基于PWM扫描算法的启动子区域统计分析

为了寻找启动子区域上转录因子结合位点的分布规律,进而研究这种规律与真核基因表达调控机制之间的关系,该文从已有数据出发,运用位置权重矩阵(PWM)扫描算法对启动子区域上4种与肝脏特异表达相关的转录因子结合位点分布情况进行了初步研究,并提出了一种新的序列评分方法。通过该方法提取的统计特征,肝脏特异基因的鉴别准确率可以达93.33%。实验结果表明:肝脏特异基因的启动子区域上结合位点的分布情况与其他基因相比存在显著差异。新的序列评分方法可以更好地反映这种差异性,实现肝脏特异基因的精确鉴别。     

识别转录因子结合位点的新方法

采用进化计算的方法, 实现了在共表达基因上游非编码区寻找转录因子的结合位点. 将此方法应用在已知的受同一种转录因子调控的基因上游启动子序列集合, 结果显示, 该算法能正确识别具有单一保守序列的调控位点; 与经典的Gibbs采样方法比较显示, 本文算法在识别较短的结合位点时更有效.     

基于位置关联性打分方程的人类转录因子结合位点的预测(英文)

转录因子结合位点的识别是阐明基因转录调控机制的重要环节,准确的转录因子结合位点的预测算法将有助于人们识别转录因子的目标基因,进而研究转录因子结合位点在上游调控区中的位置对转录调控的影响.然而,目前存在的预测转录因子结合位点的算法所得结果的特异性普遍较低,因此有必要提出一种新的有效的预测转录因子结合位点的算法.本文利用JASPAR数据库上的数据,在深入分析转录因子结合位点生物学特征的基础上,构建了考虑位点保守性和伪计数的位置关联性打分方程.预测结果表明,在最佳阈值之下,该算法对转录因子结合位点的假阳率低于0.01%.     

Ultrabithorax is required for membranous wing identity in the beetle Tribolium castaneum

The two pairs of wings that are characteristic of ancestral pterygotes (winged insects) have often undergone evolutionary modification. In the fruitfly, Drosophila melanogaster, differences between the membranous forewings and the modified hindwings (halteres) depend on the Hox gene Ultrabithorax (Ubx). The Drosophila forewings develop without Hox input, while Ubx represses genes that are important for wing development, promoting haltere identity. However, the idea that Hox input is important to the morphologically specialized wing derivatives such as halteres, and not the more ancestral wings, requires examination in other insect orders. In beetles, such as Tribolium castaneum, it is the forewings that are modified (to form elytra), while the hindwings retain a morphologically more ancestral identity. Here we show that in this beetle Ubx 'de-specializes' the hindwings, which are transformed to elytra when the gene is knocked down. We also show evidence that elytra result from a Hox-free state, despite their diverged morphology. Ubx function in the hindwing seems necessary for a change in the expression of spalt, iroquois and achaete-scute homologues from elytron-like to more typical wing-like patterns. This counteracting effect of Ubx in beetle hindwings represents a previously unknown mode of wing diversification in insects.     

Domain of Ultrabithorax expression in Drosophila visceral mesoderm from autoregulation and exclusion

Domains of differential homeotic gene activity are formed at specific positions along the anteroposterior axis of the early Drosophila embryo. Homeotic genes are required continuously throughout development, so that homeotic gene activity has to be maintained independently of the positional information provided in the early embryo. In the ectoderm, the domains of homeotic gene activity partially overlap, but we have found that in the visceral mesoderm at least three of these genes are expressed in adjacent and mutually exclusive domains. It has been proposed that stable, sharply demarcated domains of this type could be established if a homeotic gene product stimulated its own expression locally and inhibited the expression of other homeotic genes, which Meinhardt has termed autocatalysis and mutual exclusion respectively. Furthermore, autocatalysis of this kind can in principle account for the maintenance of homeotic gene activity throughout development. We find that the unique domain of Ultrabithorax (Ubx) expression in the visceral mesoderm is dependent both on autocatalysis and on an exclusion mechanism: Ubx product is required for its own synthesis, whereas the product of the posteriorly adjacent gene abdominal-A represses Ubx expression.