检索结果-内蒙古大学图书馆

Arena-Idb: a platform to build human non-coding rna interaction networks

BMC BIOINFORMATICS 2018年第10期19卷 231-244页

作者： Bonnici, Vincenzo De Caro, Giorgio Constantino, Giorgio Liuni, Sabino D'Elia, Domenica Bombieri, Nicola Licciulli, Flavio Giugno, Rosalba Univ Verona Dept Comp Sci Str Le Grazie Verona Italy Natl Res Council CNR Inst Biomed Technol Bari Italy

Background: High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. non-coding rnas (ncrnas), for a long time believed to be non-functional, are emerging as one of the most important and large family of gene regulators and key elements for genome maintenance. Functional studies have been able to assign to ncrnas a wide spectrum of functions in primary biological processes, and for this reason they are assuming a growing importance as a potential new family of cancer therapeutic targets. Nevertheless, the number of functionally characterized ncrnas is still too poor if compared to the number of new discovered ncrnas. Thus platforms able to merge information from available resources addressing data integration issues are necessary and still insufficient to elucidate ncrnas biological roles. Results: In this paper, we describe a platform called Arena-Idb for the retrieval of comprehensive and non-redundant annotated ncrnas interactions. Arena-Idb provides a framework for network reconstruction of ncrna heterogeneous interactions (i.e., with other type of molecules) and relationships with human diseases which guide the integration of data, extracted from different sources, via mapping of entities and minimization of ambiguity. Conclusions: Arena-Idb provides a schema and a visualization system to integrate ncrna interactions that assists in discovering ncrna functions through the extraction of heterogeneous interaction networks. The Arena-Idb is available at http://***

关键词： non-coding rna Database Network Data integration

来源：评论

学校读者我要写书评

暂无评论

Translational Regulation of Gene Expression by an Anaerobically Induced Small non-coding rna in Escherichia coli

引用

JOUrnaL OF BIOLOGICAL CHEMISTRY 2010年第14期285卷 10690-10702页

作者： Boysen, Anders Moller-Jensen, Jakob Kallipolitis, Birgitte Valentin-Hansen, Poul Overgaard, Martin Univ So Denmark Dept Biochem & Mol Biol DK-5230 Odense M Denmark

Small non-coding rnas (srna) have emerged as important elements of gene regulatory circuits. In enterobacteria such as Escherichia coli and Salmonella many of these srnas interact with the Hfq protein, an rna chaperone similar to mammalian Sm-like proteins and act in the post-transcriptional regulation of many genes. A number of these highly conserved ribo-regulators are stringently regulated at the level of transcription and are part of major regulons that deal with the immediate response to various stress conditions, indicating that every major transcription factor may control the expression of at least one srna regulator. Here, we extend this view by the identification and characterization of a highly conserved, anaerobically induced small srna in E. coli, whose expression is strictly dependent on the anaerobic transcriptional fumarate and nitrate reductase regulator (FNR). The srna, named FnrS, possesses signatures of base-pairing rnas, and we show by employing global proteomic and transcriptomic profiling that the expression of multiple genes is negatively regulated by the srna. Intriguingly, many of these genes encode enzymes with "aerobic" functions or enzymes linked to oxidative stress. Furthermore, in previous work most of the potential target genes have been shown to be repressed by FNR through an undetermined mechanism. Collectively, our results provide insight into the mechanism by which FNR negatively regulates genes such as sodA, sodB, cydDC, and metE, thereby demonstrating that adaptation to anaerobic growth involves the action of a small regulatory rna.

关键词： GENE expression GENETIC regulation non-coding rna ESCHERICHIA coli ENTEROBACTER

来源：评论

学校读者我要写书评

暂无评论

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

引用

Science China(Life Sciences) 2013年第10期56卷 953-959页

作者： ZHAO Yi WANG Jian CHEN XiaoWei LUO HaiTao ZHAO YunJie XIAO Yi CHEN RenSheng Bioinformatics Research Group Advanced Computing Research LaboratoryInstitute of Computing TechnologyChinese Academy ofSciences Department of Physics Huazhong University of Science and Technology Laboratory of Bioinformatics and Non-coding RNA Institute of BiophysicsChinese Academy of Sciences

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 *** roles,including as scaffolds and as guides for protein-coding genes,mainly depend on the structure and expression level of *** 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.

关键词： non-coding rna structure expression function

来源：评论

学校读者我要写书评

暂无评论

Genome-wide identification and characterization of novel non-coding rna-derived SSRs in wheat

引用

MOLECULAR BIOLOGY REPORTS 2020年第8期47卷 6111-6125页

作者： Bhandawat, Abhishek Sharma, Himanshu Pundir, Neha Madhawan, Akansha Roy, Joy Natl Agrifood Biotechnol Inst Sect 81 Mohali 140306 Punjab India

Expression of eukaryotic genes is largely regulated by non-coding rnas (ncrna). Sequence variations in the regulatory rnas may have critical biological consequences including transcriptional and post-transcriptional gene regulation. ncrna-derived markers thus can be proved useful in molecular breeding, QTL mapping and association studies for trait dissection. In present study, we identified a total of 661 SSRs dwelling in pre-mirna (15), small nuclear rna (25) and lncrna (621). Of these, 46 were validated and 100% amplification success was observed in selected wheat genotypes. A set of 36 ncrna-SSRs markers was utilized for genetic variability assessment in forty-eight Indian wheat genotypes (which includes bread wheat, durum wheat and relatives). Number of alleles ranged from 1 to 4 with an average of two alleles per SSR locus. Mean PIC, observed heterozygosity and Shannon information index were found to be 0.258, 0.37 and 0.476 which suggests ncrna-SSRs show higher polymorphism compared to genic SSRs but lower polymorphism compared to genomic SSRs. Thirty-six ncrna-SSRs showed transferability ranging from 42.1% to 100%. Average genetic dissimilarity among wheat genotypes was found to be 0.29 based on Jaccard's dissimilarity. This is the first report of ncrna-SSRs in wheat which will be useful for molecular breeding and genetic improvement of wheat.

关键词： Long non-coding rna mirna non-coding rna snrna SSRs Wheat

来源：评论

学校读者我要写书评

暂无评论

The study of the mechanism of non-coding rna regulation of programmed cell death in diabetic cardiomyopathy

引用

MOLECULAR AND CELLULAR BIOCHEMISTRY 2024年第7期479卷 1673-1696页

作者： Zhang, Bingrui Wu, Hua Zhang, Jingwen Cong, Cong Zhang, Lin Shandong Univ Tradit Chinese Med Affiliated Hosp Cardiovasc Dept Cardiovasc Dis Res Jinan 250014 Shandong Peoples R China Taian Special Care Hosp Clin Lab Med Lab Direct Tai An 271000 Shandong Peoples R China Taian Hosp Chinese Med Cardiovasc Dept Cardiovasc Dis Res 216Yingxuan St Tai An 271000 Shandong Peoples R China

Diabetic cardiomyopathy (DCM) represents a distinct myocardial disorder elicited by diabetes mellitus, characterized by aberrations in myocardial function and structural integrity. This pathological condition predominantly manifests in individuals with diabetes who do not have concurrent coronary artery disease or hypertension. An escalating body of scientific evidence substantiates the pivotal role of programmed cell death (PCD)-encompassing apoptosis, autophagy, pyroptosis, ferroptosis, and necroptosis-in the pathogenic progression of DCM, thereby emerging as a prospective therapeutic target. Additionally, numerous non-coding rnas (ncrnas) have been empirically verified to modulate the biological processes underlying programmed cell death, consequently influencing the evolution of DCM. This review systematically encapsulates prevalent types of PCD manifest in DCM as well as nascent discoveries regarding the regulatory influence of ncrnas on programmed cell death in the pathogenesis of DCM, with the aim of furnishing novel insights for the furtherance of research in PCD-associated disorders relevant to DCM.

关键词： non-coding rna Programmed cell death Diabetic cardiomyopathy Mechanisms of action

来源：评论

学校读者我要写书评

暂无评论

NCYPred: A Bidirectional LSTM Network With Attention for Y rna and Short non-coding rna Classification

引用

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023年第1期20卷 557-565页

作者： Lima, Diego de S. Amichi, Luiz J. A. Fernandez, Maria A. Constantino, Ademir A. V. Seixas, Flavio A. Univ Estadual Maringa Dept Techonol BR-87506370 Umuarama Parana Brazil Univ Estadual Maringa Dept Informat BR-87020900 Maringa Parana Brazil Univ Estadual Maringa Dept Biotechnol Genet & Cell Biol BR-87020900 Maringa Parana Brazil

