脆性X智力低下蛋白参与非编码RNA通路的研究进展

脆性X综合征(Fragile X syndrome)是一种最常见的遗传性智力低下疾病,并且伴有语言和行为障碍等。该疾病是由脆性X智力低下基因(Fragile X mental retardation 1, FMR1)突变而导致脆性X智力低下蛋白(Fragile X mental retardation protein, FMRP)表达异常造成的。近年来,研究发现FMRP参与非编码RNA通路,并发挥多种重要生物学功能,这对理解脆性X综合征发病机理具有重要的推动作用。首先发现FMRP与siRNA和miRNA通路中Dicer酶、Ago1和Ago2蛋白相互作用,参与神经活动及生殖干细胞命运决定等重要过程。随后又发现FMRP与piRNA通路中Aub、Ago1和Piwi蛋白相互作用,维持了染色体正常结构和基因组稳定性。最新研究结果发现FMRP与lncRNA相互作用,其功能和价值正引起关注。本文从FMRP与非编码RNA通路的关系展开,着重介绍了FMRP与piRNA之间的相互作用,以期为深入理解非编码RNA通路在脆性X综合征的发病过程中作用提供参考,同时期望与临床医学领域尽快形成交叉研究,早日促进理论成果转化为临床应用。     

多特征融合的植物长链非编码RNA的预测

长链非编码RNA(Long non-coding RNA, lncRNA)是一类被定义为转录本的长度大于200 nt、没有蛋白编码能力的RNA转录本。研究表明,lncRNA在调节植物生长发育、表观遗传反应以及各种胁迫反应中起重要作用。但是与人类和动物相比,植物lncRNA的研究仍然处于起步阶段。目前,如何从大量的转录本中准确地挑选出lncRNA仍然是植物lncRNA研究领域的重要问题之一。本文构建了新的植物lncRNA和mRNA数据集,分析了数据集中植物lncRNA的序列及结构特征,提取了序列的k-mer频数信息、二级结构信息、开放阅读框信息以及序列的几何柔性等特征,基于SVM(Support Vector Machine, SVM)算法,用Jackknife检验对植物lncRNA进行了预测,并且计算了各种特征融合后对植物lncRNA预测结果的影响,准确率达到了96.14%。     

R-Coffee: a method for multiple alignment of non-coding RNA

R-Coffee is a multiple RNA alignment package, derived from T-Coffee, designed to align RNA sequences while exploiting secondary structure information. R-Coffee uses an alignment-scoring scheme that incorporates secondary structure information within the alignment. It works particularly well as an alignment improver and can be combined with any existing sequence alignment method. In this work, we used R-Coffee to compute multiple sequence alignments combining the pairwise output of sequence aligners and structural aligners. We show that R-Coffee can improve the accuracy of all the sequence aligners. We also show that the consistency-based component of T-Coffee can improve the accuracy of several structural aligners. R-Coffee was tested on 388 BRAliBase reference datasets and on 11 longer Cmfinder datasets. Altogether our results suggest that the best protocol for aligning short sequences (less than 200 nt) is the combination of R-Coffee with the RNA pairwise structural aligner Consan. We also show that the simultaneous combination of the four best sequence alignment programs with R-Coffee produces alignments almost as accurate as those obtained with R-Coffee/Consan. Finally, we show that R-Coffee can also be used to align longer datasets beyond the usual scope of structural aligners. R-Coffee is freely available for download, along with documentation, from the T-Coffee web site (www.tcoffee.org).     

Large-scale study of long non-coding RNA functions based on structure and expression features

Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs (lncRNAs) that fulfill a wide variety of regulatory roles in many biological processes. These roles, including as scaffolds and as guides for protein-coding genes, mainly depend on the structure and expression level of lncRNAs. In this review, we focus on the current methods for analyzing lncRNA structure and expression, which is basic but necessary information for in-depth, large-scale analysis of lncRNA functions.     

Exocyst complexes multiple functions in plant cells secretory pathways

Endomembrane trafficking pathways involving exocyst complexes function. The two established pathways — exocytosis of TGN/EE produced vesicles mediated by EXO70A1 harbouring exocyst and EXO70B1 dependent autophagy related transport to the vacuole — are highlighted by solid arrows; other putative pathways are marked by the dashed arrows. A, autophagosome and autophagy related GA-independent traffic; CW, cell wall; ER, endoplasmic reticulum; GA, Golgi; IVB, intravacuolar bodies; MVB, multivesicular bodies; PM, cytoplasmic membrane; TGN/EE, trans-Golgi network/early endosome; TN, tonoplast; V, vacuole. Exocyst complexes with different EXO70 subunits are symbolized by diamonds connecting the transport containers to the target membranes.

