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Analysis of microRNA knockouts in mice

HUMAN MOLECULAR GENETICS 2010年第R2期19卷 R169-R175页

作者： Park, Chong Y. Choi, Yun S. McManus, Michael T. Univ Calif San Francisco UCSF Diabet Ctr San Francisco CA 94143 USA Univ Calif San Francisco Biomed Sci Grad Program San Francisco CA 94143 USA Univ Calif San Francisco Dept Microbiol & Immunol San Francisco CA 94143 USA

MicroRNAs (miRNAs) are small noncoding RNAs that act as potent regulators of gene expression. The discovery of miRNAs with specific temporal and spatial expression patterns revealed a hidden layer of post-transcriptional gene regulation. Furthermore, differential expression of miRNAs during disease progression identified miRNAs as relevant candidate genes in human pathologies. Currently the exact roles of miRNAs in human development and disease progression remain largely unknown. There have been recent efforts to study the loss of these genes in vivo and this review will discuss published miRNA knockout mouse models, highlighting their potential mechanisms of action in vivo.

关键词： .Roles knockouts miRNAs noncoding miRNA knockout

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ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder

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TRENDS IN GENETICS 2024年第11期40卷 914-916页

作者： Burns, Vanessa F. Radford, Elizabeth J. Wellcome Sanger Inst Hinxton CB10 1SA England Univ Cambridge Dept Paediat Level 8Cambridge Biomed Campus Cambridge CB2 0QQ England

Two recent papers have identified genetic variants in the noncoding gene RNU4-2 to cause a frequent neurodevelopmental disorder. This work will have a substantial impact on the rare disease community, leading to thous... 详细信息

关键词： RNU4-2 syndrome ReNU syndrome small nuclear RNA noncoding neurodevelopmental disorder rare disease

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ROLE FOR POLIOVIRUS PROTEASE 2A IN CAP INDEPENDENT TRANSLATION

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EMBO JOURNAL 1994年第4期13卷 924-927页

作者： MACADAM, AJ FERGUSON, G FLEMING, T STONE, DM ALMOND, JW MINOR, PD UNIV READING DEPT MICROBIOLREADING RG6 5AJBERKSENGLAND

Viral protein synthesis in poliovirus infected cells was found to be influenced by mutations in part of the viral 5'-non-coding region (NCR) in a temperature dependent manner. At elevated temperatures these mutations resulted in virus titre reductions that allowed selection of revertant viruses. Some revertants were found to have retained the 5'-NCR mutations but had compensating mutations in the 2A protease gene that were responsible for the suppression of the temperature sensitive phenotypes. The mutations in 2A enhanced viral protein synthesis at a stage when cap dependent translation was already abolished, suggesting that the virally encoded protein 2A is directly involved in the process of cap independent translation in addition to its role in abolishing cap dependent translation.

关键词： CAP INDEPENDENT noncoding POLIOVIRUS PROTEASE TRANSLATION

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Are there any HOTTIPs for defining coding potential of lncRNAs, or just a lot of HOTAIR?

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EPIGENOMICS 2017年第8期9卷 1045-1047页

作者： Mather, Rebecca L. Hirst, Mark Crea, Francesco Open Univ Sch Life Hlth & Chem Sci Walton Hall Milton Keynes MK7 6AA Bucks England

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Mit :: Ai :: Aim :: Aim-1530

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2016年

Mit :: Ai :: Aim :: Aim-1530 by published by

关键词： aim-1530 behavior branches coding dna dna sequences grammars languages massachusetts institute natural natural language natural languages noncoding noncoding dna noncoding regions noncoding sequences sequences word frequencies zipf

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Reversibility and heritability of liver fibrosis:Implications for research and therapy

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World Journal of Gastroenterology 2015年第17期21卷 5138-5148页

作者： Hussein M Atta Department of Surgery Faculty of MedicineMinia UniversityEl-Minia 61519Egypt

Liver fibrosis continues to be a major health problem worldwide due to lack of effective *** the etiology cannot be eliminated,liver fibrosis progresses to cirrhosis and eventually to liver failure or malignancy;both are associated with a fatal *** transplantation,the only curative therapy,is still mostly *** fibrosis was shown to be a reversible process;however,complete reversibility remains ***,the molecular markers of liver fibrosis were shown to be transmitted across *** mechanisms including DNA methylation,histone posttranslational modifications and noncoding RNA have emerged as major determinants of gene expression during liver fibrogenesis and ***,epigenetic mechanisms have been shown to be transmitted through mitosis and meiosis to daughter cells and subsequent ***,the exact epigenetic regulation of complete liver fibrosis resolution and inheritance has not been fully *** communication will highlight the recent advances in the search for delineating the mechanisms governing resolution of liver fibrosis and the potential for multigenerational and transgenerational transmission of fibrosis *** fact that epigenetic changes,unlike genetic mutations,are reversible and can be modulated pharmacologically underscores the unique opportunity to develop effective therapy to completely reverse liver fibrosis,to prevent the development of malignancy and to regulate heritability of fibrosis phenotype.

