Distinct expression patterns of natural antisense transcripts in arabidopsis
Distinct expression patterns of natural antisense transcripts in arabidopsis
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DOI：
10.1104/pp.107.100396
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发表时间：
2007-07-01
期刊：
影响因子：
7.4
通讯作者：
Schmid, Markus
中科院分区：
文献类型：
--
作者：
Henz, Stefan R.;Cumbie, Jason S.;Schmid, Markus
已有研究表明，重叠的顺式天然反义转录物（cis-NATs）可以形成一个调控回路，其中一个转录物衍生的小rna调节另一个转录物的稳定性，表现为反相关表达。然而，对cis-NATs拮抗性表达的广泛程度知之甚少。我们已经确定了在拟南芥（拟南芥）基因组中占7.4%的注释转录单位的顺式- nat对显示反相关表达模式的频率。事实上，平均而言，顺式nats对的全球表达谱比转录本不重叠的其他邻近基因对的成对Pearson相关系数要低得多。然而，仅在少数cis-NAT对中发现了大于偶然预期的反相关表达。反相关的程度不取决于重叠的长度或转录本的5'端距离。与早期的研究结果一致，顺式nas不会增加产生小RNA的可能性，这是由可用的小RNA序列和大量平行特征测序标签确定的。然而，与非重叠区域相比，顺式nats的重叠区域似乎富集了小RNA位点。此外，cis-NATs的表达在各种rna沉默突变体中没有不成比例的影响。我们的研究结果表明，在拟南芥中存在顺式- nat对反相关表达的趋势，但目前可用的数据并没有产生小rna介导的沉默这一过程的强烈特征。
It has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4% of annotated transcription units in the Arabidopsis ( Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5' ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.