Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability
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)...
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| Veröffentlicht in: | The New phytologist 2011-04, Vol.190 (2), p.442-456 |
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| creator | Licausi, Francesco Weits, Daan A. Pant, Bikram Datt Scheible, Wolf-Rüdiger Geigenberger, Peter van Dongen, Joost T. |
| description | 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. |
| doi_str_mv | 10.1111/j.1469-8137.2010.03451.x |
| format | Article |
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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.</description><identifier>ISSN: 0028-646X</identifier><identifier>EISSN: 1469-8137</identifier><identifier>DOI: 10.1111/j.1469-8137.2010.03451.x</identifier><identifier>PMID: 20840511</identifier><language>eng</language><publisher>Oxford, UK: John Wiley & Sons</publisher><subject>Anoxia ; Anoxic conditions ; Arabidopsis ; Arabidopsis - cytology ; Arabidopsis - drug effects ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Availability ; Base Sequence ; Binding sites ; Cell Hypoxia - drug effects ; Cell Hypoxia - genetics ; Deoxyribonucleic acid ; Development ; DNA ; DNA, Plant - metabolism ; Flooding ; Gene expression ; Gene Expression Profiling ; Gene expression regulation ; Gene Expression Regulation, Plant - drug effects ; Gene regulation ; Genes ; Genes, Plant - genetics ; Hypoxia ; Indoleacetic Acids - metabolism ; MicroRNA ; microRNA (miRNA) ; MicroRNAs - biosynthesis ; MicroRNAs - genetics ; MicroRNAs - metabolism ; miRNA ; Molecular Sequence Data ; Nucleotide sequence ; Oxygen ; Oxygen - pharmacology ; PCR ; Plant physiology ; Plants ; Promoter Regions, Genetic - genetics ; Protein Binding - drug effects ; quantitative real‐time PCR (qRT‐PCR) ; Ribonucleic acid ; RNA ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Time Factors ; Transcription ; transcription factor ; Transcription factors ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription, Genetic - drug effects ; Transcriptional Activation - drug effects ; Transcriptional Activation - genetics ; Up regulation ; Up-Regulation - drug effects</subject><ispartof>The New phytologist, 2011-04, Vol.190 (2), p.442-456</ispartof><rights>Copyright © 2011 New Phytologist Trust</rights><rights>The Authors (2010). Journal compilation © New Phytologist Trust (2010)</rights><rights>The Authors (2010). Journal compilation © New Phytologist Trust (2010).</rights><rights>Copyright Wiley Subscription Services, Inc. Apr 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5001-98a4df9eaa596e3d8e68de4f6bb7b9e23a11eceec619a72cb35b4806f20221573</citedby><cites>FETCH-LOGICAL-c5001-98a4df9eaa596e3d8e68de4f6bb7b9e23a11eceec619a72cb35b4806f20221573</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/29783452$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/29783452$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20840511$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Licausi, Francesco</creatorcontrib><creatorcontrib>Weits, Daan A.</creatorcontrib><creatorcontrib>Pant, Bikram Datt</creatorcontrib><creatorcontrib>Scheible, Wolf-Rüdiger</creatorcontrib><creatorcontrib>Geigenberger, Peter</creatorcontrib><creatorcontrib>van Dongen, Joost T.</creatorcontrib><title>Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability</title><title>The New phytologist</title><addtitle>New Phytol</addtitle><description>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.