关键词： Epigenetics Epimutations Inheritance Livercirrhosis Hepatic stellate cells Histone modification DNA methylation MicroRNA Long noncoding RNA Transcription regulation

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Integrative transcriptomic analysis unveils lncRNA-miRNA-mRNA interplay in tomato plants responding to Ralstonia solanacearum

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2023年第Part3期253卷 126891页

作者： Si, Xiuyang Liu, Hongyan Cheng, Xi Xu, Chengcui Han, Zhanghui Dai, Zhongren Wang, Rongqing Pan, Changtian Lu, Gang Zhejiang Univ Coll Agr & Biotechnol Dept Hort Hangzhou 310058 Peoples R China Harbin Acad Agr Sci Branch Acad Hort Res Harbin 150029 Peoples R China Zhejiang Acad Agr Sci Inst Vegetables Hangzhou 310022 Peoples R China Zhejiang Univ Key Lab Hort Plant Growth Dev & Qual Improvement Minist Agr Hangzhou 310058 Peoples R China

Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.

关键词： Tomato noncoding Ralstonia solanacearum ceRNA Plant-pathogen interactions

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Classification of short human exons and introns based on statistical features

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Physical Review E 2003年第6期67卷 061916-061916页

作者： Yonghui Wu Alan Wee-Chung Liew Hong Yan Mengsu Yang []Department of Computer Engineering and Information Technology 83 Tat Chee Avenue City University of Hong Kong Kowloon Hong Kong

The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this paper, we define a set of features, called the simple Z (SZ) features, which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that SZ features, while fewer in numbers (three in total), can preserve the high recognition rate of the original nine Z-curve features. Since the size of SZ features is one-third of the Z-curve features, the dimensionality of the feature space is much smaller, and better recognition efficiency is achieved. If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of length <140bp can be obtained.

关键词： .sequences DNA Sequence PHYSICAL REVIEW curve introns set of features stop codon noncoding human exons statistical features Tat Chee SZ features recognition rate used together

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Lévy scaling: The diffusion entropy analysis applied to DNA sequences

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Physical Review E 2002年第3期66卷 031906-031906页

作者： Nicola Scafetta Vito Latora Paolo Grigolini Pratt School EE Department Duke University P.O. Box 90291 Durham North Carolina 27708 Center for Nonlinear Science University of North Texas P.O. Box 311427 Denton Texas 76203-1427 Dipartimento di Fisica e Astronomia Università di Catania and INFN Corso Italia 57 95129 Catania Italy Dipartimento di Fisica dell’Università di Pisa and INFM Piazza Torricelli 2 56127 Pisa Italy Istituto di Biofisica CNR Area della Ricerca di Pisa Via Alfieri 1 San Cataldo 56010 Ghezzano-Pisa Italy

We address the problem of the statistical analysis of a time series generated by complex dynamics with the diffusion entropy analysis (DEA) [N. Scafetta, P. Hamilton, and P. Grigolini, Fractals 9, 193 (2001)]. This method is based on the evaluation of the Shannon entropy of the diffusion process generated by the time series imagined as a physical source of fluctuations, rather than on the measurement of the variance of this diffusion process, as done with the traditional methods. We compare the DEA to the traditional methods of scaling detection and prove that the DEA is the only method that always yields the correct scaling value, if the scaling condition applies. Furthermore, DEA detects the real scaling of a time series without requiring any form of detrending. We show that the joint use of DEA and variance method allows to assess whether a time series is characterized by Lévy or Gauss statistics. We apply the DEA to the study of DNA sequences and prove that their large-time scales are characterized by Lévy statistics, regardless of whether they are coding or noncoding sequences. We show that the DEA is a reliable technique and, at the same time, we use it to confirm the validity of the dynamic approach to the DNA sequences, proposed in earlier work.

关键词： .DNA sequences applies noncoding SDA

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Phylogeny derived from homodimeric endonuclease correlates with its pre-RNA substrates

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Advances in Bioscience and Biotechnology 2011年第3期2卷 117-122页

作者： Sanga Mitra Smarajit Das Satyabrata Sahoo Chandana Sinha Jayprokas Chakrabarti 不详

Amongst endonuclease, the homodimeric variety is found in many prokaryotes for processing of the introns out from pre-RNAs. But as the variety and the complexity of introns rise with evolution, do the homodimeric endonuclease adapt to the changes? The correlations between evolving pre-RNAs and adapting homodimeric endonuclease in lower prokaryotes is investigated in this paper. First, we construct and observe the appearance of a long branch in the phylogeny based on homodimeric endonuclease. To appreciate the finer aspects of accelerating evolution near this long branch, we delve deeper into the pre-RNA substrates of the endonuclease. Computational evidence of an as-yet-unreported noncoding RNA gene then emerges from this study. The capabilities of homodimeric endonuclease and the complexities of its pre-RNA substrates appear to evolve in steps together.

关键词： Phylogeny Maximum Likelihood Method Homodimeric Endonuclease noncoding RNA Intron Methanogen

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