The long non-coding RNA Dali is an epigenetic regulator of neural differentiation.
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation.
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DOI：
10.7554/elife.04530
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发表时间：
2014-11-21
期刊：
影响因子：
7.7
通讯作者：
Ponting CP
中科院分区：
文献类型：
--
作者：
Chalei V;Sansom SN;Kong L;Lee S;Montiel JF;Vance KW;Ponting CP
许多基因间长链非编码RNA （lncRNA）位点调控邻近蛋白编码基因的表达。不太清楚的是，基因间lncrna是否通常通过调节基因组上较远位点的染色质来调节转录。在这里，我们报告了Dali的基因组局部和远端rna依赖作用，Dali是一种保守的中枢神经系统表达的基因间lncRNA。Dali位于Pou3f3转录因子基因的下游，其缺失会破坏神经母细胞瘤细胞的分化。Dali转录本局部调控Pou3f3位点的转录。在远端，它优先靶向活性启动子并调节神经分化基因的表达，部分通过与POU3F3蛋白的物理关联。Dali在小鼠和人类中与DNMT1 DNA甲基转移酶相互作用，并调节反式中CpG岛相关启动子的DNA甲基化状态。这些结果首次表明，单个基因间lncRNA控制基因组远端调控元件的活性和甲基化，从而调节大规模的转录程序。传统上，基因被认为包含了构建蛋白质所需的所有指令。为了遵循这些指令，它们需要被“转录”成称为信使RNA的分子，然后被“翻译”成蛋白质。信使RNA并不是细胞中制造的唯一类型的RNA分子；例如，长链非编码rna（或lncrna）被转录，但从未被翻译成蛋白质。相反，一些lncrna控制附近基因的表达，一些改变DNA在细胞内的包装方式。已经发现一些lncrna可以控制邻近的基因，但目前尚不清楚这些分子中有多少也可以调节更远的基因，甚至是其他染色体上的基因。一种名为Dali的lncRNA是在哺乳动物的神经系统细胞中产生的。在基因组中，达利的基因位于一个名为Pou3f3的基因旁边，该基因编码一种蛋白质，这种蛋白质有助于神经和肾脏的生长和发育。Chalei等人现在已经证明，人为减少Dali lncRNA的数量会限制小鼠N2A细胞的发育，而N2A细胞通常用于研究神经细胞的发育。这些细胞中Dali lncRNA水平的降低导致Pou3f3信使RNA水平的降低，这表明Dali是一种控制其邻近基因的lncRNA。当Dali水平降低时，许多其他基因的水平也发生了变化，包括许多生长工作神经细胞所需的基因。Chalei等人也发现Dali lncRNA与N2A细胞基因组的1427个不同区域结合，最常在活性基因的起始位置附近；Dali可以通过POU3F3蛋白携带到这些位点。大理lncRNA结合的DNA序列都是不同的。Chalei等人发现Dali还与一种名为DNMT1的酶结合，这种酶可以化学修饰DNA以改变其包装成细胞的方式，他们预测这种酶可以帮助Dali找到其结合位点。此外，当人为降低Dali lncRNA水平时，影响细胞中DNA包装的化学修饰——从而改变了由这种DNA编码的基因的表达——对几个基因来说也发生了变化。其中一些基因位于距离编码Dali的基因较远的地方，表明该lncRNA可以调节远端基因的包装和表达。许多受Dali调控的基因也受POU3F3蛋白调控；这表明lncRNA可能与该蛋白一起影响某些基因的表达。现在需要进一步的工作来揭示有多少其他lncrna在其合成位点之外起作用，以及有多少lncrna也与dna结合蛋白和dna修饰蛋白形成复合物。DOI: http://dx.doi.org/10.7554/eLife.04530.002
Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. DOI: http://dx.doi.org/10.7554/eLife.04530.001 Traditionally genes are considered to contain all the instructions necessary to build proteins. For these instructions to be followed they need to be ‘transcribed’ into molecules called messenger RNA, which are then ‘translated’ to form the protein. Messenger RNAs are not the only type of RNA molecule made in a cell; long non-coding RNAs (or lncRNAs), for example, are transcribed but never translated into proteins. Instead, some lncRNAs control the expression of nearby genes and some alter how the DNA is packaged within the cell. Several lncRNAs have been found to control their neighbouring genes, but it is unclear how many of these molecules can also regulate genes that are much further away, even on other chromosomes. One lncRNA called Dali is made in cells of the nervous system of mammals. In the genome, the gene for Dali is situated next to a gene called Pou3f3, which encodes a protein that contributes to the growth and development of nerves and the kidneys. Chalei et al. have now shown that artificially reducing the amount of the Dali lncRNA restricts the development of mouse cells called N2A cells, which are commonly used to study the development of nerve cells. Reducing Dali lncRNA levels in these cells caused Pou3f3 messenger RNA levels to also decrease, which demonstrates that Dali is a lncRNA that controls its neighbouring gene. The levels of many other genes were also changed when Dali levels were reduced, including many genes that are needed to grow working nerve cells. Chalei et al. also showed that the Dali lncRNA binds to 1427 different regions of the genome of N2A cells, most often near to the start of active genes; Dali could be carried to these sites by the POU3F3 protein. The DNA sequences with which the Dali lncRNA binds were all different. Chalei et al. found that Dali also binds to an enzyme, called DNMT1, that chemically modifies DNA to change how it is packaged into a cell, and they predict that this enzyme helps Dali to find its binding sites. Furthermore, when Dali lncRNA levels were artificially reduced, the chemical modifications that affect the packaging of DNA in the cell—and hence the expression of genes encoded by this DNA—were changed for several genes. Some of these genes were located far away from the gene that encodes Dali, indicating that this lncRNA can regulate the packaging and expression of distant genes. Many genes that are regulated by Dali are also regulated by the POU3F3 protein; this suggests that the lncRNA might work together with this protein to affect the expression of some genes. Further work is now needed to uncover how many other lncRNAs act away from their sites of synthesis, and how many also form complexes with DNA-binding and DNA-modifying proteins. DOI: http://dx.doi.org/10.7554/eLife.04530.002