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<title cf:type="text"><![CDATA[Progress in Biochemistry and Biophysics -->Special Topic: Noncoding RNAs]]></title>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Editorial: Noncoding RNAs: an lmportant Area to be Studied in Life Science]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130305]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[进入21世纪以来，非编码RNA和非编码基因的研究越来越引起人们的关注。2010年12月7日的《科学》杂志(Science)在评选本世纪前10年的十大科学突破时，首先提到的就是基因组中的暗物质(the genome's "dark matter")。近10年非编码RNA领域发展如此迅速，首先源于20世纪90年代开展的基因组研究和随后的比较基因组研究。海量的基因组序列数据证实：DNA上编码蛋白质的区域(也就是通常说的基因)只占人类和其他高等动、植物基因组的极小部分，在人类不会超过整个基因组的3%，其余部分都不编码蛋白质或多肽。而且，随着生物从简单到复杂、从低级到高级，非编码序列在基因组中所占的比例也单调地增加，说明非编码序列是有功能的；近年来大量转录组的新实验结果表明，基因组中的非编码序列是可以表达的，其表达产物就是非编码RNA，转录组的研究说明基因组中的非编码序列是有信息发放的；此后，越来越多的事实证明非编码RNA具有重要的生物功能，microRNA(miRNA)的研究就是最突出的例子。上述的进展明确地告诉我们数量巨大的非编码RNA是有待挖掘的生物宝库。当今，非编码序列、非编码基因和非编码RNA的研究已成为生物学领域的研究热点，重新唤起了科学家们对“RNA世界”的重视及对“生命起源于RNA分子”这一命题的兴趣。目前，这一领域值得关注的问题很多，比如：<br>
1  长非编码RNA系统发现和功能研究<br>
尽管长度小于50个碱基的非编码RNA(如microRNA和piRNA等)的研究已取得突破性进展，但长度大于100个碱基的非编码RNA，还有数以万计功能尚未发现。长非编码RNA不仅数量巨大，更为重要的是它们能折叠为特定的空间结构，因此它们与其他生物分子相互作用的方式是不同于microRNA的。虽然到目前为止，才知道了几百个长非编码RNA的功能，但已涉及到：转录调控、转录后调控、翻译调控、表观遗传调控、基因印迹以及端粒系统等。近年来还发现了一些新类型的长非编码RNA，如ceRNA和环RNA等。所以，进一步开展非编码序列、非编码基因和非编码RNA的研究，系统发现新的长非编码RNA，研究它们的空间结构与功能，可能为我们带来更多的创新机会。<br>

2  非编码RNA是生物网络的元件<br>
近年来的大量新研究成果表明非编码RNA是许多生命过程中富有活力的参与者。一些科学家认为成千上万非编码RNA分子组成了巨大的分子网络调节着细胞中的生命活动，它们与蛋白质网络相对应，同时这两类网络必然有紧密的相互作用，从而构成更复杂的网络。所以未来的网络至少是双色的才更符合生命活动的实际。<br>
3  非编码RNA调节的多样性<br>
非编码RNA在发挥生物学功能时的作用方式是多种多样的，以miRNA为例：它的负调控作用不仅存在于靶mRNA的3'UTR区，也可发生在5'UTR区；miRNA不仅具有负调控作用，在特定条件下也可以激活基因的表达；最近的研究表明，miRNA不仅可通过调节mRNA的表达发挥生物作用，还可以通过调节蛋白来发挥生物功能。<br>
miRNA的作用方式尚且如此复杂，其他非编码RNA行使功能的途径可能更为多样。<br>
4  非编码RNA与疾病紧密相关<br>
非编码RNA，特别是miRNA，与疾病相关的研究已数不胜数。长非编码RNA也和人类疾病紧密相关，仅以肿瘤为例：PCGEM1与前列腺癌有关；His-1是白血病致病因素，而且参与了癌变代谢通路和细胞周期调控； MALAT-1的转录本是一条8000多个碱基长度的非编码RNA，该基因与非小细胞肺癌有关。上述一些成果正逐渐走向临床。非编码RNA研究是一个紧密结合实际，又可迅速用于实际的领域，应特别关注从基础到应用的转化。
为了让广大读者了解非编码RNA领域的进展，本刊特意组织了这个专辑。邀请国内RNA研究领域的5位知名专家对该领域当前的进展与挑战作了综述。屈良鹄教授介绍了microRNA和细胞信号通路间的相互作用及其对两者功能发挥的关键作用，并探讨了其生物学意义；邵宁生教授的综述介绍了在不同细胞或同一细胞的不同状态下microRNA发挥生物学功能的时序特异性和组织特异性，说明microRNA在机体内工作的复杂性；张辰宇教授结合自己多年的研究实践叙述了人体体液中microRNA的起源与功能，对分泌RNA和循环RNA概念作了论述，并探讨了它们在临床医学领域的潜在诊断功能；施蕴渝教授从结构生物学出发综述了RNA分子伴侣Hfq是如何促进sRNA和mRNA相互配对的；鲁志教授介绍了长非编码RNA研究中的各种生物信息学的工具与方法。希望大家对这些文章感兴趣，也希望它们能给大家带来知识与帮助。]]></description>
<pubDate>2013/7/25 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[CHEN Run-Sheng]]></author>
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<atom:name>CHEN Run-Sheng</atom:name>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Review: The Reciprocal Interactions of microRNAs and Cell Signaling Pathways]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130255]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[MicroRNAs(miRNAs), widely existed in various organisms, play important roles in the regulation of gene expression at the post-transcriptional level. Cell signaling pathways transduce extracellular stimuli into cells and provoke a series of physiological and pathological effects, resulting in cell fate determination. This review summarizes the reciprocal interactions of microRNAs and cell signaling pathways, revealing a miRNA-integrated signaling pathways and network in cells.]]></description>
<pubDate>2013/7/24 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[LI Bin,GUO Yan-Hua,XU Hui,ZHOU Hui and QU Liang-Hu]]></author>
