Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
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DOI：
10.1101/gr.080275.108
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发表时间：
2009-01-01
期刊：
影响因子：
7
通讯作者：
Crespi, Martin
中科院分区：
文献类型：
--
作者：
Ben Amor, Besma;Wirth, Sonia;Crespi, Martin
长链非蛋白编码RNA（npcRNA）代表了一类新兴的核糖核酸调节因子，它们要么以这种长链形式直接发挥作用，要么被加工成较短的miRNA和siRNA。全长cDNA数据库的全基因组生物信息学分析鉴定了76个拟南芥npcRNA。14个npcRNA与蛋白质编码mRNA反义，表明顺式调节作用。许多24-nt siRNA与5种不同的npcRNA匹配，表明这些npcRNA是这种类型siRNA的前体。76个npcRNA的表达分析鉴定了一种新的npcRNA，其在dcl 1突变体中积累，但似乎不产生反式作用的siRNA或miRNA。此外，另一个npcRNA是miR 869的前体，并且在dcl 4中被上调，但在dcl 1突变体中没有，这表明一个年轻的miRNA基因。非生物胁迫改变了76个中22个npcRNA的积累，这一分数显著高于转录组的RNA结合蛋白编码分数。在拟南芥中的过表达分析确定了两个npcRNA作为调节剂的根生长在盐胁迫和叶片形态，分别。因此，与小RNA一起，长npcRNA包含转录组的敏感组分，其在生长和分化期间具有不同的作用。
Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcl1 mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcl1 mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation.