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dc.contributor.author Liu, Jun
dc.contributor.author Jung, Choonkyun
dc.contributor.author Xu, Jun
dc.contributor.author Wang, Huan
dc.contributor.author Deng, Shulin
dc.contributor.author Bernad, Lucia
dc.contributor.author Arenas-Huertero, Catalina
dc.contributor.author Chua, Nam-Hai
dc.coverage.spatial New York
dc.date.accessioned 2012-11-13T15:51:51Z
dc.date.available 2012-11-13T15:51:51Z
dc.date.issued 2012-11-13
dc.identifier doi:10.5061/dryad.n40hc
dc.identifier.citation Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua N (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. The Plant Cell 24(11): 4333-4345.
dc.identifier.uri http://hdl.handle.net/10255/dryad.42447
dc.description Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis transcriptome datasets, we identified 13,230 intergenic transcripts of which 6,480 can be classified as lincRNAs. Expression of 2,708 lincRNAs was detected by RNA-seq experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and pri-miRNAs. A subset of lincRNA genes show organ-specific expression whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CBP20, and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these 3 proteins are also needed for splicing of a small group of intron-containing lincRNAs.
dc.relation.haspart doi:10.5061/dryad.n40hc/1
dc.relation.haspart doi:10.5061/dryad.n40hc/2
dc.relation.haspart doi:10.5061/dryad.n40hc/3
dc.relation.haspart doi:10.5061/dryad.n40hc/4
dc.relation.haspart doi:10.5061/dryad.n40hc/5
dc.relation.haspart doi:10.5061/dryad.n40hc/6
dc.relation.haspart doi:10.5061/dryad.n40hc/7
dc.relation.haspart doi:10.5061/dryad.n40hc/8
dc.relation.haspart doi:10.5061/dryad.n40hc/9
dc.relation.haspart doi:10.5061/dryad.n40hc/10
dc.relation.haspart doi:10.5061/dryad.n40hc/11
dc.relation.haspart doi:10.5061/dryad.n40hc/12
dc.relation.haspart doi:10.5061/dryad.n40hc/13
dc.relation.haspart doi:10.5061/dryad.n40hc/14
dc.relation.haspart doi:10.5061/dryad.n40hc/15
dc.relation.haspart doi:10.5061/dryad.n40hc/16
dc.relation.haspart doi:10.5061/dryad.n40hc/17
dc.relation.haspart doi:10.5061/dryad.n40hc/18
dc.relation.haspart doi:10.5061/dryad.n40hc/19
dc.relation.isreferencedby doi:10.1105/tpc.112.102855
dc.relation.isreferencedby PMID:23136377
dc.subject Noncoding RNA
dc.subject lincRNA
dc.subject transcriptome
dc.subject RNA-seq
dc.title Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
dc.type Article *
dwc.ScientificName Arabidopsis thaliana
dc.contributor.correspondingAuthor Liu, Jun
prism.publicationName The Plant Cell

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Title Supplemental Dataset 1. Classification of TAIR9 other RNAs
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Title Supplemental Dataset 2. Classification of the TUs identifed by ESTs
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Title Supplemental Dataset 3. Classification of the TUs previously reported by Matsui.A et.al 2008
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Title Supplemental Dataset 4. Classification of the TUs previously reported by Okamoto.M et.al 2010
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Title Supplemental Dataset 5. Tiling array datasets we used for analysis
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Title Supplemental Dataset 6. Classification of the TUs identifed by RepTAS
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Title Supplemental Dataset 7. RCTUs identifed by RepTAS
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Title Supplemental Dataset 8. Design of ATH LincRNA v1 Array
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Title Supplemental Dataset 9. LincRNAs identified by both RepTAS and RNA-seq
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Title Supplemental Dataset 10. Summary of assambled transcripts by RNA-seq
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Title Supplemental Dataset 11. Classification of the TUs identified by RNAseq
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Title Supplemental Dataset 12. Verfication of organ-preferencially expressed lincRNA by qRT-PCR
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Download Supplemental Dataset 12. Verfication of o...CR.xls (27.13 Kb)
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Title Supplemental Dataset 13. Comparison of lincRNAs identifed by mutiple platforms
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Title Supplemental Dataset 14. Predicted introns of lincRNAs
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Title Supplemental Dataset 15. Stresses-responsive lincRNAs
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Download Supplemental Dataset 15 Stresses-responsi...As.xls (2.650 Mb)
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Title Supplemental Dataset 16. LincRNAs associated with smRNAs
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Download Supplemental Dataset 16.LincRNAs associat...As.xls (76.28 Kb)
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Title Supplemental Dataset 17. LincRNAs regulated by SERRATE and CBPs
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Download Supplemental Dataset 17. lincRNAs regulat...Ps.xls (176.6 Kb)
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Title Supplemental Dataset 18. Verfication of SE and CBPs regulated lincRNAs by qRT-PCR
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Download Supplemental Dataset 18. Verfication of S...CR.xls (35.32 Kb)
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Title Supplemental Dataset 19. Summary of expression evidence of lincRNA
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Download Supplemental Dataset 19 Summary of expres...NA.xls (311.2 Kb)
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