Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium
MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound...
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| description | MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants. |
| doi_str_mv | 10.1371/journal.pone.0049662 |
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Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2012 Ong, Wickneswari 2012 Ong, Wickneswari</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-d629474720fc14aca6dd283ae4aad81b94325a763f767b1923d1cb3ae90588783</citedby><cites>FETCH-LOGICAL-c692t-d629474720fc14aca6dd283ae4aad81b94325a763f767b1923d1cb3ae90588783</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507875/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507875/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23251324$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ong, Seong Siang</creatorcontrib><creatorcontrib>Wickneswari, Ratnam</creatorcontrib><title>Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.</description><subject>Acacia</subject><subject>Acacia - cytology</subject><subject>Acacia - genetics</subject><subject>Acacia - metabolism</subject><subject>Analysis</subject><subject>Arabidopsis</subject><subject>Base Sequence</subject><subject>Biology</subject><subject>Biosynthesis</subject><subject>Cell Wall - metabolism</subject><subject>Cell walls</subject><subject>Compression</subject><subject>Conserved sequence</subject><subject>Flowers & plants</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genomics</subject><subject>Lignin</subject><subject>Lignin - biosynthesis</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Plant Proteins - metabolism</subject><subject>Plants (botany)</subject><subject>Populus tremuloides</subject><subject>Regulatory sequences</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA Precursors - genetics</subject><subject>Studies</subject><subject>Thermodynamics</subject><subject>Tissues</subject><subject>Transcription Factors - metabolism</subject><subject>Transcriptome</subject><subject>Wood</subject><subject>Wood - cytology</subject><subject>Wood - genetics</subject><subject>Wood - metabolism</subject><subject>Woody plants</subject><subject>Xylem</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1uL1DAUx4so7jr6DUQLgujDjLm0SfoiDIOXgcWF9fIkhNMk7WTpJGPS6q6f3ozTXaayD5KHhOR3_ueSc7LsKUYLTDl-c-mH4KBb7LwzC4SKijFyLzvFFSVzRhC9f3Q-yR7FeIlQSQVjD7MTQkmJKSlOs--rDQRQvQn2N_TWu9w3-daq4C8-LWNurnbBxGh0rodgXZtHo7zTEK7zX9B1eW19vHb9xkQbc-vypQJlId-Ca-2wfZw9aKCL5sm4z7Kv7999WX2cn51_WK-WZ3PFKtLPNSNVwQtOUKNwAQqY1kRQMAWAFriuihQucEYbzniNK0I1VnV6r1ApBBd0lj0_6O46H-VYmCgxLVGFcJnKMMvWB0J7uJS7YLcpBenByr8XPrQSQm9VZ6TWgiNW6JILVFCjRQWiUQygNpiTkiWtt6O3od4arYzrA3QT0emLsxvZ-p8yhcMFL5PAq1Eg-B-Dib3c2qhM14EzfkhxE04pFhjRhL74B707u5FqISVgXeOTX7UXlcuCc5T6he3dLu6g0tImfXjqosam-4nB64lBYnpz1bcwxCjXny_-nz3_NmVfHrEbA12_ib4b9u0Xp2BxAFM7xhhMc1tkjOR-CG6qIfdDIMchSGbPjj_o1uim6-kf9tgBkw</recordid><startdate>20121127</startdate><enddate>20121127</enddate><creator>Ong, Seong Siang</creator><creator>Wickneswari, Ratnam</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20121127</creationdate><title>Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium</title><author>Ong, Seong Siang ; Wickneswari, Ratnam</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-d629474720fc14aca6dd283ae4aad81b94325a763f767b1923d1cb3ae90588783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Acacia</topic><topic>Acacia - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ong, Seong Siang</au><au>Wickneswari, Ratnam</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2012-11-27</date><risdate>2012</risdate><volume>7</volume><issue>11</issue><spage>e49662</spage><epage>e49662</epage><pages>e49662-e49662</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23251324</pmid><doi>10.1371/journal.pone.0049662</doi><tpages>e49662</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acacia Acacia - cytology Acacia - genetics Acacia - metabolism Analysis Arabidopsis Base Sequence Biology Biosynthesis Cell Wall - metabolism Cell walls Compression Conserved sequence Flowers & plants Gene expression Gene Expression Regulation, Plant Genes Genomics Lignin Lignin - biosynthesis MicroRNA MicroRNAs MicroRNAs - genetics miRNA Plant Proteins - metabolism Plants (botany) Populus tremuloides Regulatory sequences Ribonucleic acid RNA RNA Precursors - genetics Studies Thermodynamics Tissues Transcription Factors - metabolism Transcriptome Wood Wood - cytology Wood - genetics Wood - metabolism Woody plants Xylem |
| title | Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium |
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