Genetic - genetics; Protein Binding; Protein Binding - drug effects; quantitative real‐time PCR (qRT‐PCR); Ribonucleic acid; RNA; RNA, Messenger; RNA, Messenger - genetics; RNA, Messenger - metabolism; roots; Time Factors; Transcription; transcription factor; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; Transcription, Genetic - drug effects; Transcriptional Activation; Transcriptional Activation - drug effects; Transcriptional Activation - genetics; Up regulation; Up-Regulation - drug effects
• ISSN: 0028-646X; 1469-8137; 1469-8137
• DOI: 10.1111/j.1469-8137.2010.03451.x

Reduced oxygen availability is not only associated with flooding, but occurs also during growth and development. It is largely unknown how hypoxia is perceived and what signaling cascade is involved in activating adaptive responses. We analysed the expression of over 1900 transcription factors (TFs) and 180 microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots exposed to different hypoxic conditions by means of quantitative PCR. We also analysed the promoters of genes induced by hypoxia with respect to over-represented DNA elements that can act as potential TF binding sites and their in vivo interaction was verified. We identified various subsets of TFs that responded differentially through time and in an oxygen concentration-dependent manner. The regulatory potential of selected TFs and their predicted DNA binding elements was validated. Although the expression of pri-miRNAs was differentially regulated under hypoxia, only one corresponding mature miRNA changed accordingly. Putative target transcripts of the miRNAs were not significantly affected. Our results show that the regulation of hypoxia-induced genes is controlled via simultaneous interaction of various combinations of TFs. Under anoxic conditions, an additional set of TFs is induced. Regulation of gene expression via miRNAs appears to play a minor role during hypoxia.