Short non-coding rnas (sncrnas) are involved in multiple cellular processes and can be divided into dozens of classes. Among such classes, Y rnas have been gaining attention, being essential factors for the initiation of DNA replication on vertebrates, as well as potential tumor biomarkers. Homologs have also been described in nematodes and insects, as well as related sequences in bacteria. Methods capable of accurately predicting Y rna transcripts are lacking. In this work, we developed an attention-based LSTM network and built a classification model able to classify sncrnas (including Y rna) directly from nucleotide sequences. A dataset consisting of 45,447 sncrna sequences, from a wide range of organisms, obtained from Rfam 14.3 was built. Performance evaluation demonstrated that our proposed method, NCYPred (non-coding/Y rna Prediction), can accurately predict Y rna sequences and their homologs, as well as 11 additional classes, achieving results comparable with state-of-the-art methods. We also demonstrate that applying t-SNE on learned sequence representations could be useful for sequence analysis. Our model is freely available as a web-server (https://***/ncypred/).

关键词： non-coding rna Y rna recurrent neural network sequence classification web server

来源：评论

学校读者我要写书评

暂无评论

Loss of non-coding rna expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines

引用

STEM CELL RESEARCH & THERAPY 2015年第1期6卷 1页

作者： Mo, Chu-Fan Wu, Fang-Chun Tai, Kang-Yu Chang, Wei-Chun Chang, Kai-Wei Kuo, Hung-Chih Ho, Hong-Nerng Chen, Hsin-Fu Lin, Shau-Ping Natl Taiwan Univ Inst Biotechnol Taipei 106 Taiwan Natl Taiwan Univ Hosp Coll Med Dept Obstet & Gynecol Taipei 100 Taiwan Natl Taiwan Univ Hosp Taipei 100 Taiwan Natl Taiwan Univ Coll Med Grad Inst Med Genom & Prote Taipei 100 Taiwan Natl Taiwan Univ Genome & Syst Biol Degree Program Taipei 106 Taiwan Acad Sinica Genome & Syst Biol Degree Program Taipei 115 Taiwan Acad Sinica Genom Res Ctr Taipei 115 Taiwan Acad Sinica Inst Cellular & Organism Biol Taipei 115 Taiwan Acad Sinica Agr Biotechnol Res Ctr Taipei 115 Taiwan Natl Taiwan Univ Res Ctr Dev Biol & Regenerat Med Taipei 106 Taiwan Natl Taiwan Univ Ctr Syst Biol Taipei 106 Taiwan

Introduction: Pluripotent stem cells are increasingly used to build therapeutic models, including the transplantation of neural progenitors derived from human embryonic stem cells (hESCs). Recently, long non-coding rnas (lncrnas), including delta-like homolog 1 gene and the type III iodothyronine deiodinase gene (DLK1-DIO3) imprinted locus-derived maternally expressed gene 3 (MEG3), were found to be expressed during neural development. The deregulation of these lncrnas is associated with various neurological diseases. The imprinted locus DLK1-DIO3 encodes abundant non-coding rnas (ncrnas) that are regulated by differential methylation of the locus. We aim to study the correlation between the DLK1-DIO3-derived ncrnas and the capacity of hESCs to differentiate into neural lineages. Methods: We classified hESC sublines into MEG3-ON and MEG3-OFF based on the expression levels of MEG3 and its downstream micrornas as detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A cDNA microarray was used to analyze the gene expression profiles of hESCs. To investigate the capacity of neural differentiation in MEG3-ON and MEG3-OFF hESCs, we performed neural lineage differentiation followed by neural lineage marker expression and neurite formation analyses via qRT-PCR and immunocytochemistry, respectively. MEG3-knockdown via small interfering rna (sirna) and small hairpin rna (shrna) was used to investigate the potential causative effect of MEG3 in regulating neural lineage-related gene expression. Results: DLK1-DIO3-derived ncrnas were repressed in MEG3-OFF hESCs compared with those in the MEG3-ON hESCs. The transcriptome profile indicated that many genes related to nervous system development and neural-type tumors were differentially expressed in MEG3-OFF hESCs. Three independent MEG3-knockdown assays using different sirna and shrna constructs consistently resulted in downregulation of some neural lineage genes. Lower expression levels of stage-speci

关键词： HUMAN embryonic stem cells PLURIPOTENT stem cells STEM cell transplantation non-coding rna NEURAL development REVERSE transcriptase polymerase chain reaction GENE expression

来源：评论

学校读者我要写书评

暂无评论

Dissecting non-coding rna mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting

