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An Integrated Analysis Method for miRNA, lncRNA and mRNA Profiles Based on Their Functional and Positional Relationships  [PDF]
Li Guo, Sheng Yang, Yang Zhao, Qian Wu, Feng Chen, Hui Zhang
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.510B008

ncRNAs have been identified as potential regulatory molecules and have multiple biological roles. Aberrant expression of specific ncRNAs contributes to multiple biological processes and many human diseases. Herein, we simultaneously profiled miRNA, lncRNA and mRNA in human HepG2 and L02 cells applying high-throughput sequencing and micro-array technologies. Abnormal miRNA, lncRNA and mRNA profiles were assessed through fold change filtering. A cross-platform integrated analysis method was developed to analyze differentially expressed miRNA, lncRNA and mRNA profiles. miRNA-mRNA interaction was analyzed according to their functional relationships. Target mRNAs of aberrantly expressed miRNAs were obtained from experimentally validated datasets or predicted using some programs. Generally, multiple target mRNAs were involved, and they have versatile roles by functional enrichment analysis. Ac-cording to actual expression datasets in the study, compared to deregulated miRNAs, these theoretical target mRNAs showed various expression patterns. The consistent or inconsistent expression was mainly derived from complex, mul-tiple, flexible and alternative regulatory relationships between miRNA and mRNA. Further, miRNA/mRNA and lncRNA were completely surveyed based on their location distributions on human chromosomes. Many miRNA-lncRNA and mRNA-lncRNA pairs always were located on the same strand or different strands in the specific genomic region. Due to the location distributions, they might have partly or completely overlapped regions or they could be reverse complementarily binding. These miRNA/mRNA-lncRNA pairs showed consistent or inconsistent expression pat-terns, although they might have functional relationships through reverse complementarily binding events. Moreover, we also detected and analyzed various isomiRs from a given miRNA locus, including those isomiRs with 3’ additional non-template nucleotides. These isomiRs, especially for those 5’ isomiRs with the new “seed sequences” through “seed shifting” events, maybe have potential biological roles as well as isomiR repertoire and their expression patterns. The integrative analysis provides potential functional relationships between miRNA, lncRNA and mRNA across different datasets. The complex and various expression patterns suggest a robust regulatory network across different regulatory molecules and their targets.

Deep Sequencing of Porphyromonas gingivalis and Comparative Transcriptome Analysis of a LuxS Mutant
Takanori Hirano,David A. C. Beck,Murray Hackett,Richard J. Lamont
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00079
Abstract: Porphyromonas gingivalis is a major etiological agent in chronic and aggressive forms of periodontal disease. The organism is an asaccharolytic anaerobe and is a constituent of mixed species biofilms in a variety of microenvironments in the oral cavity. P. gingivalis expresses a range of virulence factors over which it exerts tight control. High-throughput sequencing technologies provide the opportunity to relate functional genomics to basic biology. In this study we report qualitative and quantitative RNA-Seq analysis of the transcriptome of P. gingivalis. We have also applied RNA-Seq to the transcriptome of a ΔluxS mutant of P. gingivalis deficient in AI-2-mediated bacterial communication. The transcriptome analysis confirmed the expression of all predicted ORFs for strain ATCC 33277, including 854 hypothetical proteins, and allowed the identification of hitherto unknown transcriptional units. Twelve non-coding RNAs were identified, including 11 small RNAs and one cobalamin riboswitch. Fifty-seven genes were differentially regulated in the LuxS mutant. Addition of exogenous synthetic 4,5-dihydroxy-2,3-pentanedione (DPD, AI-2 precursor) to the ΔluxS mutant culture complemented expression of a subset of genes, indicating that LuxS is involved in both AI-2 signaling and non-signaling dependent systems in P. gingivalis. This work provides an important dataset for future study of P. gingivalis pathophysiology and further defines the LuxS regulon in this oral pathogen.
