一种基于综合信息的剪接位点识别方法

为提高剪接位点识别的精度,提出一种基于综合信息的剪接位点识别方法.通过分析供体位点与受体位点的剪接信号、剪接序列、位点附近序列的二级结构,以及剪接因子作用过程等特征,分别为供体位点与受体位点建立信号模型和序列模型;应用Vienna软件中的Mfold包预测每个剪接位点附近序列最稳定的二级结构,将传统的四字符核酸表转化为八字符核酸表,每个序列用八字符进行描述,用结合了结构信息的序列对信号模型和序列模型进行训练学习;最后用训练好的模型进行剪接位点的识别.实验结果证明:该方法对剪接位点的识别取得了很好的效果,其识别精度可达95%以上.     

基于卷积神经网络的基因剪接位点预测

研究剪接位点可以更深入地探索剪接机制和基因预测方法,准确预测剪接位点至关重要。基于深度学习技术提出一种新的预测方法,无需人工提取样本特征,以基因序列的K-MER编码向量作为输入,采用训练后的卷积神经网络(CNN)模型进行预测。基于人类基因HS3D供体数据集,与传统机器学习方法进行预测比较,结果表明预测模型的主要性能指标,包含马修斯相关系数(MCC)、灵敏度(SN)均超过传统的机器学习方法。     

利用条件随机场实现DNA剪接位点的预测

为解决传统的基因识别算法主要关注编码区的整体特性,而并不着重考虑个别位点的信息,因此难以准确地识别出剪接位点的缺点,提出了基于条件随机场的剪接位点预测方法,条件随机场能够更好的处理标记数据之间的依赖关系,并且能够避免数据标记偏置的问题。实验结果表明基于条件随机场的剪接位点预测方法是一种合适的方法,能够取得更好的效果。     

基于序列信息理论预测线虫基因选择性剪切位点

基因的选择性剪切使得在DNA上一段相同的序列翻译成多个不同的蛋白质序列.选择性剪切的出现把剪切位点分为选择性供体位点、组成性供体位点、选择性受体位点和组成性受体位点.基于EBI中的线虫基因选择性剪切位点数据库,选取不同位点的单碱基频率和序列片段的三联体频数作为参数,利用位置权重矩阵和离散增量结合支持向量机,对选择性剪切位点进行了理论预测.对选择性供体位点和选择性受体位点的预测成功率分别为63.78%和72.63%,特异性分别为68.02%和83.96%.     

模式生物的外显子、内含子和基因间序列的识别

基于核酸序列在剪切位点上保守性、组分的不同和编码序列阅读框架的3周期性,模式生物全基因组序列分为外显子、内含子和基因间序列三类.三个标准离散源分别由64个三联体在整条序列上的概率和4个碱基序列首尾(剪切位点附近)共30个位点上的概率共同构成.某条序列的类型就由该序列的离散量同相应区间上三个标准离散量的离散增量确定.结果表明:具有184个信号参数的离散量预测比只有64个三联体参数的结果要高出5%,总体预测成功率:线虫为87.37%,拟南芥为91.08%,果蝇为92.28%,原核生物大肠杆菌的二种序列预测率为92.88%,酵母菌为94.88%.     

Splicing-site recognition of rice （Oryza sativa L. ） DNA sequences by support vector machines

Motivation: It was found that high accuracy splicing-site recognition of rice ( Oryza satlva L. ) DNA sequence is especially difficult. We described a new method for the splicing-site recognition of rice DNA sequences. Method: Based on the intron in eukaryotic organisms conforming to the principle of GT-AG, we used support vector machines (SVM) to predict the splicing sites. By machine learning, we built a model and used it to test the effect of the test data set of true and pseudo splicing sites. Results : The prediction accuracy we obtained was 87.53% at the true 5‘ end splicing site and 87.37% at the true 3‘ end splicing sites. The results suggested that the SVM approach could achieve higher accuracy than the previous approaches.     

Mechanism of recognition of the 5' splice site in self-splicing group I introns

Group I introns include many mitochondrial ribosomal RNA and messenger RNA introns and the nuclear rRNA introns of Tetrahymena and Physarum. The splicing of precursor RNAs containing these introns is a two-step reaction. Cleavage at the 5' splice site precedes cleavage at the 3' splice site, the latter cleavage being coupled with exon ligation. Following the first cleavage, the 5' exon must somehow be held in place for ligation. We have now tested the reactivity of two self-splicing group I RNAs, the Tetrahymena pre-rRNA and the intron 1 portion of the Neurospora mitochondrial cytochrome b (cob) pre-mRNA, in the intermolecular exon ligation reaction (splicing in trans) described by Inoue et al. The different sequence specificity of the reactions supports the idea that the nucleotides immediately upstream from the 5' splice site are base-paired to an internal, 5' exon-binding site, in agreement with RNA structure models proposed by Davies and co-workers and others. The internal binding site is proposed to be involved in the formation of a structure that specifies the 5' splice site and, following the first step of splicing, to hold the 5' exon in place for exon ligation.     

Takagi-Sugeno模型在剪接位点识别中的应用

为降低基因剪接位点识别算法复杂度和计算量,根据剪接位点上下游序列的保守特性及碱基组成随位点邻近序列GC含量变化等统计特征,建立Takagi-Sugeno模糊模型.通过模型输出值和阈值比较,判断真实的剪接位点.基于模糊似然函数的模糊聚类算法确定模型结构和前件参数,并结合最小二乘法完成该模型后件参数的识别.仿真结果表明,该算法简单,可使模糊模型的结构辨识和参数辨识同时完成,从而实现模糊模型的快速识别;能够很好地提取剪接位点附近保守序列的统计特征,为剪接位点的识别提供一种新的方法.     

Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells.

Exon sequences present on separate RNA molecules can be joined by trans-splicing in trypanosomatids, Euglena, and in the nematode and trematode worms. Trans-splicing involves an interaction between a 5' splice site present in a spliced leader RNA and a 3' splice site located near the 5' end of pre-messenger RNAs. In vitro trans-splicing of artificial mammalian pre-mRNAs has been reported, but the efficiency of splicing appears to depend on sequence complementarity between the two substrates. There has been speculation that some natural pre-mRNAs can be trans-spliced in mammalian cells in vivo, but alternative interpretations have not been ruled out. Here we show that spliced leader RNAs can be accurately trans-spliced in mammalian cells in vivo and in vitro. Both nematode and mammalian 3' splice sites can function as acceptors for trans-splicing in vivo. These results reveal functional conservation in the splicing machinery between lower eukaryotes and mammals, and they directly demonstrate the potential for trans-splicing in mammalian cells.     

Scanning from an independently specified branch point defines the 3' splice site of mammalian introns

During pre-messenger RNA splicing the lariat branch point in mammalian introns is specified independently of the 3' splice site by the sequence surrounding the branch point and by an adjacent downstream polypyrimidine tract. The 3' splice site is dispensable for spliceosome assembly and cleavage at the 5' splice site, and is itself determined by a scanning process that recognizes the first AG located 3' of the branch point/polypyrimidine tract, irrespective of distance or sequence environment.     

Both subunits of U2AF recognize the 3' splice site in Caenorhabditis elegans

Introns are defined by sequences that bind components of the splicing machinery. The branchpoint consensus, polypyrimidine (poly(Y)) tract, and AG at the splice boundary comprise the mammalian 3' splice site. Although the AG is crucial for the recognition of introns with relatively short poly(Y) tracts, which are termed 'AG-dependent introns', the molecule responsible for AG recognition has never been identified. A key player in 3' splice site definition is the essential heterodimeric splicing factor U2AF, which facilitates the interaction of the U2 small nuclear ribonucleoprotein particle with the branch point. The U2AF subunit with a relative molecular mass (Mr 65K) of 65,000 (U2AF65) binds to the poly(Y) tract, whereas the role of the 35K subunit (U2AF35) has not been clearly defined. It is not required for splicing in vitro but it plays a critical role in vivo. Caenorhabditis elegans introns have a highly conserved U4CAG/ R at their 3' splice sites instead of branch-point and poly(Y) consensus sequences. Nevertheless, C. elegans has U2AF, 12). Here we show that both U2AF subunits crosslink to the 3' splice site. Our results suggest that the U2AF65-U2AF35 complex identifies the U4CAG/R, with U2AF35 being responsible for recognition of the canonical AG.     

DNA splice site sequences clustering method for conservativeness analysis

DNA sequences that are near to splice sites have remarkable conservativeness, and many researchers have contributed to the prediction of splice site. In order to mine the underlying biological knowledge, we analyze the conservativeness of DNA splice site adjacent sequences by clustering. Firstly, we propose a kind of DNA splice site sequences clustering method which is based on DBSCAN, and use four kinds of dissimilarity calculating methods. Then, we analyze the conservative feature of the clustering results and the experimental data set.     

Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing

Alternative splicing of pre-messenger RNAs diversifies gene products in eukaryotes and is guided by factors that enable spliceosomes to recognize particular splice sites. Here we report that alternative splicing of Saccharomyces cerevisiae SRC1 pre-mRNA is promoted by the conserved ubiquitin-like protein Hub1. Structural and biochemical data show that Hub1 binds non-covalently to a conserved element termed HIND, which is present in the spliceosomal protein Snu66 in yeast and mammals, and Prp38 in plants. Hub1 binding mildly alters spliceosomal protein interactions and barely affects general splicing in S. cerevisiae. However, spliceosomes that lack Hub1, or are defective in Hub1-HIND interaction, cannot use certain non-canonical 5' splice sites and are defective in alternative SRC1 splicing. Hub1 confers alternative splicing not only when bound to HIND, but also when experimentally fused to Snu66, Prp38, or even the core splicing factor Prp8. Our study indicates a novel mechanism for splice site utilization that is guided by non-covalent modification of the spliceosome by an unconventional ubiquitin-like modifier.     

Effects of temperature on the expression of STN7 and phosphorylation of LHCII proteins in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

In Arabidopsis thaliana, STN7 kinase is required for phosphorylation of LHCII and for state transitions. In this paper, a hydrophilic polypeptide, derived from the amino acid sequence of STN7, was conjugated to a carrier protein, bovine serum albumin （BSA）, to obtain the polyclonal antibody. Immunogenicity and specificity of the polyclonal antibody were evaluated by agar gel immunodiffusion （AGID） test and Western blot analysis. The results show that besides the phosphorylation of LHCII proteins, also the expression of STN7 was regulated by temperature conditions. In addition, the change tendency of LHCII proteins phosphorylation was not only coherent with expression of STN7 with respect to increasing temperature, but also closely related to state transitions. These results would provide useful information for studying regulatory mechanism of LHCII proteins phosphorylation and expression of STN7.