</description><subject>Anoxia</subject><subject>Anoxic conditions</subject><subject>Arabidopsis</subject><subject>Arabidopsis - cytology</subject><subject>Arabidopsis - drug effects</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis Proteins - metabolism</subject><subject>Availability</subject><subject>Base Sequence</subject><subject>Binding sites</subject><subject>Cell Hypoxia - drug effects</subject><subject>Cell Hypoxia - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>Development</subject><subject>DNA</subject><subject>DNA, Plant - metabolism</subject><subject>Flooding</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene expression regulation</subject><subject>Gene Expression Regulation, Plant - drug effects</subject><subject>Gene regulation</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Hypoxia</subject><subject>Indoleacetic Acids - metabolism</subject><subject>MicroRNA</subject><subject>microRNA (miRNA)</subject><subject>MicroRNAs - biosynthesis</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>Oxygen</subject><subject>Oxygen - pharmacology</subject><subject>PCR</subject><subject>Plant physiology</subject><subject>Plants</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Protein Binding - drug effects</subject><subject>quantitative real‐time PCR (qRT‐PCR)</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Time Factors</subject><subject>Transcription</subject><subject>transcription factor</subject><subject>Transcription factors</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription, Genetic - drug effects</subject><subject>Transcriptional Activation - drug effects</subject><subject>Transcriptional Activation - genetics</subject><subject>Up regulation</subject><subject>Up-Regulation - drug effects</subject><issn>0028-646X</issn><issn>1469-8137</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkcFu1DAQhiMEotvCI4AsceCUxXZixz5wqKrSRaoKQiBxs5xkQh0lcbCdJXkWXhanKUXiAr7YGn_zj0ZfkiCC9ySeN-2e5FymgmTFnuJYxVnOyH5-lOwePh4nO4ypSHnOv54kp963GGPJOH2anFAscswI2SU_D8toZ6ORAz_awZsjoG8wAIJ5jCVv7ICMRz3URgeoUbmgo3bGTh75qfQQPLINCk4PvnJmDCvf6CpY55EeatSbTzfnHoVbHZB2gGoI4HozbFHhFlCEJ90hOy9xLtJHbTpdms6E5VnypNGdh-f391ny5d3l54tDev3h6v3F-XVaMYxJKoXO60aC1kxyyGoBXNSQN7wsi1ICzTQhUAFUnEhd0KrMWJkLzBuKKSWsyM6S11vu6Oz3CXxQvfEVdJ0eIC6qhMwopzTL_00ymRFG7shXf5GtndwQ11CUCC4lo5xESmxU5az3Dho1OtNrtyiC1WpatWoVqlahajWt7kyrOba-vB8wldHOQ-NvtRF4uwE_TAfLfwerm4-H9RX7X2z9rY82_-TLQsR_mv0CZejD3A</recordid><startdate>201104</startdate><enddate>201104</enddate><creator>Licausi, Francesco</creator><creator>Weits, Daan A.</creator><creator>Pant, Bikram Datt</creator><creator>Scheible, Wolf-Rüdiger</creator><creator>Geigenberger, Peter</creator><creator>van Dongen, Joost T.</creator><general>John Wiley & Sons</general><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>201104</creationdate><title>Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability</title><author>Licausi, Francesco ; 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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.</abstract><cop>Oxford, UK</cop><pub>John Wiley & Sons</pub><pmid>20840511</pmid><doi>10.1111/j.1469-8137.2010.03451.x</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Anoxia Anoxic conditions Arabidopsis Arabidopsis - cytology Arabidopsis - drug effects Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Availability Base Sequence Binding sites Cell Hypoxia - drug effects Cell Hypoxia - genetics Deoxyribonucleic acid Development DNA DNA, Plant - metabolism Flooding Gene expression Gene Expression Profiling Gene expression regulation Gene Expression Regulation, Plant - drug effects Gene regulation Genes Genes, Plant - genetics Hypoxia Indoleacetic Acids - metabolism MicroRNA microRNA (miRNA) MicroRNAs - biosynthesis MicroRNAs - genetics MicroRNAs - metabolism miRNA Molecular Sequence Data Nucleotide sequence Oxygen Oxygen - pharmacology PCR Plant physiology Plants Promoter Regions, Genetic - genetics Protein Binding - drug effects quantitative real‐time PCR (qRT‐PCR) Ribonucleic acid RNA RNA, Messenger - genetics RNA, Messenger - metabolism Time Factors Transcription transcription factor Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcription, Genetic - drug effects Transcriptional Activation - drug effects Transcriptional Activation - genetics Up regulation Up-Regulation - drug effects |
| title | Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability |
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