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Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora
White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐...
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Published in: | The EMBO journal 2009-04, Vol.28 (8), p.1029-1042 |
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description | White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light‐responsive submerged protoperithecia‐1 (SUB‐1), a GATA family transcription factor, is essential for most late light gene expression. After a 15‐min light stimulus, the WCC directly binds the sub‐1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild‐type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis‐ and trans‐acting elements comprising the regulatory signalling cascade that governs the photobiological response. |
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Unsupervised hierarchical clustering of genome‐wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light‐responsive submerged protoperithecia‐1 (SUB‐1), a GATA family transcription factor, is essential for most late light gene expression. After a 15‐min light stimulus, the WCC directly binds the sub‐1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild‐type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis‐ and trans‐acting elements comprising the regulatory signalling cascade that governs the photobiological response.</description><identifier>ISSN: 0261-4189</identifier><identifier>EISSN: 1460-2075</identifier><identifier>DOI: 10.1038/emboj.2009.54</identifier><identifier>PMID: 19262566</identifier><identifier>CODEN: EMJODG</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>Base Sequence ; Biological Clocks - physiology ; Circadian rhythm ; Circadian Rhythm - physiology ; Cluster Analysis ; DNA-Binding Proteins - genetics ; DNA-Binding Proteins - metabolism ; Fungal Proteins - genetics ; Fungal Proteins - metabolism ; Fungi ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Genomics ; Light ; microarray ; Molecular biology ; Molecular Sequence Data ; Neurospora ; Neurospora crassa - genetics ; Neurospora crassa - metabolism ; Oligonucleotide Array Sequence Analysis ; photoreceptors ; Promoter Regions, Genetic ; Signal Transduction - physiology ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcription, Genetic ; wc-1</subject><ispartof>The EMBO journal, 2009-04, Vol.28 (8), p.1029-1042</ispartof><rights>Copyright © 2009 European Molecular Biology Organization</rights><rights>Copyright Nature Publishing Group Apr 22, 2009</rights><rights>Copyright © 2009, European Molecular Biology Organization 2009</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5224-3671929a97c43095a5b924f76b34326761cb1e5d2efd284fd409b06b20e0a1f33</citedby><cites>FETCH-LOGICAL-c5224-3671929a97c43095a5b924f76b34326761cb1e5d2efd284fd409b06b20e0a1f33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1038%2Femboj.2009.54$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1038%2Femboj.2009.54$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,315,733,786,790,891,27957,27958,50923,51032,53827,53829</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19262566$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Chen-Hui</creatorcontrib><creatorcontrib>Ringelberg, Carol S</creatorcontrib><creatorcontrib>Gross, Robert H</creatorcontrib><creatorcontrib>Dunlap, Jay C</creatorcontrib><creatorcontrib>Loros, Jennifer J</creatorcontrib><title>Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora</title><title>The EMBO journal</title><addtitle>EMBO J</addtitle><description>White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light‐responsive submerged protoperithecia‐1 (SUB‐1), a GATA family transcription factor, is essential for most late light gene expression. After a 15‐min light stimulus, the WCC directly binds the sub‐1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild‐type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis‐ and trans‐acting elements comprising the regulatory signalling cascade that governs the photobiological response.