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<atom:name>LI Bin,GUO Yan-Hua,XU Hui,ZHOU Hui and QU Liang-Hu</atom:name>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Review: The Origin, Function and Diagnostic Potential of Extracellular microRNA in Human Body Fluids]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130260]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[Recently, numerous studies have documented the importance of microRNAs (miRNAs) as an essential cornerstone of the genetic system. Once thought as unstable RNA molecules, miRNAs are now known to circulate in the bloodstream and other body fluids in a stable, cell-free form. Importantly, extracellular miRNAs are aberrantly present in plasma, serum and other body fluids during the pathogenesis of many diseases and, thus, are promising noninvasive or minimally invasive biomarkers to assess the pathological status of the body. However, the origin and biological function of extracellular miRNAs remains incompletely understood. In this review, we summarize the recent literature on the biogenesis and working models of extracellular miRNAs, and we highlight the impact of extending these ongoing extracellular miRNA studies to clinical applications.]]></description>
<pubDate>2013/7/25 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[ZHANG Sun-Yang,XIE Jia-Yun,LIANG Hong-Wei,CHEN Xi and ZHANG Chen-Yu]]></author>
<atom:author xmlns:atom="http://www.w3.org/2005/Atom">
<atom:name>ZHANG Sun-Yang,XIE Jia-Yun,LIANG Hong-Wei,CHEN Xi and ZHANG Chen-Yu</atom:name>
</atom:author>
<guid><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130260]]></guid><cfi:id>4</cfi:id><cfi:read>true</cfi:read></item>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Review: Time and Space Specificity and Dynamic Change of microRNA and Its Targets]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130281]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[MicroRNA(miRNA) are endogenous ～22 nt non- coding small RNAs broadly expressed in plants and mammalians. MiRNAs are involved in the negative regulation of gene expression through the targeting of mRNAs during the process and activity of life such as cell proliferation and differentiation, apoptosis  as well as the development of diseases. Recently, numerous studies have demonstrated that the expression of miRNA is of time and tissue specificity. It has been predicted that each miRNA may target more than one or hundreds of mRNAs. In addition, the functional targets of miRNAs may be different in different cells or the different states of the same cell. All these results suggested that miRNA and its functional targets may be dynamically variable with the time and space. MiRNAs may play complex roles in human body. In this paper the dynamic change of miRNA and its targets has been reviewed and it may provide new idea for the study of miRNAs.]]></description>
<pubDate>2013/7/24 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[LI Jie,QIN Xing-Liang and SHAO Ning-Sheng]]></author>
<atom:author xmlns:atom="http://www.w3.org/2005/Atom">
