标题： 核酸轨道上的混合分子马达交通：转录干扰和基因表达调控的模型 显示英文标题

标题： Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

摘要： RNA聚合酶（RNAP）是一种分子机器，它使用单链DNA（ssDNA）作为相应的模板来聚合一个RNA分子，这是一种线性杂聚物；RNA的单体序列由ssDNA模板上的单体序列决定。 在聚合RNA时，RNAP沿着ssDNA模板以特定方向逐步移动。 因此，RNAP也可以被视为一种分子马达，其在DNA上的起始和停止位点标记了它转录成RNA的遗传信息的两端。 两个重叠基因的转录干扰被认为通过其中一个对另一个的抑制作用来调节它们的表达水平，即相应RNA合成的总体速率。 在这里，我们将这个过程建模为两个群体的RNAP马达的混合交通，这两个群体由两对不同的起始和停止位点所表征。 每个群体聚合相同副本的RNA，而两个群体聚合的RNA是不同的。 这些模型也可以被看作是两个相互干扰的完全不对称简单排除过程，尽管它们非常简单，但可以解释所有转录干扰模式。 这些模型的平均场理论和计算机模拟相结合，揭示了在两个RNAP马达群体的同向和反向交通中，两个相互干扰基因的开关式调控的物理起源。 显示英文摘要

摘要： RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on the ssDNA template. While polymerizing a RNA, the RNAP walks step-by-step on the ssDNA template in a specific direction. Thus, a RNAP can be regarded also as a molecular motor and the sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes is believed to regulate the levels of their expression, i.e., the overall rate of the corresponding RNA synthesis, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of start and stop sites. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptional interference in spite of their extreme simplicity. A combination of mean-field theory and computer simulation of these models demonstrate the physical origin of the switch-like regulation of the two interfering genes in both co-directional and contra-directional traffic of the two groups of RNAP motors.