</description><subject>Base Sequence</subject><subject>Biological Clocks - physiology</subject><subject>Circadian rhythm</subject><subject>Circadian Rhythm - physiology</subject><subject>Cluster Analysis</subject><subject>DNA-Binding Proteins - genetics</subject><subject>DNA-Binding Proteins - metabolism</subject><subject>Fungal Proteins - genetics</subject><subject>Fungal Proteins - metabolism</subject><subject>Fungi</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Fungal</subject><subject>Genome, Fungal</subject><subject>Genomics</subject><subject>Light</subject><subject>microarray</subject><subject>Molecular biology</subject><subject>Molecular Sequence Data</subject><subject>Neurospora</subject><subject>Neurospora crassa - genetics</subject><subject>Neurospora crassa - metabolism</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>photoreceptors</subject><subject>Promoter Regions, Genetic</subject><subject>Signal Transduction - physiology</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription, Genetic</subject><subject>wc-1</subject><issn>0261-4189</issn><issn>1460-2075</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNp9kUuP0zAUhSMEYsrAki0KLNil-J14gwTVTAFNBwnBsLSc5KZ1cZxiJzPTf4_TVOWxYOUr-TtH596TJM8xmmNEizfQlt12ThCSc84eJDPMBMoIyvnDZIaIwBnDhTxLnoSwRQjxIsePkzMsiSBciFkCS3BdC9mdqSHVTtt9MCHtmtSa9abPjKuHypQWUg9h17kAIU63oG1INwa89tXGVNpOeBrMOlpY49apcek1DL6LKq-fJo-aKIFnx_c8-XZ58XXxIbv6vPy4eHeVVZwQllGRx2RSy7xiFEmueSkJa3JRUkaJyAWuSgy8JtDUpGBNzZAskSgJAqRxQ-l58nby3Q1lC3UFrvfaqp03rfZ71Wmj_v5xZqPW3a0ioqA5Gg1eHw1893OA0KvWhAqs1Q66IagYkOVYyAi--gfcdoOPyweFJR-vW5AIZRNUxTsED80pCUZqbE8d2lNje4qzyL_4M_5v-lhXBPgE3BkL-_-7qYvV-0_jfDB-Oemc7gcPJ-FBcGKOYU3o4f6EaP8jbk1zrr5fL9XNYvUlZzcrJegvNg_DVw</recordid><startdate>20090422</startdate><enddate>20090422</enddate><creator>Chen, Chen-Hui</creator><creator>Ringelberg, Carol S</creator><creator>Gross, Robert H</creator><creator>Dunlap, Jay C</creator><creator>Loros, Jennifer J</creator><general>John Wiley & Sons, Ltd</general><general>Blackwell Publishing Ltd</general><general>Nature Publishing Group</general><scope>BSCLL</scope><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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20090422</creationdate><title>Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora</title><author>Chen, Chen-Hui ; Ringelberg, Carol S ; Gross, Robert H ; Dunlap, Jay C ; Loros, Jennifer J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5224-3671929a97c43095a5b924f76b34326761cb1e5d2efd284fd409b06b20e0a1f33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Base Sequence</topic><topic>Biological Clocks - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The EMBO journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Chen-Hui</au><au>Ringelberg, Carol S</au><au>Gross, Robert H</au><au>Dunlap, Jay C</au><au>Loros, Jennifer J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora</atitle><jtitle>The EMBO journal</jtitle><addtitle>EMBO J</addtitle><date>2009-04-22</date><risdate>2009</risdate><volume>28</volume><issue>8</issue><spage>1029</spage><epage>1042</epage><pages>1029-1042</pages><issn>0261-4189</issn><eissn>1460-2075</eissn><coden>EMJODG</coden><notes>istex:03EA88327238C6280D3EA0CB735DACA4A4D25DA3</notes><notes>ArticleID:EMBJ200954</notes><notes>Supplementary Figures 1-6Supplementary Figure LegendsSupplementary TablesSupplementary data</notes><notes>ark:/67375/WNG-VCMR74VM-6</notes><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light‐responsive submerged protoperithecia‐1 (SUB‐1), a GATA family transcription factor, is essential for most late light gene expression. After a 15‐min light stimulus, the WCC directly binds the sub‐1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild‐type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis‐ and trans‐acting elements comprising the regulatory signalling cascade that governs the photobiological response.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>19262566</pmid><doi>10.1038/emboj.2009.54</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Base Sequence Biological Clocks - physiology Circadian rhythm Circadian Rhythm - physiology Cluster Analysis DNA-Binding Proteins - genetics DNA-Binding Proteins - metabolism Fungal Proteins - genetics Fungal Proteins - metabolism Fungi Gene expression Gene Expression Profiling Gene Expression Regulation, Fungal Genome, Fungal Genomics Light microarray Molecular biology Molecular Sequence Data Neurospora Neurospora crassa - genetics Neurospora crassa - metabolism Oligonucleotide Array Sequence Analysis photoreceptors Promoter Regions, Genetic Signal Transduction - physiology Transcription Factors - genetics Transcription Factors - metabolism Transcription, Genetic wc-1 |
title | Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora |
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