果蝇中顺式调控序列的进化

顺式调控序列(cis-regularory sequences)是与基因表达调控相关、能够被调控因子特异性识别和结合的非编码DNA序列。顺式调控序列可以通过增减所含转录因子结合位点的数目,重构转录调控网络,以精准调控基因的时空表达模式,从而调控动物的生理和形态表型。顺式调控假说认为顺式调控序列进化是自然界丰富的动物表型进化的主要遗传机制。本文首先简述了顺式调控序列的结构和功能,然后重点讨论了近年来顺式调控序列进化调控果蝇表型进化如刚毛表型进化、色素沉积表型进化和胚胎发育方面的研究进展,阐释了顺式调控序列进化是动物表型进化的主要遗传机制之一。最后本文展望了顺式调控序列未来研究方向,例如应用功能基因组研究、开展ENCODE计划等,为进化发育生物学中顺式调控序列的研究提供了参考。     

调控进化与形态多样性

揭示导致生物体形态和结构多样性产生的原因和机制, 是进化生物学研究的重要内容。进化发育生物学的研究表明, 许多复杂的形态结构及其多样性, 都是通过对古老调控网络的修饰或改造来完成的。也就是说, 生物体形态和结构的多样化并不是像以前认为的是由基因编码区的变化造成的, 而更多的是取决于基因的调控进化。作为控制基因表达的关键组分, 基因调控区的顺式调控元件通过与特定反式作用因子结合, 精细调控基因表达的时、空和量。因此, 调控元件的获得、丢失、修饰或者改变都能引起基因表达模式的变化, 是形态和结构多样性产生的主要原因。本文结合近年来国际上在基因的调控进化方面所取得的进展, 总结了真核生物中基因调控的方式和特点, 阐述了调控进化的基本式样, 揭示了调控进化在生物进化(特别是形态和结构多样化)中的作用。     

顺式调控元件对“头对头”基因对共表达的影响

转录调控是生物学过程中最关键的环节之一, 其中顺式调控元件在基因表达调控中发挥了极其重要的作用. 本研究通过对公共顺式调控元件的活性和行为进行分析, 从而推断“头对头”基因对共表达的原理. 用网络组分分析法估测顺式调控元件在不同条件下对基因启动子及其活性的影响. 结果揭示了生物系统如何利用这些调控元件调控“头对头”基因对的表达模式和整个转录调控系统.     

顺式调控元件对“头对头”基因对共表达的影响

转录调控是生物学过程中最关键的环节之一,其中顺式调控元件在基因表达调控中发挥了极其重要的作用.本研究通过对公共顺式调控元件的活性和行为进行分析,从而推断"头对头"基因对共表达的原理.用网络组分分析法估测顺式调控元件在不同条件下对基因启动子及其活性的影响.结果揭示了生物系统如何利用这些调控元件调控"头对头"基因对的表达模式和整个转录调控系统.     

石榴WRKY基因家族全基因组鉴定与表达分析

WRKY蛋白是一类在植物生长发育过程及生物与非生物胁迫过程中起重要调控作用的转录因子。该研究利用石榴全基因组数据,采用生物信息学的方法,对石榴WRKY转录因子家族成员蛋白理化性质、系统进化、基因结构、保守基序、顺式作用元件、蛋白互作及基因共表达和转录组表达模式进行系统分析。结果共鉴定出69个PgWRKY基因;分组鉴定和进化分析显示WRKY蛋白可分为Ⅰ、Ⅱ和Ⅲ共三大类型。顺式作用元件分析表明,PgWRKY基因广泛参与到非生物胁迫中;蛋白互作网络与共表达分析暗示PgWRKY基因在同一胁迫应答中可能作用一致并同时诱导表达;RNA-Seq数据分析表明,PgWRKY基因有一定的组织表达特异性,广泛参与植物营养、生殖生长以及根部逆境胁迫应答过程。     

利用进化比较的方法确定β珠蛋白基因簇调控的顺式元件

利用进化比较的方法对我、兔子和灵长类Ｇａｌａｇｏ的β珠蛋白基因以及所在的β珠蛋白基因簇进行分析,确定了可能的基因调控的顺式元件,并与一些实验结果进行比较,发现利用进行比较的方法确定基因调控的顺式元件是一种简单可行的方法。     

脊椎动物肌动蛋白顺式作用元件分布的进化

具有组织和发育表达特异性的基因,很可能具有独特的顺式作用元件的分布模式,这种模式在很大程度上决定表达的特异性。脊椎动物肌动蛋白各亚型的表达具有严格的组织特异性。为改进和完善１种顺式元件匹配预测方法,在实验资料的基础上,统计出５各顺式元件的核苷酸分布权重矩阵模式,对脊椎动物肌动蛋白基因的５’７调控区进行顺式元件的区配预测和序列分析,获得了相应亚型的物异性的顺式元件编码分布模式,并分析了其进化趋势。     

拟南芥GA2ox基因家族启动子分析

赤霉素是一类重要的植物激素,它参与调节植物生长发育的各个阶段。真核基因的表达受多种因素的调控,其中启动子在转录水平上的调节作用至关重要,但是目前对拟南芥GA2ox基因家族上游顺式元件的详细分析较少。本研究分析了AtGA2ox基因家族染色体定位、进化关系、蛋白模体以及顺式元件。分析结果表明：AtGA2ox基因家族分为2个亚类;具有相对集中的染色体分布：具有相似的内含子和外显子结构;AtGA2ox基因家族成员进化关系越相近,模体和顺式元件则越保守且分布位置更接近。PLACE和Plant CARE以及DMB分析显示,AtGA2ox基因家族存在许多保守元件,受多因素的调控,在此家族的上游调控区域普遍存在组织和器官特异性表达元件、光响应元停、激素响应元件以及其他环境响应元件。基因表达谱分析结果表明,在激素诱导下,AtGA2ox基因家族均有响应。这些元件不仅作为正调控元件,诱导部分AtGA2ox基因的表达,而且还能作为负调控元件．抑制其他AtGA2ox基因的表达。     

