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A novel method for constructing pathogen-regulated small RNA cDNA library
Pathogen-responsive endogenous small non-coding RNAs regulate gene expression in relation to plant immune responses by serving as RNA silencing machinery. Decay caused by the bacterium, Erwinia carotovora subsp . carotovora ( Ecc), often leads to soft rot disease in the plant Brassica campestris L....
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| Published in: | Biochemical and biophysical research communications 2010-07, Vol.397 (3), p.532-536 |
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| Main Authors: | , , |
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| Language: | English |
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| cites | cdi_FETCH-LOGICAL-c387t-97c8f8b3d449ce52d8241f7aa29087389662e232dd097d35e677290a42c2da743 |
| container_end_page | 536 |
| container_issue | 3 |
| container_start_page | 532 |
| container_title | Biochemical and biophysical research communications |
| container_volume | 397 |
| creator | Sun, Chuan Bao Du, Xian Ming He, Yu Ke |
| description | Pathogen-responsive endogenous small non-coding RNAs regulate gene expression in relation to plant immune responses by serving as RNA silencing machinery. Decay caused by the bacterium,
Erwinia carotovora subsp
. carotovora (
Ecc), often leads to soft rot disease in the plant
Brassica campestris L. ssp
. pekinensis (
Bcp). To discover endogenous small RNA species in
Bcp in response to
Ecc infection, we developed a highly efficient approach for cloning pathogen-regulated small RNAs. A group of degenerate stem–loop reverse primers was designed to synthesize first single-stranded cDNA (sscDNA) and the sscDNA was then tailed with a poly(C) at its 3′ end to create a forward priming site. A novel cDNA/RNA subtractive hybridization was performed to capture
Ecc-regulated small RNAs and this subsequently allowed construction of small RNA cDNA libraries for sequencing. |
| doi_str_mv | 10.1016/j.bbrc.2010.05.151 |
| format | article |
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Erwinia carotovora subsp
. carotovora (
Ecc), often leads to soft rot disease in the plant
Brassica campestris L. ssp
. pekinensis (
Bcp). To discover endogenous small RNA species in
Bcp in response to
Ecc infection, we developed a highly efficient approach for cloning pathogen-regulated small RNAs. A group of degenerate stem–loop reverse primers was designed to synthesize first single-stranded cDNA (sscDNA) and the sscDNA was then tailed with a poly(C) at its 3′ end to create a forward priming site. A novel cDNA/RNA subtractive hybridization was performed to capture
Ecc-regulated small RNAs and this subsequently allowed construction of small RNA cDNA libraries for sequencing.</description><identifier>ISSN: 0006-291X</identifier><identifier>EISSN: 1090-2104</identifier><identifier>DOI: 10.1016/j.bbrc.2010.05.151</identifier><identifier>PMID: 20515661</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Base Sequence ; Brassica - genetics ; Brassica - microbiology ; Brassica campestris ; cDNA/RNA subtractive hybridization ; Cloning, Molecular - methods ; DNA, Single-Stranded - genetics ; Erwinia carotovora ; Gene Library ; Host-Pathogen Interactions - genetics ; MicroRNAs - genetics ; Nucleic Acid Hybridization ; Pectobacterium carotovorum - physiology ; Plant Diseases - genetics ; Plant Diseases - microbiology ; Small non-coding RNA ; Stem–loop primer</subject><ispartof>Biochemical and biophysical research communications, 2010-07, Vol.397 (3), p.532-536</ispartof><rights>2010 Elsevier Inc.</rights><rights>Copyright 2010 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c387t-97c8f8b3d449ce52d8241f7aa29087389662e232dd097d35e677290a42c2da743</citedby><cites>FETCH-LOGICAL-c387t-97c8f8b3d449ce52d8241f7aa29087389662e232dd097d35e677290a42c2da743</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20515661$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Chuan Bao</creatorcontrib><creatorcontrib>Du, Xian Ming</creatorcontrib><creatorcontrib>He, Yu Ke</creatorcontrib><title>A novel method for constructing pathogen-regulated small RNA cDNA library</title><title>Biochemical and biophysical research communications</title><addtitle>Biochem Biophys Res Commun</addtitle><description>Pathogen-responsive endogenous small non-coding RNAs regulate gene expression in relation to plant immune responses by serving as RNA silencing machinery. Decay caused by the bacterium,
Erwinia carotovora subsp
. carotovora (
Ecc), often leads to soft rot disease in the plant
Brassica campestris L. ssp
. pekinensis (
Bcp). To discover endogenous small RNA species in
Bcp in response to
Ecc infection, we developed a highly efficient approach for cloning pathogen-regulated small RNAs. A group of degenerate stem–loop reverse primers was designed to synthesize first single-stranded cDNA (sscDNA) and the sscDNA was then tailed with a poly(C) at its 3′ end to create a forward priming site. A novel cDNA/RNA subtractive hybridization was performed to capture