杨勇飞 李政 樊启昶 龙漫远,张文霞
科学通报 , 2007,
Abstract: 以果蝇为材料,检测ncRNA在物种间表达的保守性.选取在黑腹果蝇(D.melanogaster)研究中获得的12个性腺特异表达的ncRNA基因,用RT—PCR技术分别对黑腹果蝇及其近缘物种D.simulans,D.yakuba,D.pseudoobscura和D.virilis的头部、精巢和卵巢进行了ncRNA转录信号的检测.结果显示,在果蝇中,ncRNA的表达与否及表达强度(表达图谱)在种间有显著差异,并体现出组织特异性的明显变动,表明ncRNA的表达在近缘物种间的保守性很低.
科学通报 , 2007,
Abstract: 以果蝇为材料,检测ncRNA在物种间表达的保守性.选取在黑腹果蝇(D.melanogaster)研究中获得的12个性腺特异表达的ncRNA基因,用RT-PCR技术分别对黑腹果蝇及其近缘物种D.simulans,D.yakuba,D.pseudoobscura和D.virilis的头部、精巢和卵巢进行了ncRNA转录信号的检测.结果显示,在果蝇中,ncRNA的表达与否及表达强度(表达图谱)在种间有显著差异,并体现出组织特异性的明显变动,表明ncRNA的表达在近缘物种间的保守性很低.
中国生物工程杂志 , 2015,
Abstract: 长链非编码rna(long-noncodingrna,lncrna)是一类长度大于200nt的非编码rna(noncodingrna,ncrna),不具有编码蛋白质的功能,直接以rna的形式发挥作用,以诱饵分子、信号分子、引导分子和支架分子的方式在转录水平和转录后水平调节蛋白质编码基因的表达,参与细胞分化和个体发育等生命过程.lncrna存在普遍的转录现象,但与蛋白质编码基因相比表达水平较低.基因组测序结果显示生物体内仅有少量的编码基因,绝大部分基因以非编码的形式存在于动物和植物体内起调控作用.近年来以mirna和sirna为代表的ncrna的研究已经取得了丰硕的成果,而lncrna的研究才刚刚开始,但是已经有研究表明lncrna有广泛的生物学功能,如染色体修饰、x染色体沉默、干扰或激活转录和核内运输等.以转录组测序、微阵列和荧光原位杂交为代表的研究方法也在发展完善.
Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature
Mathew W Wright, Elspeth A Bruford
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-2-90
Abstract: At the beginning of this century, many geneticists were predicting that the human genome contained around 100,000 protein-coding genes, partly based on the assumption that more complex organisms would have a greater number of genes. Ten years later, with far more genomic data from a wide variety of organisms and a much better-quality, well-annotated human genome, this original expectation has been downsized to around 20,000 protein-coding genes. This means that highly complex organisms like the human have about the same number of protein-coding genes as much simpler life forms such as the roundworm, Caenorhabditis elegans. If we look to the human's closest living relative, the chimpanzee, we see that the equivalent proteins in human and chimpanzee typically differ by only two amino acids, and approximately 29 per cent of all the orthologous proteins encoded in human and chimpanzee are identical [1]. Why, then, when the protein-coding components of our genomes are so similar, are humans and chimpanzees so strikingly different? Since protein-coding genes comprise only two per cent of the human genome, the answer may lie in the large swathes of the genome previously regarded as 'junk DNA'. Indeed, the ENCyclopedia Of DNA Elements (ENCODE) Consortium,[2] which is aiming to identify all the functional elements in the human genome, suggests that the vast majority of the genome is transcribed as non-protein-coding RNA (ncRNA). These RNAs could be responsible for some of the complex differences between humans and other primates, especially since the expression of many genes is now thought to be regulated by ncRNAs. They are also known to be involved in many other diverse and vital roles within our bodies, including protein biosynthesis and the splicing of messenger RNAs (mRNAs), and have been implicated in many diseases, such as Prader-Willi syndrome and various cancers (for review, see Taft et al.[3]). It is not surprising, then, that interest in ncRNAs has accelerated eve
中国科学 生命科学 , 2009,
Abstract: 非编码RNA(non-coding RNA,ncRNA)是指不翻译产生蛋白质的RNA.近年来,对ncRNA在基因表达调控中的功能进行了广泛的研究,ncRNA在发育、代谢和疾病等生命活动中都起着重要的作用.本文总结了ncRNA在胚胎发育、干细胞维持和器官发生等动物发育过程中的作用.