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ADAR-mediated RNA editing in non-coding RNA sequences

Adenosine to inosine (A-to-I) RNA editing is the most abundant editing event in animals. It converts adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase acting on RNA (ADAR) proteins. Editing of pre-mRNA coding regions can alter the protein codon and increase functional diversity. However, most of the A-to-I editing sites occur in the non-coding regions of pre-mRNA or mRNA and non-coding RNAs. Untranslated regions (UTRs) and introns are located in pre-mRNA non-coding regions, thus A-to-I editing can influence gene expression by nuclear retention, degradation, alternative splicing, and translation regulation. Non-coding RNAs such as microRNA (miRNA), small interfering RNA (siRNA) and long non-coding RNA (lncRNA) are related to pre-mRNA splicing, translation, and gene regulation. A-to-I editing could therefore affect the stability, biogenesis, and target recognition of non-coding RNAs. Finally, it may influence the function of non-coding RNAs, resulting in regulation of gene expression. This review focuses on the function of ADAR-mediated RNA editing on mRNA non-coding regions (UTRs and introns) and non-coding RNAs (miRNA, siRNA, and lncRNA).     

RNA interference in fungi: pathways, functions, and applications

Small RNA molecules of about 20 to 30 nucleotides function in gene regulation and genomic defense via conserved eukaryotic RNA interference (RNAi)-related pathways. The RNAi machinery consists of three core components: Dicer, Argonaute, and RNA-dependent RNA polymerase. In fungi, the RNAi-related pathways have three major functions: genomic defense, heterochromatin formation, and gene regulation. Studies of Schizosaccharomyces pombe and Neurospora, and other fungi have uncovered surprisingly diverse small RNA biogenesis pathways, suggesting that fungi utilize RNAi-related pathways in various cellular processes to adapt to different environmental conditions. These studies also provided important insights into how RNAi functions in eukaryotic systems in general. In this review, we will discuss our current understanding of the fungal RNAi-related pathways and their functions, with a focus on filamentous fungi. We will also discuss how RNAi can be used as a tool in fungal research.     

长链非编码RNA与宫颈癌

长链非编码RNA (Long non-coding RNA,lncRNAs)是RNA的其中一员,其结构类似于mRNA,但由于没有保守的开放阅读框,因此不能编码蛋白质。LncRNAs曾被认为是基因转录后的异常现象或噪音,没有任何的生物学功能。随着研究的进一步深入,发现其可作为重要的调控分子参与人类正常或异常的生物学活动过程。LncRNAs与神经系统功能、机体代谢紊乱以及肿瘤等疾病的发生发展密切相关。异常表达于宫颈癌的lncRNAs通过发挥抑制肿瘤或促进肿瘤的作用,参与调控宫颈癌的各个生物学过程。文中结合最新报道就lncRNAs在宫颈癌的异常调节、分子调节机制和潜在临床应用方面进行综述。     

Expanding the plant non-coding RNA world

Journal of Plant Research - Small nuclear RNA (snRNA) represents a distinct class of non-coding RNA molecules. As these molecules have fundamental roles in RNA metabolism, including pre-mRNA...     

长非编码RNA编码微肽的研究进展

长非编码RNA(long non-coding RNA,lncRNA)是长度超过200 nt的非编码RNA,具有一个或多个短开放阅读框,可编码功能性微肽。这些功能性微肽在各种生物过程中扮演着重要角色,例如Ca2+转运、线粒体代谢、肌细胞融合和细胞衰老等过程。同时,这些生物过程又在机体稳态调控、疾病和癌症的发生与发展、胚胎发育等重要生理过程中起关键作用。因此,研究由lncRNA编码的微肽在生物体的潜在的调控机制,将有助于进一步解析生物体潜在调控过程,并为后续疾病的靶向治疗及动物生长性能的提高提供新的理论依据。本文综述了现阶段lncRNA编码微肽领域的最新研究进展,并对当前微肽在肌肉生理、炎症与免疫、人类常见癌症、胚胎发育等领域的研究进展进行描述与总结,最后简单阐述了lncRNA编码微肽现阶段面临的问题和存在的挑战,以期为后续微肽的深入研究提供科学参考及新思路。     

长非编码RNA与蛋白质的相互作用

长非编码RNA(long non-coding RNA,lncRNA)是一类长度大于200个核苷酸但缺乏蛋白质编码潜力的调控型RNA。lncRNA在真核生物基因组中广泛转录,并且能够在多种层次以灵活的方式对基因表达进行调控。lncRNA能够与染色质修饰复合物及转录因子等蛋白质相互作用,这种相互作用提高了基因表达调控的灵活性和复杂性。本文将介绍部分具有代表性的lncRNA-蛋白质相互作用及其在基因表达调控中的作用。