Long ncRNA expression associates with tissue-specific enhancers

Long non-coding RNAs (ncRNA) have recently been demonstrated to be expressed from a subset of enhancers and to be required for the distant regulation of gene expression. Several approaches to predict enhancers have been developed based on various chromatin marks and occupancy of enhancer-binding proteins. Despite the rapid advances in the field, no consensus how to define tissue specific enhancers yet exists. Here, we identify 2,695 long ncRNAs annotated by ENCODE (corresponding to 28% of all ENCODE annotated long ncRNAs) that overlap tissue-specific enhancers. We use a recently developed algorithm to predict tissue-specific enhancers, PreSTIGE, that is based on the H3K4me1 mark and tissue specific expression of mRNAs. The expression of the long ncRNAs overlapping enhancers is significantly higher when the enhancer is predicted as active in a specific cell line, suggesting a general interdependency of active enhancers and expression of long ncRNAs. This dependency is not identified using previous enhancer prediction algorithms that do not account for expression of their downstream targets. The predicted enhancers that overlap annotated long ncRNAs generally have a lower ratio of H3K4me1 to H3K4me3, suggesting that enhancers expressing long ncRNAs might be associated with specific epigenetic marks. In conclusion, we demonstrate the tissue-specific predictive power of PreSTIGE and provide evidence for thousands of long ncRNAs that are expressed from active tissue-specific enhancers, suggesting a particularly important functional relationship between long ncRNAs and enhancer activity in determining tissue-specific gene expression.近年来研究证实，长链非编码RNA（long non-coding RNAs, ncRNA）可由部分增强子转录生成，并在基因表达的远端调控中发挥必要功能。目前已基于多种染色质修饰标记及增强子结合蛋白的占据特征，开发出多款增强子预测方法。尽管该领域进展迅猛，但目前尚未就组织特异性增强子的定义达成统一共识。本研究共鉴定出2695个由ENCODE注释的长链非编码RNA（占ENCODE注释的全部长链非编码RNA的28%），这些RNA与组织特异性增强子存在序列重叠区域。我们采用了新近开发的组织特异性增强子预测算法PreSTIGE，该算法以H3K4me1修饰标记及mRNA的组织特异性表达为核心依据。当增强子在特定细胞系中被预测为活性状态时，与之重叠的长链非编码RNA的表达水平会显著升高，这提示活性增强子与长链非编码RNA的表达之间存在普遍的相互依存关系。而采用未考虑下游靶基因表达的传统增强子预测算法，则无法识别出这种依存关联。与已注释长链非编码RNA重叠的预测增强子，其H3K4me1与H3K4me3的修饰比值普遍更低，这提示转录长链非编码RNA的增强子可能与特定表观遗传修饰标记相关。综上，本研究验证了PreSTIGE算法的组织特异性增强子预测能力，并为数千个由活性组织特异性增强子转录的长链非编码RNA提供了实验证据，提示长链非编码RNA与增强子活性之间存在极为重要的功能关联，该关联在组织特异性基因表达调控过程中发挥关键作用。