Ecc-regulated small RNAs and this subsequently allowed construction of small RNA cDNA libraries for sequencing.</description><subject>Base Sequence</subject><subject>Brassica - genetics</subject><subject>Brassica - microbiology</subject><subject>Brassica campestris</subject><subject>cDNA/RNA subtractive hybridization</subject><subject>Cloning, Molecular - methods</subject><subject>DNA, Single-Stranded - genetics</subject><subject>Erwinia carotovora</subject><subject>Gene Library</subject><subject>Host-Pathogen Interactions - genetics</subject><subject>MicroRNAs - genetics</subject><subject>Nucleic Acid Hybridization</subject><subject>Pectobacterium carotovorum - physiology</subject><subject>Plant Diseases - genetics</subject><subject>Plant Diseases - microbiology</subject><subject>Small non-coding RNA</subject><subject>Stem–loop primer</subject><issn>0006-291X</issn><issn>1090-2104</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNqFkEtLxDAUhYMozvj4Ay6kO1cdbx5NWnAz-AZREAV3IU1uxw59jEkr-O_NMKNL3dwL555z4H6EnFCYUaDyfDkrS29nDKIA2YxmdIdMKRSQMgpil0wBQKasoG8TchDCEoBSIYt9MmGQ0UxKOiX386TrP7FJWhzee5dUvU9s34XBj3aou0WyMlFfYJd6XIyNGdAloTVNkzw_zhN7FUdTl974ryOyV5km4PF2H5LXm-uXy7v04en2_nL-kFqeqyEtlM2rvOROiMJixlzOBK2UMayAXPG8kJIh48w5KJTjGUql4skIZpkzSvBDcrbpXfn-Y8Qw6LYOFpvGdNiPQSvJWMwI_r-TcylAynUn2zit70PwWOmVr9v4lKag16z1Uq9Z6zVrDZmOrGPodFs_li2638gP3Gi42Bgw4vis0etga-wsutqjHbTr67_6vwHSe43J</recordid><startdate>20100702</startdate><enddate>20100702</enddate><creator>Sun, Chuan Bao</creator><creator>Du, Xian Ming</creator><creator>He, Yu Ke</creator><general>Elsevier 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>7X8</scope><scope>7QL</scope><scope>7TM</scope><scope>C1K</scope></search><sort><creationdate>20100702</creationdate><title>A novel method for constructing pathogen-regulated small RNA cDNA library</title><author>Sun, Chuan Bao ; Du, Xian Ming ; He, Yu Ke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c387t-97c8f8b3d449ce52d8241f7aa29087389662e232dd097d35e677290a42c2da743</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Base Sequence</topic><topic>Brassica - genetics</topic><topic>Brassica - microbiology</topic><topic>Brassica campestris</topic><topic>cDNA/RNA subtractive hybridization</topic><topic>Cloning, Molecular - methods</topic><topic>DNA, Single-Stranded - genetics</topic><topic>Erwinia carotovora</topic><topic>Gene Library</topic><topic>Host-Pathogen Interactions - genetics</topic><topic>MicroRNAs - genetics</topic><topic>Nucleic Acid Hybridization</topic><topic>Pectobacterium carotovorum - physiology</topic><topic>Plant Diseases - genetics</topic><topic>Plant Diseases - microbiology</topic><topic>Small non-coding RNA</topic><topic>Stem–loop primer</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Chuan Bao</creatorcontrib><creatorcontrib>Du, Xian Ming</creatorcontrib><creatorcontrib>He, Yu Ke</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Nucleic Acids Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><jtitle>Biochemical and biophysical research communications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Chuan Bao</au><au>Du, Xian Ming</au><au>He, Yu Ke</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A novel method for constructing pathogen-regulated small RNA cDNA library</atitle><jtitle>Biochemical and biophysical research communications</jtitle><addtitle>Biochem Biophys Res Commun</addtitle><date>2010-07-02</date><risdate>2010</risdate><volume>397</volume><issue>3</issue><spage>532</spage><epage>536</epage><pages>532-536</pages><issn>0006-291X</issn><eissn>1090-2104</eissn><abstract>Pathogen-responsive endogenous small non-coding RNAs regulate gene expression in relation to plant immune responses by serving as RNA silencing machinery. Decay caused by the bacterium,
Erwinia carotovora subsp
. carotovora (
Ecc), often leads to soft rot disease in the plant
Brassica campestris L. ssp
. pekinensis (
Bcp). To discover endogenous small RNA species in
Bcp in response to
Ecc infection, we developed a highly efficient approach for cloning pathogen-regulated small RNAs. A group of degenerate stem–loop reverse primers was designed to synthesize first single-stranded cDNA (sscDNA) and the sscDNA was then tailed with a poly(C) at its 3′ end to create a forward priming site. A novel cDNA/RNA subtractive hybridization was performed to capture
Ecc-regulated small RNAs and this subsequently allowed construction of small RNA cDNA libraries for sequencing.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>20515661</pmid><doi>10.1016/j.bbrc.2010.05.151</doi><tpages>5</tpages></addata></record> |
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| ispartof | Biochemical and biophysical research communications, 2010-07, Vol.397 (3), p.532-536 |
| issn | 0006-291X 1090-2104 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_762267743 |
| source | ScienceDirect Journals |
| subjects | Base Sequence Brassica - genetics Brassica - microbiology Brassica campestris cDNA/RNA subtractive hybridization Cloning, Molecular - methods DNA, Single-Stranded - genetics Erwinia carotovora Gene Library Host-Pathogen Interactions - genetics MicroRNAs - genetics Nucleic Acid Hybridization Pectobacterium carotovorum - physiology Plant Diseases - genetics Plant Diseases - microbiology Small non-coding RNA Stem–loop primer |
| title | A novel method for constructing pathogen-regulated small RNA cDNA library |
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