<atom:name>LI Jie,QIN Xing-Liang and SHAO Ning-Sheng</atom:name>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Review: Research Progress of <i>Escherichia coli</i> RNA Chaperone Hfq Interaction With DsrA and <i>rpoS</i>]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130277]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[Hfq is a bacterial post-transcriptional regulator. It facilitates base-pairing between sRNA and target mRNA. The mRNA <i>rpoS</i>, which encodes the master regulator σ<sup>S</sup> of general stress response, requires Hfq-facilitated base pairing with DsrA small RNA for efficient translation at low temperatures. Two mutually non-exclusive mechanisms have been proposed to explain the process of how Hfq facilitates base pairing of sRNA DsrA to mRNA <i>rpoS</i>: Hfq may form ternary complex with two RNAs <i>via</i> co-binding to bring the RNA strands into close proximity for optimal annealing; Hfq may bind one or both RNAs, and change its (or their) secondary (or tertiary) structure to facilitate the RNA pairing. Recently, several complex crystal structures of AU<sub>6</sub>A-Hfq-ATP, A<sub>7</sub>-Hfq, and AU<sub>6</sub>A-Hfq-A<sub>7</sub> were acquired, and interesting structural features were extracted from them to deepen our understanding in the RNA binding properties of Hfq and its RNA complexes. Furthermore, the formation of ternary complex sRNA-Hfq-mRNA is proved to be necessary for translation activation of <i>rpoS</i> mRNA <i>in vivo</i>. This mini-review summarizes some recent structural biology advances in the research of DsrA-regulated translation of <i>rpoS</i> and the biological implications of the transient ternary complex are discussed.]]></description>
<pubDate>2013/7/24 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[WANG Li-Jun,WANG Wei-Wei,GONG Qing-Guo,WU Ji-Hui and SHI Yun-Yu]]></author>
<atom:author xmlns:atom="http://www.w3.org/2005/Atom">
<atom:name>WANG Li-Jun,WANG Wei-Wei,GONG Qing-Guo,WU Ji-Hui and SHI Yun-Yu</atom:name>
</atom:author>
<guid><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130277]]></guid><cfi:id>2</cfi:id><cfi:read>true</cfi:read></item>
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<title xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="text"><![CDATA[Review: Progress on Bioinformatic Research of lncRNA]]></title>
<link><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130266]]></link>
<description xmlns:cf="http://www.microsoft.com/schemas/rss/core/2005" cf:type="html"><![CDATA[Noncoding RNA (ncRNA) refers to any RNA that is functional without being translated into proteins. Recently, people have paid more and more attention on various types of novel ncRNAs. Some small ncRNAs have already been identified and well studied, such as microRNAs, snoRNAs, tRNA, etc. However, the fields of long noncoding RNA (lncRNA) have not been well explored. This paper reviewed the research progress of ncRNA, especially the lncRNA, including the historical overview, the basic characteristics and the relationship with diseases.  We also compared the prediction methods of ncRNA, and introduced an integrative strategy to combine the high throughput sequencing data in the prediction of ncRNA.]]></description>
<pubDate>2013/7/25 0:00:00</pubDate>
<category><![CDATA[Special Topic: Noncoding RNAs]]></category>
<author><![CDATA[YUAN Jia-Pei,ZHANG Hao-Wen and LU Zhi]]></author>
<atom:author xmlns:atom="http://www.w3.org/2005/Atom">
<atom:name>YUAN Jia-Pei,ZHANG Hao-Wen and LU Zhi</atom:name>
</atom:author>
<guid><![CDATA[http://www.pibb.ac.cn/pibben/article/abstract/20130266]]></guid><cfi:id>1</cfi:id><cfi:read>true</cfi:read></item>
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