Striking circadian neuron diversity and cycling of Drosophila alternative splicing.
Striking circadian neuron diversity and cycling of Drosophila alternative splicing.
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作者：
Wang Q;Abruzzi KC;Rosbash M;Rio DC
尽管选择性前mRNA剪接(AS)显著地使神经元蛋白质组多样化，但AS的程度仍不清楚，部分原因是大脑中有大量不同类型的细胞。为了解决这个复杂的问题，我们使用了一种无注释的计算方法来分析和比较小的特定果蝇昼夜节律神经元组之间的AS谱。该方法，连接使用模型(JUM)，允许从特定的RNA-SEQ文库中对已知和新的AS事件进行综合分析。结果表明，在一类时钟神经元中，许多不同的和新的Pre-mRNA亚型优先表达，而在更标准的果蝇头部RNA制备中也没有表达。这些AS事件富含对神经元放电重要的钾通道，也有循环异构体，没有可检测到的潜在转录振荡。结果表明，大脑中存在大量的AS调节，这可能对昼夜节律也很重要。地球上几乎所有生物的生活都遵循着昼夜的节奏。例如，在果蝇中，黑暗和光明决定了昆虫何时进食、休息、移动或交配。这要归功于生物钟，这是一种与环境同步的内部程序，它告诉体内的细胞何时执行特定的角色。果蝇体内维持生物钟运转的结构由大约150个“昼夜节律神经元”组成，这些神经元被分成几个亚群。在这些细胞中，一个复杂的遗传程序正在发挥作用，基因网络以一种循环的方式被打开。为了了解这个程序是如何工作的，科学家需要知道哪些基因在什么时候被激活，以及根据这些基因中包含的信息产生了哪些蛋白质。这可能很困难，因为一个基因不一定只编码一种蛋白质。事实上，当一个基因被激活时，它被复制到由几个模块组成的前信使RNA(前信使RNA)中。然后，前信使核糖核酸可以经历一种称为选择性剪接的过程，该过程可以洗牌或移除不同的模块。这意味着一个基因可以产生不同的前信使核糖核酸分子，每个分子都将作为模板来构建不同的蛋白质。到目前为止，很少有研究检查在昼夜节律神经元中发现的不同类型的前mRNAs，以及这些前mRNAs是如何随着一天中的时间变化的。在这里，王，阿布鲁齐等人。从果蝇的大脑中提取三个昼夜节律神经元亚群和一个非昼夜节律神经元亚群。分离出前信使核糖核酸，然后一种名为Jum的新计算方法对不同神经元组中的前信使核糖核酸分子进行识别、计数和分类。这项分析揭示了数百个以前未知的前信使核糖核酸分子，其中许多分子在不同类型的脑细胞之间存在很大差异。当比较昼夜节律神经元和非昼夜节律神经元时，Wang，ABruzzi等人。表明昼夜节律细胞有更多的前mRNAs，这些mRNAs编码帮助细胞与其他神经元交流的蛋白质。最后，昼夜节律神经元中的许多基因使用选择性剪接在一天中的不同时间以一种循环的方式打开不同类型的前mRNA分子；这表明这些前信使RNA可能参与了遗传昼夜节律程序。当生物钟失去平衡时，许多人类疾病，如某些形式的失眠，就会出现。王、阿布鲁齐等人报道的结果。表明替代剪接可能是塑造这个复杂程序的一个被忽视的机制。
Although alternative pre-mRNA splicing (AS) significantly diversifies the neuronal proteome, the extent of AS is still unknown due in part to the large number of diverse cell types in the brain. To address this complexity issue, we used an annotation-free computational method to analyze and compare the AS profiles between small specific groups of Drosophila circadian neurons. The method, the Junction Usage Model (JUM), allows the comprehensive profiling of both known and novel AS events from specific RNA-seq libraries. The results show that many diverse and novel pre-mRNA isoforms are preferentially expressed in one class of clock neuron and also absent from the more standard Drosophila head RNA preparation. These AS events are enriched in potassium channels important for neuronal firing, and there are also cycling isoforms with no detectable underlying transcriptional oscillations. The results suggest massive AS regulation in the brain that is also likely important for circadian regulation. The life of nearly all creatures on Earth follows the rhythm of day and night. For example, in fruit flies, darkness and light dictate when the insects feed, rest, move or mate. This is possible thanks to the circadian clock, an internal program which is synchronized with the environment to tell cells in the body when to perform certain roles. In fruit flies, the structure that keeps the body clock ticking is formed of about 150 ‘circadian neurons’, which are divided into several subgroups. In these cells, a complex genetic programis at work, with networks of genes being ‘switched on’ in a cyclical way. To understand how this program works, scientists need to know which genes are turned on and when, as well as which proteins are created based on the information contained in these genes. This can be difficult because one gene does not necessarily code for only one protein. Indeed, when a gene is turned on, it gets copied into a pre-messenger RNA (pre-mRNA), which is formed of several modules. The pre-mRNA can then go through a process called alternative splicing that shuffles or removes the different modules. This means that one gene can give rise to different pre-mRNA molecules that will each serve as a template to build a distinct protein. Until now, there have been few studies that examine the different types of pre-mRNAs found in circadian neurons, and how these change with the time of day. Here, Wang, Abruzzi et al. extract three subgroups of circadian neurons, and one subgroup of non-circadian neurons, from the brain of fruit flies. The pre-mRNAs are isolated, and then a new computational method, called JUM, identifies, counts and categorizes the pre-mRNA molecules in the different groups of neurons. This analysis reveals hundreds of previously unknown pre-mRNA molecules, many of which differed extensively between the types of brain cells. When comparing circadian and non-circadian neurons, Wang, Abruzzi et al. show that the circadian cells had more pre-mRNAs that code for proteins that help the cell communicate with other neurons. Finally, many genes in the circadian neurons use alternative splicing to turn on different types of pre-mRNA molecules at different times of the day in a cyclical way; this suggests that these pre-mRNAs might be participating in the genetic circadian program. Many human disorders, such as certain forms of insomnia, emerge when the circadian clock is thrown off balance. The results reported by Wang, Abruzzi et al. show that alternative splicing may be an overlooked mechanism that shapes this complex program.