齐力旺,Xinmin Li,张守攻,安道昌
中国科学 生命科学 , 2006,
Abstract: 大规模cDNA文库的测序和Tiling基因芯片研究结果表明,人类基因组中大约50%的DNA可以转录为RNA,其中只有2%能够翻译蛋白质(即mRNA),其余98%为非编码蛋白RNAs(ncRNAs).最近研究初步显示,这些ncRNAs可以通过多种遗传机理调控DNA的结构、RNA的表达及蛋白质的翻译和功能,进而在细胞、组织或个体水平上影响生物体的正常生长发育.迄今,人们仍对这占转录RNA 95%以上的ncRNA的功能了解甚少,但弄清这些ncRNAs在遗传信息传递过程中的作用机理和个体发育过程中的生物功能,是揭示生命奥妙不可缺少的环节.为促进当今生命科学中这个最活跃研究领域的进展,特综述ncRNA的历史和现状、作用机理及功能、发现和鉴定方法,以及功能研究手段和应用理论、方法与实例.
Funcionalidades dos RNA n o codificantes (ncRNA) e pequenos RNA reguladores, nos mamíferos (RNA non-coding -ncRNA- functionalities and small RNA regulators in mammals
Dias Correia, J. H. R.:,Dias Correia, A.A.:
REDVET , 2007,
Abstract: Os ácidos ribonucleicos n o codificadores de proteínas (ncRNA) s o um importante conjunto de RNA dentro da totalidade dos transcritos existentes nas células animais. Os ncRNA contêm nas suas moléculas informa es variadas que lhes permitem ter diversas fun es. Nos ncRNA há que considerar diversos tipos , mas para o seu funcionamento há que atender aos aspectos subjacentes ao emparelhamento entre moléculas. O fenómeno do RNA de interferência (RNAi) desencadeado pelos ncRNA (mi/siRNA) revelou que a estabilidade e tradu o dos RNA mensageiros (mRNA) e a estrutura da cromatina podem ser reguladas por esses ncRNA nos animais. A biogénese, mecanismos de ac o (cis o ou repress o da tradu o) , tal como a distin o entre miRNA e siRNA v o sendo descobertas correlativamente com a respectiva identifica o e especificidade celular. A presen a de miRNA específicos no tecido muscular está bem assinalada tal como a sua possível regula o em hipertrofias musculares notáveis em ovinos (Texel). As potencialidades do conhecimento aprofundado dos fenómenos de RNAi e a constru o de miRNA exógenos específicos e sua introdu o em células, tecidos ou órg os, antevêm diversas hipóteses biotecnológicas, terapêuticas, produtivas ou preventivas, acauteladas que estejam as muitas implica es envolvidas.
Why YRNAs? About Versatile RNAs and Their Functions
Marcel K?hn,Nikolaos Pazaitis,Stefan Hüttelmaier
Biomolecules , 2013, DOI: 10.3390/biom3010143
Abstract: Y?RNAs constitute a family of highly conserved small noncoding RNAs (in humans: 83-112 nt; Y1, Y3, Y4 and Y5). They are transcribed from individual genes by RNA-polymerase?III and fold into conserved stem-loop-structures. Although discovered 30 years ago, insights into the cellular and physiological role of Y?RNAs remains incomplete. In this review, we will discuss knowledge on the structural properties, associated proteins and discuss proposed functions of Y?RNAs. We suggest Y?RNAs to be an integral part of ribonucleoprotein networks within cells and could therefore have substantial influence on many different cellular processes. Putative functions of Y?RNAs include small RNA quality control, DNA replication, regulation of the cellular stress response and proliferation. This suggests Y?RNAs as essential regulators of cell fate and indicates future avenues of research, which will provide novel insights into the role of small noncoding RNAs in gene expression.
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