植物中小RNA基因和功能多样化
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Field: Biology & Biochemistry
Article Title: Genetic and functional diversification of small RNA pathways in plants
Authors: Xie, ZX;Johansen, LK;Gustafson, AM;Kasschau, KD;Lellis, AD;Zilberman, D;Jacobsen, SE;Carrington, JC
Journal: PLOS BIOL
Volume: 2 (5)
Q：Why do you think your paper is highly cited?
A：Plants have proven to be great models for the discovery of RNA silencing pathways and mechanisms, partly because of the many different ways in which plants deploy the basic RNA silencing apparatus. Plants have multigene families encoding the core factors required for RNA silencing. The contribution of this paper centers on the identification of distinct functions for specific members of the Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) families. We showed that biogenesis of specific classes of endogenous siRNAs and microRNAs required distinct silencing pathways, and that knocking out these pathways had unique effects on either transcriptional or posttranscriptional silencing. For example, the roles of DCL3 and RDR2 in transcriptional silencing through heterochromatin formation were demonstrated. By no means did we identify all functions for each family member, but this paper laid a foundation that a lot of other labs have used to explore the roles of RNA silencing in many biological processes.
Q：Does it describe a new discovery or a new methodology that's useful to others?
A：The most useful discoveries in the paper involved the assignment of functions to specific RNA silencing factors, especially those involved in the transcriptional silencing pathway. The mutant series we developed and the approaches used to link RNA silencing functions to heterochromatin formation have been used by many other groups. Some of the key methodologies were developed by our collaborators, Steve Jacobson and his group at UCLA.
Q：Could you summarize the significance of your paper in layman's terms?
A：This work is a small part of a much larger revolution in how we understand genetics and how genes are regulated. RNA silencing?or RNA interference (RNAi)?processes that are described in this paper occur in most complex organisms such as plants, flies, and people. This means that the RNAi mechanism has been around since before plants diverged from animals in evolution. We used the plant Arabidopsis thaliana as a productive model to explore some of the basic mechanisms that control RNAi. Recent research in animals shows that deviations in RNAi-related processes, involving small RNAs called microRNAs, likely play a role in various pathologies. Additionally, small RNAs that function in RNAi are being developed as drugs in many labs and companies. So, understanding the silencing pathways and mechanisms, we believe, may have important benefits in the future.
Q：How did you become involved in this research?
A：This lab became involved in RNA silencing back in the mid-1990s, when it was only poorly understood and before anyone was aware of how widespread the process occurs in complex organisms. We were one of several labs exploring how RNA silencing functioned as an antiviral defense response in plants, and how viruses counteracted the silencing response to establish systemic infections. This led to the discovery, along with a few other labs, of RNA silencing suppressor proteins encoded by viruses. We reasoned that if the silencing response was effective against viruses, perhaps there were endogenous RNA silencing pathways regulating cellular genes. This led to the identification of endogenous siRNAs resulting from silencing of transposons, retroelements, and other repeated sequences, as well as some of the initially recognized plant microRNAs. Most of our work since then has focused on understanding plant silencing pathways and how the system evolved to engage so many different cellular and defense processes.
Q：What are the social or political implications of your research?
A：There actually are some social and political implications of this work, but not how you might guess. This was one of the early papers published in PLoS Biology, an open access journal founded on principles that differed considerably from many or most other scientific journals. We believed in the philosophy behind the PLoS journals?open and immediate access to all scientists and anyone else. We also believed in the way PLoS Biology was organized, and felt it would rapidly emerge as one of the major biological journals. We are very pleased that this paper has received the citations it has, in part because, in a small way, it validates the open access publishing model.
Zhixin Xie, Ph.D.
