Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals.
Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals.
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DOI：
10.1186/s12864-017-3662-1
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发表时间：
2017-04-07
期刊：
影响因子：
4.4
通讯作者：
Imamura T
中科院分区：
文献类型：
--
作者：
Uesaka M;Agata K;Oishi T;Nakashima K;Imamura T
最近的转录组分析表明，长的非编码RNA(NcRNAs)在转录调控中发挥着广泛的作用。特别是，我们已经报道了启动子相关的ncRNAs(PancRNAs)通过局部表观遗传变化激活伙伴基因的表达。在这里，我们鉴定了pancRNA介导的转录激活下的数千个基因在五个哺乳动物物种中的共同之处。在小鼠中，1)与pancRNA配对的基因相比，pancRNA配对基因的表达模式仅限于某些组织，2)pancRNA的表达与配对基因启动子区域活性染色质标记的丰富显著相关，H3K4三甲基化和H3K27乙酰化，3)H3K4me1标记pancRNA配对基因，无论其表达水平如何，以及4)C-或G-倾斜基序在−200和−1之间相对于pancRNA配对基因的转录起始位置唯一地过度表达。更重要的是，使用总共25个对应组织对5个不同哺乳动物物种进行的比较转录组分析表明，总体pancRNA表达谱与总mRNA相比表现出极高的物种特异性，这表明pancRNA谱带的物种间差异可能导致了mRNA表达谱的多样化。本研究提出了一种有趣的可能性，即在进化过程中，由于基因组GC倾斜结构的形成或破坏而导致的基因激活相关pancRNA谱系的获得和/或丢失，精细地塑造了根据给定物种的基因表达的组织特异性模式。本文的在线版本(doi：10.1186/s12864-0173662-1)包含补充材料，授权用户可以使用。
Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activate the partner gene expression via local epigenetic changes. Here, we identify thousands of genes under pancRNA-mediated transcriptional activation in five mammalian species in common. In the mouse, 1) pancRNA-partnered genes confined their expression pattern to certain tissues compared to pancRNA-lacking genes, 2) expression of pancRNAs was significantly correlated with the enrichment of active chromatin marks, H3K4 trimethylation and H3K27 acetylation, at the promoter regions of the partner genes, 3) H3K4me1 marked the pancRNA-partnered genes regardless of their expression level, and 4) C- or G-skewed motifs were exclusively overrepresented between−200 and−1 bp relative to the transcription start sites of the pancRNA-partnered genes. More importantly, the comparative transcriptome analysis among five different mammalian species using a total of 25 counterpart tissues showed that the overall pancRNA expression profile exhibited extremely high species-specificity compared to that of total mRNA, suggesting that interspecies difference in pancRNA repertoires might lead to the diversification of mRNA expression profiles. The present study raises the interesting possibility that the gain and/or loss of gene-activation-associated pancRNA repertoires, caused by formation or disruption of the genomic GC-skewed structure in the course of evolution, finely shape the tissue-specific pattern of gene expression according to a given species. The online version of this article (doi:10.1186/s12864-017-3662-1) contains supplementary material, which is available to authorized users.