CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110020, India.
Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi, 110020, India.
J Transl Med. 2017 Sep 2;15(1):186. doi: 10.1186/s12967-017-1282-9.
Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not been studied extensively. In the present study, we explore whether lncRNAs could modulate genomic regulation by interacting with DNA through the formation of highly stable DNA:DNA:RNA triplexes.
We computationally screened 23,898 lncRNA transcripts as annotated by GENCODE, across the human genome for potential triplex forming sequence stretches (PTS). The PTS frequencies were compared across 5'UTR, CDS, 3'UTR, introns, promoter and 1000 bases downstream of the transcription termination sites. These regions were annotated by mapping to experimental regulatory regions, classes of repeat regions and transcription factors. We validated few putative triplex mediated interactions where lncRNA-gene pair interaction is via pyrimidine triplex motif using biophysical methods.
We identified 20,04,034 PTS sites to be enriched in promoter and intronic regions across human genome. Additional analysis of the association of PTS with core promoter elements revealed a systematic paucity of PTS in all regulatory regions, except TF binding sites. A total of 25 transcription factors were found to be associated with PTS. Using an interaction network, we showed that a subset of the triplex forming lncRNAs, have a positive association with gene promoters. We also demonstrated an in vitro interaction of one lncRNA candidate with its predicted gene target promoter regions.
Our analysis shows that PTS are enriched in gene promoter and largely associated with simple repeats. The current study suggests a major role of a subset of lncRNAs in mediating chromatin organization modulation through CTCF and NSRF proteins.
只有少数长链非编码 RNA 具有功能特征。已知它们通过与细胞内的其他生物分子（DNA、RNA 和蛋白质）相互作用来调节调节。尽管已经对 lncRNA-miRNA 和 lncRNA-蛋白质相互作用进行了详细研究，但尚未广泛研究 lncRNA 与 DNA 的相互作用。在本研究中，我们通过形成高度稳定的 DNA:DNA:RNA 三螺旋来探索 lncRNA 是否可以通过与 DNA 相互作用来调节基因组调节。
我们在人类基因组中计算筛选了 23898 个 lncRNA 转录本，作为 GENCODE 注释的潜在三螺旋形成序列（PTS）。比较了 PTS 在 5'UTR、CDS、3'UTR、内含子、启动子和转录终止位点下游 1000 个碱基处的频率。这些区域通过映射到实验调节区域、重复区域和转录因子的类别进行注释。我们使用生物物理方法验证了一些潜在的三螺旋介导的相互作用，其中 lncRNA-基因对的相互作用是通过嘧啶三螺旋基序。
我们确定了 2004034 个 PTS 位点在人类基因组中富含启动子和内含子区域。对 PTS 与核心启动子元件的关联的进一步分析表明，除了 TF 结合位点外，所有调节区域中 PTS 都普遍缺乏。总共发现 25 个转录因子与 PTS 相关。使用交互网络，我们表明一组形成三螺旋的 lncRNA 与基因启动子呈正相关。我们还证明了一个 lncRNA 候选物与其预测的基因靶标启动子区域的体外相互作用。
我们的分析表明，PTS 在基因启动子中富集，并且与简单重复高度相关。本研究表明，一组 lncRNA 在通过 CTCF 和 NSRF 蛋白介导染色质组织调节中起主要作用。