Assistant Professor
Department of Biological Sciences
Texas Tech University
Lubbock, TX, USA
领域：生物科学生物化学
文章标题:：植物中小RNA基因和功能多样化
作者:：
杂志：PLoSBiol
问：为什么你认为你的文件是引用高？
对于发现小RNA沉默机制和途径，植物已证明是非常好的模式：部分原因是许多不同的方式在植物中被应用。 植物拥有很多基因编码小RNA沉默的核心因子。本文的贡献在于，对具体的dicer式（DCL)）小RNA依赖Polymerase小RNA（RDR）员的不同功能的鉴定。我们发现了特定种类内源性的siRNAs和microRNAs需要不同的沉默途径的biogenesis，这些途径的封闭会引起posttranscriptional或transcriptional的不同效果。例如，在dcl3和rdr2通过异染色质的形成从而引起转录沉默的作用被阐明了。我们并没有确定每个成员的全部功能，但该文件奠定使用的小RNA在许多生物进程引起沉默的作用。
问：是否有新的发现或新的方法的有用吗？
最有用的发现是获得小RNA沉默的因素，特别是那些从事transcriptional沉默途径的。我们发展的方法把沉默和异染色质形成联系到一起被很多研究人员使用。一些主要的方法是由我们的合作者即加大洛杉矶分校的Steve Jacobson小组。
问：你能否用大众语言总结您的文章的意义？
这项工作的一小部分。是一个更大的革命怎样理解基因是遗传的，怎样调控的、小RNA沉默、或小RNA干扰（RNAi）。过程中描述发生在这个文件中最复杂的生物，如植物、苍蝇和人。这意味着在当植物偏离动物演变进化中，RNAi机制已出现了。我们用植物Arabidopsis作为模型研究控制RNAi基本机制。最近在动物研究显示偏差RNAi相关过程，包括小RNAs称为microRNAs，在各种疾病可能扮演的角色。在许多实验室这些小RNAs，RNAi正在开发为药物。因此，了解沉默途径和机制，我们认为，未来可能有重大利益。
问：您如何介入这项研究的？
我们实验室进行小RNA早在九十年代中期，当时人们知之甚少，没有一是到这个过程普遍出现复杂有机体。我们是几个实验室之一，探讨RNA沉默功能是如何保持作为一个植物抗病毒防御反应,，以及如何保持对病毒的作用完成系统性感染。这就导致这一发现，同其它几个实验室，RNA沉默抑制病毒编码蛋白.。我们想，如果这种沉默反应能有效对付病毒，或许有内源性小RNA途径调节细胞基因。这一结果导致了由于转座子、逆转录因子、重复序列和初步发现的microRNAs导致的沉默后对内源性siRNA的鉴定。从那时起，我们的工作多数集中在如何理解植物沉默途径和植物如何在不同的细胞和防御过程中起作用。
问：您的发现对政治或社会问题的研究意义是什么？
确实是有社会和政治意义的，但不是你能猜测的。这是该论文发表在开放的PLoS生物学年初，和其他的许多其他大多数科学期刊有大的不同。我们认为PLoS杂志的理念是立即获得所有的科学家的资料和信息，我们也相信PLoS生物学是这样的组织的，感到它将很快成为一个主要的生物期刊。我们很高兴这个文章收到引用，部分原因是，在一个小角度来说，这证明了开放出版模式是正确的。
【全文连接】http://biology.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371%2Fjournal%2Epbio%2E0020104
【点评】
RNAi无疑是近几年中的亮点。
对于RNAi作用机制，似乎人们知道的不多。
作者就是通过对（这一过程）特定的dicer样（DCL）成员和小RNA依赖Polymerase （RDR）成员的不同功能的鉴定， 从而试图帮助我们理解这个过程。
如果想知道复杂机体中RNAi究竟是启动了哪个沉默途径，这篇文章可能部分回答您。
编辑：西门吹血
Article Title: Genetic and functional diversification of small RNA pathways in plants
Authors: Xie, ZX;Johansen, LK;Gustafson, AM;Kasschau, KD;Lellis, AD;Zilberman, D;Jacobsen, SE;Carrington, JC
Journal: PLOS BIOL
Volume: 2 (5)
Q：Why do you think your paper is highly cited?
A：Plants have proven to be great models for the discovery of RNA silencing pathways and mechanisms, partly because of the many different ways in which plants deploy the basic RNA silencing apparatus. Plants have multigene families encoding the core factors required for RNA silencing. The contribution of this paper centers on the identification of distinct functions for specific members of the Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) families. We showed that biogenesis of specific classes of endogenous siRNAs and microRNAs required distinct silencing pathways, and that knocking out these pathways had unique effects on either transcriptional or posttranscriptional silencing. For example, the roles of DCL3 and RDR2 in transcriptional silencing through heterochromatin formation were demonstrated. By no means did we identify all functions for each family member, but this paper laid a foundation that a lot of other labs have used to explore the roles of RNA silencing in many biological processes.
Q：Does it describe a new discovery or a new methodology that's useful to others?
A：The most useful discoveries in the paper involved the assignment of functions to specific RNA silencing factors, especially those involved in the transcriptional silencing pathway. The mutant series we developed and the approaches used to link RNA silencing functions to heterochromatin formation have been used by many other groups. Some of the key methodologies were developed by our collaborators, Steve Jacobson and his group at UCLA.
Q：Could you summarize the significance of your paper in layman's terms?
A：This work is a small part of a much larger revolution in how we understand genetics and how genes are regulated. RNA silencing?or RNA interference (RNAi)?processes that are described in this paper occur in most complex organisms such as plants, flies, and people. This means that the RNAi mechanism has been around since before plants diverged from animals in evolution. We used the plant Arabidopsis thaliana as a productive model to explore some of the basic mechanisms that control RNAi. Recent research in animals shows that deviations in RNAi-related processes, involving small RNAs called microRNAs, likely play a role in various pathologies. Additionally, small RNAs that function in RNAi are being developed as drugs in many labs and companies. So, understanding the silencing pathways and mechanisms, we believe, may have important benefits in the future.
Q：How did you become involved in this research?