烟草TIR-NBS基因家族的生物信息学分析

TIR-NBS基因是一类与植物抗病调节和生长发育密切相关的基因,其特征解析有助于对植物免疫和发育调节的认识。该研究通过生物信息学分析方法,从基因鉴定、染色体分布、基因结构、蛋白性质和结构、信号肽、亚细胞定位和顺式作用元件等方面,对烟草TIR-NBS基因家族进行了鉴定和分子特性分析。结果表明:烟草TIR-NBS基因家族含有30条成员,分布在21条染色体上,含有3～8个保守基序;编码蛋白均为不稳定蛋白,无信号肽,主要分布于细胞核、细胞质和叶绿体中,二级结构以α-螺旋和无规则卷曲为主要构成元件;进化时主要受纯化选择作用,与番茄的TIR-NBS基因亲缘关系最近;顺式作用元件分析表明其可能受光照、温度以及生长素、茉莉酸甲酯、脱落酸、水杨酸、赤霉素等激素调控。该研究结果为进一步探究TIR-NBS基因的生物学功能及提高植物产量和品质提供了依据。     

高粱SbSBP17基因的克隆及表达分析

SBP box(Squamosa promoter Binding Protein box)蛋白是绿色植物中特有的一类转录因子,其功能涉及植物叶片发育、胚胎发生、间隔期长度、营养到生殖生长的更替、育性维持等生长发育的重要过程。该研究以高粱材料BTx623花序总RNA为模板进行RT PCR,克隆了高粱SbSBP17基因,并对其进行了系统进化及半定量PCR表达分析,为进一步研究SbSBP17基因的生物学功能奠定基础。结果表明：SbSBP17含有2个内含子和3个外显子,编码1个444氨基酸的蛋白质,在其195~269 aa区域含有一个典型的SBP box结构域;系统进化分析表明,18个SBP17蛋白可分为三组,第Ⅰ和Ⅱ组只有单子叶植物基因,而第Ⅲ组只有双子叶植物基因,SbSBP17与玉米PWZ17260.1亲缘关系最近;启动子顺式作用元件分析显示,SbSBP17启动子含有细胞周期调控元件MSA like、分生组织发育调控相关元件CAT box和组织特异性表达元件RY element等。基因表达分析显示,SbSBP17是花序特异性表达基因,随着花序发育(长度增加),SbSBP17基因表达量逐渐增高,当花序长至10 cm时基因表达量达到峰值,约是花序长度最小点(≤2 cm)时的40倍,随后表达量逐渐降低,并于花序长度20 cm时显著降低50%以上。研究推测,随着高粱花序进一步发育,SbSBP17基因的表达量可能逐渐降低,最终消失。     

Adaptive cis-regulatory changes may involve few mutations

A long-standing debate in evo-devo research concerns the relative role of protein-coding and cis-regulatory regions in adaptation. Recent studies of genetic adaptation have revealed that the number of substitutions contributing to phenotypic variation is lower in cis-regulatory than in structural regions, which has led to the idea that cis-regulatory regions are less important in phenotypic adaptation. However, the number of substitutions is not the only important factor, the "size" of the adaptive contribution of these substitutions is important too. A geometrical reasoning predicts that, given their lesser pleiotropic effects, cis-regulatory substitutions should have a larger average adaptive contribution than protein-coding substitutions. Thus it is possible that even with a lower number of adaptive mutations, cis-regulatory regions may contribute at the same level or even more than protein-coding regions.     

A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis

Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.     

Evo-devo: extending the evolutionary synthesis

Evolutionary developmental biology (evo-devo) explores the mechanistic relationships between the processes of individual development and phenotypic change during evolution. Although evo-devo is widely acknowledged to be revolutionizing our understanding of how the development of organisms has evolved, its substantial implications for the theoretical basis of evolution are often overlooked. This essay identifies major theoretical themes of current evo-devo research and highlights how its results take evolutionary theory beyond the boundaries of the Modern Synthesis.     

Arabidopsis thaliana regulatory element analyzer

In the Arabidopsis thaliana regulatory element analyzer (AtREA) server, we have integrated sequence data, genome-wide expression data and functional annotation data in three application modules which will be useful to identify major regulatory targets of a user-provided cis-regulatory element (CRE), study different features of CRE distribution and evaluate the role of a set of CREs in the regulation of gene expression--independently as well as in combination with other user-provided CREs. AVAILABILITY: AtREA is freely available at http://www.bioinformatics.org/grn/atrea.html.     

How developmental is evolutionary developmental biology?

Evolutionary developmental biology (evo-devo) offers both an account of developmental processes and also new integrative frameworks for analyzing interactions between development and evolution. Biologists and philosophers are keen on evo-devo in part because it appears to offer a comfort zone between, on the one hand, what some take to be the relative inability of mainstream evolutionary biology to integrate a developmental perspective; and, on the other hand, what some take to be more intractable syntheses of development and evolution. In this article, I outline core concerns of evo-devo, distinguish theoretical and practical variants, and counter Sterelny's recent argument that evo-devo's attention to development, while important, offers no significant challenge to evolutionary theory as we know it. This revised version was published online in July 2006 with corrections to the Cover Date.