Computational analyses of transcriptome regulation on RNA level

我的生物信息学小组研究生物体的转录组，如人类，以及它是如何调节的。转录组对应于在给定细胞中被激活的一组基因。它由所谓的转录物，线性RNA分子组成，这些分子要么编码蛋白质产物，要么作为所谓的RNA基因发挥作用。这两类分子，即蛋白质和RNA基因，是决定细胞状态的关键。与蛋白质及其相互作用相反，人们对转录组及其调控方式知之甚少。 我们已经知道发挥关键功能作用的特定调控机制（例如，所谓的miRNA-mRNA相互作用，2006年诺贝尔奖），并有助于生物体（如人类）的复杂性（所谓的选择性剪接），但我们目前缺乏全面和详细的观点。 为了解决这个问题，我的生物信息学小组开发了新的计算方法，使我们能够研究RNA结构特征（即转录本与自身的相互作用）和RNA-蛋白质相互作用在调节转录组中的作用。我们工作的一个特殊目标是捕获可能与活细胞相关的特征，并检测编码蛋白质的转录本中的调控特征。 我们的研究有可能产生计算预测方法，使我们能够（1）检测转录组调控的未知机制，（2）显着增加我们目前对已知调控过程的理解，如RNA编辑，选择性剪接，翻译起始，转录本定位和降解。

My Bioinformatics group investigates the transcriptome of organisms such as the human, and how it is regulated. The transcriptome corresponds to the set of genes that are activated in a given cell. It consists of so-called transcripts, linear RNA molecules that either encode a protein product or function as so-called RNA genes. Both classes of molecules, i.e. proteins and RNA genes, are key to determining the state of a cell. In contrast to proteins and their interactions, comparatively little is known about the transcriptome and how it is regulated. We already know of specific mechanisms of regulation that play key functional roles (e.g. so-called miRNA-mRNA interactions, Nobel prize in 2006) and that contribute to the complexity of organisms such as the human (so-called alternative-splicing), yet we currently lack both a comprehensive and a detailed view. To address this, my Bioinformatics group develops new computational methods that will allow us to investigate the role that RNA structural features (i.e. interactions of a transcript with itself) and RNA-protein interactions play in regulating the transcriptome. A special goal of our work is to capture features that are likely to be relevant in the living cell and to detect regulatory features in transcripts that encode proteins. Our research has the potential to yield computational prediction methods that will allow us (1) to detect yet unknown mechanisms of transcriptome regulation and (2) to significantly increase our current understanding of known regulatory processes such as RNA-editing, alternative splicing, translation initiation, transcript localization and degradation.