Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065, USA.
Plant Cell. 2012 Nov;24(11):4333-45. doi: 10.1105/tpc.112.102855. Epub 2012 Nov 6.
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 thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of intron-containing lincRNAs.
长链非编码 RNA（lncRNA）是从酵母和动物基因组的基因间区转录而来的，在关键的生物过程中发挥着重要作用。然而，植物 lncRNA 的特征仍然知之甚少，lncRNA 生物发生的调控机制也不清楚。本研究采用基于可重复性的生物信息学策略，分析了 200 个拟南芥转录组数据集，鉴定出 13230 个基因间转录本，其中 6480 个可归类为 lincRNA。通过 RNA 测序实验检测到 2708 个 lincRNA 的表达。定制微阵列的转录组分析表明，这些 lincRNA 中的大多数表达水平介于 mRNA 和 miRNA 前体之间。一部分 lincRNA 基因具有器官特异性表达，而其他 lincRNA 基因则对生物和/或非生物胁迫有反应。在 11 个突变体中的转录组数据的进一步分析表明，SERRATE、CAP BINDING PROTEIN20（CBP20）和 CBP80 是 lincRNA 表达和生物发生的调节因子。RT-PCR 实验证实，这三种蛋白也需要剪接一小部分含有内含子的 lincRNA。