A：This lab became involved in RNA silencing back in the mid-1990s, when it was only poorly understood and before anyone was aware of how widespread the process occurs in complex organisms. We were one of several labs exploring how RNA silencing functioned as an antiviral defense response in plants, and how viruses counteracted the silencing response to establish systemic infections. This led to the discovery, along with a few other labs, of RNA silencing suppressor proteins encoded by viruses. We reasoned that if the silencing response was effective against viruses, perhaps there were endogenous RNA silencing pathways regulating cellular genes. This led to the identification of endogenous siRNAs resulting from silencing of transposons, retroelements, and other repeated sequences, as well as some of the initially recognized plant microRNAs. Most of our work since then has focused on understanding plant silencing pathways and how the system evolved to engage so many different cellular and defense processes.
Q：What are the social or political implications of your research?
A：There actually are some social and political implications of this work, but not how you might guess. This was one of the early papers published in PLoS Biology, an open access journal founded on principles that differed considerably from many or most other scientific journals. We believed in the philosophy behind the PLoS journals?open and immediate access to all scientists and anyone else. We also believed in the way PLoS Biology was organized, and felt it would rapidly emerge as one of the major biological journals. We are very pleased that this paper has received the citations it has, in part because, in a small way, it validates the open access publishing model.
Zhixin Xie, Ph.D.
Assistant Professor
Department of Biological Sciences
Texas Tech University
Lubbock, TX, USA
领域：生物科学生物化学
文章标题:：植物中小RNA基因和功能多样化
作者:：
杂志：PLoSBiol
问：为什么你认为你的文件是引用高？
对于发现小RNA沉默机制和途径，植物已证明是非常好的模式：部分原因是许多不同的方式在植物中被应用。 植物拥有很多基因编码小RNA沉默的核心因子。本文的贡献在于，对具体的dicer式（DCL)）小RNA依赖Polymerase小RNA（RDR）员的不同功能的鉴定。我们发现了特定种类内源性的siRNAs和microRNAs需要不同的沉默途径的biogenesis，这些途径的封闭会引起posttranscriptional或transcriptional的不同效果。例如，在dcl3和rdr2通过异染色质的形成从而引起转录沉默的作用被阐明了。我们并没有确定每个成员的全部功能，但该文件奠定使用的小RNA在许多生物进程引起沉默的作用。
问：是否有新的发现或新的方法的有用吗？
最有用的发现是获得小RNA沉默的因素，特别是那些从事transcriptional沉默途径的。我们发展的方法把沉默和异染色质形成联系到一起被很多研究人员使用。一些主要的方法是由我们的合作者即加大洛杉矶分校的Steve Jacobson小组。
问：你能否用大众语言总结您的文章的意义？
这项工作的一小部分。是一个更大的革命怎样理解基因是遗传的，怎样调控的、小RNA沉默、或小RNA干扰（RNAi）。过程中描述发生在这个文件中最复杂的生物，如植物、苍蝇和人。这意味着在当植物偏离动物演变进化中，RNAi机制已出现了。我们用植物Arabidopsis作为模型研究控制RNAi基本机制。最近在动物研究显示偏差RNAi相关过程，包括小RNAs称为microRNAs，在各种疾病可能扮演的角色。在许多实验室这些小RNAs，RNAi正在开发为药物。因此，了解沉默途径和机制，我们认为，未来可能有重大利益。
问：您如何介入这项研究的？
我们实验室进行小RNA早在九十年代中期，当时人们知之甚少，没有一是到这个过程普遍出现复杂有机体。我们是几个实验室之一，探讨RNA沉默功能是如何保持作为一个植物抗病毒防御反应,，以及如何保持对病毒的作用完成系统性感染。这就导致这一发现，同其它几个实验室，RNA沉默抑制病毒编码蛋白.。我们想，如果这种沉默反应能有效对付病毒，或许有内源性小RNA途径调节细胞基因。这一结果导致了由于转座子、逆转录因子、重复序列和初步发现的microRNAs导致的沉默后对内源性siRNA的鉴定。从那时起，我们的工作多数集中在如何理解植物沉默途径和植物如何在不同的细胞和防御过程中起作用。
问：您的发现对政治或社会问题的研究意义是什么？
确实是有社会和政治意义的，但不是你能猜测的。这是该论文发表在开放的PLoS生物学年初，和其他的许多其他大多数科学期刊有大的不同。我们认为PLoS杂志的理念是立即获得所有的科学家的资料和信息，我们也相信PLoS生物学是这样的组织的，感到它将很快成为一个主要的生物期刊。我们很高兴这个文章收到引用，部分原因是，在一个小角度来说，这证明了开放出版模式是正确的。
【全文连接】http://biology.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371%2Fjournal%2Epbio%2E0020104
【点评】
RNAi无疑是近几年中的亮点。
对于RNAi作用机制，似乎人们知道的不多。
作者就是通过对（这一过程）特定的dicer样（DCL）成员和小RNA依赖Polymerase （RDR）成员的不同功能的鉴定， 从而试图帮助我们理解这个过程。
如果想知道复杂机体中RNAi究竟是启动了哪个沉默途径，这篇文章可能部分回答您。
编辑：西门吹血
作者: Zhixin Xie
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