Data from: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
Data files
Nov 13, 2012 version files 27.65 MB
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Supplemental Dataset 1. Classification of TAIR9 other RNAs.xls
264.19 KB
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Supplemental Dataset 10. Summary of assambled transcripts by RNA-seq.xls
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Supplemental Dataset 11. Classification of the TUs identified by RNAseq.xls
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Supplemental Dataset 12. Verfication of organ-preferencially expressed lincRNA by qRT-PCR.xls
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Supplemental Dataset 13.comparison of lincRNAs identifed by mutiple platforms .xls
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Supplemental Dataset 14. Predicted introns of lincRNAs.xls
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Supplemental Dataset 15 Stresses-responsive lincRNAs.xls
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Supplemental Dataset 16.LincRNAs associated with smRNAs.xls
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Supplemental Dataset 17. lincRNAs regulated by SERRATE and CBPs.xls
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Supplemental Dataset 18. Verfication of SE and CBPs regulated lincRNAs by qRT-PCR.xls
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Supplemental Dataset 19 Summary of expression evidence of lincRNA.xls
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Supplemental Dataset 2. Classification of the TUs identifed by ESTs.xls
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Supplemental Dataset 3. Classification of the TUs previously reported by Matsui.A et.al 2008.xls
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Supplemental Dataset 4. Classification of the TUs previously reported by Okamoto.M et.al 2010.xls
1.44 MB
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Supplemental Dataset 5. Tiling array datasets we used for analysis.xls
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Supplemental Dataset 6. Classification of the TUs identifed by RepTAS.xls
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Supplemental Dataset 7. RCTUs identifed by RepTAS.xls
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Supplemental Dataset 8. Design of ATH LincRNA v1 Array.xls
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Supplemental Dataset 9. LincRNAs identified by both RepTAS and RNA-seq .xls
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Abstract
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.