染色质构象调控真核基因的表达

真核基因的表达受到各种顺式调控元件、反式作用因子、染色质DNA以及组蛋白表观遗传修饰等多因素、多层次的调控。染色质三维空间结构的变化在调控真核基因表达方面也发挥了至关重要的作用。染色质构象的变化一方面可以使增强子等调控元件与靶基因相互靠近,从而促进基因表达;同时也可能通过形成空间位阻结构阻碍调控元件作用于靶基因,抑制基因表达。虽然染色质结构变化调控真核基因表达的机制仍缺乏较为精确的分子模型,但在组蛋白修饰、核小体定位、染色体领域以及染色质间相互作用等表观遗传学研究中,已经发现有诸多证据支持染色质构象在真核基因表达调控中的重要地位。文章主要综述了染色质结构及其构象的变化等对真核基因表达调控的影响。     

花、基因、禾本科

进化发育生物学的一个重要任务就是揭示形态多样性的分子基础, 该领域的研究包含形态、形态发育相关基因和形态所属类群等三个要素。花/花序是进化发育生物学研究的首要对象, 系统发育重建和个体发育剖析的结合将促进认知花的形态进化。发育相关基因的进化表现为等位基因遗传或表观遗传的突变, 基因家族生与死的进化, 不同基因组拥有独特的基因。运用形态学或序列分析方法很大程度揭示了禾本科植物花进化过程中的基因进化。试从学科问题、思路方法以及具体例子介绍植物进化发育生物学。     

花、基因、禾本科

进化发育生物学的一个重要任务就是揭示形态多样性的分子基础,该领域的研究包含形态、形态发育相关基因和形态所属类群等三个要素。花/花序是进化发育生物学研究的首要对象,系统发育重建和个体发育剖析的结合将促进认知花的形态进化。发育相关基因的进化表现为等位基因遗传或表观遗传的突变,基因家族生与死的进化,不同基因组拥有独特的基因。运用形态学或序列分析方法很大程度揭示了禾本科植物花进化过程中的基因进化。试从学科问题、思路方法以及具体例子介绍植物进化发育生物学。     

基因及其顺式调控元件在动物表型进化中的作用

顺式调控假说是当前进化发育生物学中重要的理论之一, 该假说认为顺式调控元件的进化是调控外表性状进化的主要遗传机制。然而越来越多的实验结果表明, 仅靠顺式调控假说远不足以解释复杂的进化发育过程, 其他因素也会导致表型的进化, 如：与顺式调控元件相联基因的蛋白序列改变; 基因及染色体组复制; 蛋白结构域与顺式调控元件的灵活性等。文章回顾了近年来顺式调控元件以及与顺式调控元件相联基因的进化发育研究, 探讨了进化发育生物学研究的新方法与新思路。     

北京中医药大学中药学院

转录因子是能够结合某基因上游特异核苷酸序列上的蛋白质,活化后从胞质转位至胞核,通过识别和结合基因启动子区的顺式作用元件,启动和调控基因表达。真核生物在转录水平上的基因表达调控,影响和控制着细胞和生物个体的许多生物学过程。本文综述了转录因子的结构、分类以及其在植物干旱胁迫中发挥的作用。     

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。     

《自然》《基因与发育》:科学家破译"组蛋白密码"识别新机制

<正>清华大学医学院基础医学系和结构生物学中心李海涛课题组利用上海光源生物大分子晶体学线站,从结构生物学角度解析组蛋白甲基化修饰识别新机制,进一步揭开了错综复杂的表观遗传调控的神秘面纱。相关成果近期分别在线发表于《自然》和《基因与发育》杂志。据了解,真核生物基因表达调控不仅依赖于特定的DNA序列元件,还受到特定组蛋白翻译后修饰的精密调节。组蛋白变体和组蛋白修饰赋     

转座元件、表观遗传调控与细胞命运决定

转座元件是哺乳动物基因组内含量最多的元素。尽管转座元件的存在对基因组稳定性具有潜在的危险,但它们同时还是潜在的基因调控序列、蛋白质编码序列和染色质结构序列,并参与物种进化过程。因此,基因组中转座元件的有害性和有益性保持着谨慎的平衡,并且这种平衡主要由表观遗传修饰来调控。本文详细介绍了异染色质类型表观遗传修饰如H3K9me3和DNA甲基化在转座元件沉默中的功能;转座元件作为增强子元件富集激活型表观遗传修饰如H3K4me1和H3K27ac,以及作为转录因子结合靶点、染色质构象锚点等方式参与基因表达调控的模式;从体内胚胎发育到体外细胞命运转变,阐述了转座元件在细胞命运决定中的潜在功能及作用方式;最后,对转座元件领域研究存在的挑战及潜在解决方法提出了见解。总之,本文对转座元件与表观遗传、基因表达调控以及细胞命运决定等方面的研究及存在的问题进行了较全面的综述,旨在为相关领域的研究人员提供参考。     

基于信息量的调控元件预测方法

设计基于信息含量的调控元件识别算法,对酵母的基因表达数据聚类结果进行分析,旨在预测共表达基因上游非编码区可能存在的转录因子结合位点。分析已知受相同调控因子作用的基因上游序列的结果表明,算法能正确识别具有单一保守核心序列的调控元件和具有间隔子(spacer)的保守序列．通过分析共表达基因,算法提取出的候选调控元件,部分可能具有生物学意义,这还有待于生物学实验的进一步验证。     

真核生物转录调控进化的研究进展

转录调控进化在真核生物的表型进化中发挥了重要作用.首先介绍了基因转录调控元件,包括基因上游调控序列和转录因子的进化特点,然后阐述了转录调控进化在生物体进化中所起的作用,最后提出了当前研究转录调控进化所面临的问题和挑战.     

Gene regulatory landscape of the sonic hedgehog locus in embryonic development

The organs of vertebrate species display a wide variety of morphology. A remaining challenge in evolutionary developmental biology is to elucidate how vertebrate lineages acquire distinct morphological features. Developmental programs are driven by spatiotemporal regulation of gene expression controlled by hundreds of thousands of cis-regulatory elements. Changes in the regulatory elements caused by the introduction of genetic variants can confer regulatory innovation that may underlie morphological novelties. Recent advances in sequencing technology have revealed a number of potential regulatory variants that can alter gene expression patterns. However, a limited number of studies demonstrate causal dependence between genetic and morphological changes. Regulation of Shh expression is a good model to understand how multiple regulatory elements organize tissue-specific gene expression patterns. This model also provides insights into how evolution of molecular traits, such as gene regulatory networks, lead to phenotypic novelty.     

Functional evolutionary developmental biology (evo‐devo) of morphological novelties in plants

Abstract The origin of morphological and ecological novelties is a long‐standing problem in evolutionary biology. Understanding these processes requires investigation from both the development and evolution standpoints, which promotes a new research field called “evolutionary developmental biology” (evo‐devo). The fundamental mechanism for the origin of a novel structure may involve heterotopy, heterochrony, ectopic expression, or loss of an existing regulatory factor. Accordingly, the morphological and ecological traits controlled by the regulatory genes may be gained, lost, or regained during evolution. Floral morphological novelties, for example, include homeotic alterations (related to organ identity), symmetric diversity, and changes in the size and morphology of the floral organs. These gains and losses can potentially arise through modification of the existing regulatory networks. Here, we review current knowledge concerning the origin of novel floral structures, such as “evolutionary homeotic mutated flowers”, floral symmetry in various plant species, and inflated calyx syndrome (ICS) within Solanaceae. Functional evo‐devo of the morphological novelties is a central theme of plant evolutionary biology. In addition, the discussion is extended to consider agronomic or domestication‐related traits, including the type, size, and morphology of fruits (berries), within Solanaceae.     

单端孢霉烯族毒素的产生及分子调控机制

禾谷镰刀菌复合种(Fusarium graminearum species complex,FGSC)引起的赤霉病是小麦生产上危害最为严重的病害之一。赤霉病除了造成减产外,感病籽粒中含有多种镰刀菌毒素,如单端孢霉烯族的呕吐毒素,可引起人畜中毒和重大疾病,给食品安全构成严重威胁。过去20年,随着禾谷镰刀菌全基因组序列的公布和遗传转化体系的成熟,禾谷镰刀菌Fusarium graminearum的功能基因组学的研究取得了较大进展,单端孢霉烯族毒素的产生、调控机制及网络研究成为热点。本文综述国内外单端孢霉烯族毒素的生物合成和分子调控机制,包括合成基因簇及决定不同产毒化学型的基因、产毒调控元件、环境因子调控产毒的分子机制,可为小麦抗赤霉病的育种提供新思路,为新型药剂的研发提供分子靶标,为赤霉病的持续防控和毒素污染的有效治理提供理论依据。     

Non-periodic cues generate seven ftz stripes in the Drosophila embryo

We have examined the expression pattern of the segmentation gene fushi tarazu (ftz) by in situ hybridization to whole mount embryos using digoxygenin labeled probes. This method has revealed previously undetected stages in the development of the ftz RNA pattern. The ftz stripes arise individually in a distinct, non-linear order along the anterior-posterior axis of the embryo. In addition, the stripes develop differentially along the dorsal-ventral axis; most stripes emerge on the ventral side and then gradually spread dorsally until they surround the entire circumference of the embryo. The order of appearance of ftz stripes is not inversely correlated with the order of appearance of hairy (h) stripes as would be expected if ftz stripes were generated by h repression. Furthermore, the seven ftz stripes are correctly established in embryos carrying mutations in h, eve or runt, with normal expression patterns decaying only after cellularization. Thus, the so called primary pair-rule genes are involved in the refinement rather than establishment of the ftz stripes. The contribution of cis-acting regulatory elements to the ftz pattern was examined. The zebra and upstream elements interact to generate seven correctly positioned stripes at the end of cellularization. However, stripe establishement is not correctly mimicked by any ftz/lac fusion gene: stripes arise in an order drastically different from the endogenous ftz gene suggesting the existence of ftz regulatory elements outside the 10-kb region examined to date. These observations suggest that the ftz pattern is directed by at least two independent regulatory systems: first, stripe establishment is directed by regionally distributed factors that act differentially in individual stripes along both anterior-posterior and dorsal-ventral axes of the egg and, second, stripe refinement and maintenance are mediated by pair-rule gene products that interact with previously identified ftz regulatory elements. This multi-level regulation provides a back-up system that ensures the development of seven stripes in the blastoderm.