引用

METHODS 2013年第2期63卷 188-199页

作者： Pitchiaya, Sethuramasundaram Krishnan, Vishalakshi Custer, Thomas C. Walter, Nils G. Univ Michigan Single Mol Anal Real Time SMART Ctr Ann Arbor MI 48109 USA Univ Michigan Single Mol Anal Grp Dept Chem Ann Arbor MI 48109 USA Univ Michigan Program Chem Biol Ann Arbor MI 48109 USA

non-coding rnas (ncrnas) recently were discovered to outnumber their protein-coding counterparts, yet their diverse functions are still poorly understood. Here we report on a method for the intracellular Single-molecule High-Resolution Localization and Counting (iSHiRLoC) of micrornas (mirnas), a conserved, ubiquitous class of regulatory ncrnas that controls the expression of over 60% of all mammalian protein coding genes post-transcriptionally, by a mechanism shrouded by seemingly contradictory observations. We present protocols to execute single particle tracking (SPT) and single-molecule counting of functional microinjected, fluorophore-labeled mirnas and thereby extract diffusion coefficients and molecular stoichiometries of micro-ribonucleoprotein (miRNP) complexes from living and fixed cells, respectively. This probing of mirnas at the single molecule level sheds new light on the intracellular assembly/disassembly of miRNPs, thus beginning to unravel the dynamic nature of this important gene regulatory pathway and facilitating the development of a parsimonious model for their obscured mechanism of action. (C) 2013 Elsevier Inc. All rights reserved.

关键词： rna silencing microrna non-coding rna Single molecule microscopy Single particle tracking

来源：评论

学校读者我要写书评

暂无评论

Leishmania-induced repression of selected non-coding rna genes containing B-box element at their promoters in alternatively polarized M2 macrophages

引用

MOLECULAR AND CELLULAR BIOCHEMISTRY 2011年第1-2期350卷 47-57页

作者： Farrow, Anitra L. Rana, Tanu Mittal, Mukul K. Misra, Smita Chaudhuri, Gautam Meharry Med Coll Dept Microbiol & Immunol Nashville TN 37208 USA

Leishmania is a group of parasitic protozoa that infect blood and tissue phagocytes including macrophages. We hypothesize that Leishmania is capable of establishing infection inside the macrophages because (a) they infect a subpopulation of macrophages;and (b) they "renovate" the macrophages before the establishment of infection. We found that only alternatively activated polarized M2 macrophages support Leishmania growth. Exposure of M2 macrophages to Leishmania promastigotes represses several selected rna polymerase III (PolIII)-transcribed non-coding rna (ncrna) genes including those of 7SL rna, vault rna, and B2 rna which have B-box element at their promoters. The B-box-binding transcription factor TFIIIC110 is down-regulated in Leishmania-exposed macrophages. Both the surface protease gp63 and the surface glycolipid LPG are required for the down-regulation of the ncrnas in the M2 macrophages. We conclude that Leishmania surface gp63 collaborates with LPG to down-regulate TFIIIC110 in M2 macrophages to repress B-box containing ncrna gene promoters.

关键词： Leishmania non-coding rna 7SL rna Vault rna H1 rna B2 rna gp63 LPG Scavenger receptor SR-AII TFIIIC110 B-box rna polymerase III

来源：评论

学校读者我要写书评

暂无评论

Strand-specific rna sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding rna and circular rna

引用

BMC GENOMICS 2015年第1期16卷 1-22页

作者： Broadbent, Kate M. Broadbent, Jill C. Ribacke, Ulf Wirth, Dyann Rinn, John L. Sabeti, Pardis C. Harvard Univ Sch Med Dept Syst Biol Boston MA 02115 USA Broad Inst Cambridge MA USA Harvard Univ FAS Ctr Syst Biol Boston MA 02115 USA Harvard Univ Dept Organism & Evolutionary Biol Boston MA 02115 USA Harvard Univ Sch Publ Hlth Dept Immunol & Infect Dis Boston MA 02115 USA Uppsala Univ BMC Dept Cell & Mol Biol Uppsala Sweden Harvard Univ Dept Stem Cell & Regenerat Biol Boston MA 02115 USA

Background: The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding rnas (lncrnas) could represent a missing regulatory layer across a broad range of organisms. Results: To investigate the regulatory capacity of lncrna in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected rna sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from rna sequencing data. This approach enabled the annotation of over one thousand lncrna transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncrnas with compelling properties. non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular rnas, six of which we validated experimentally. Conclusions: We found that a subset of lncrnas, including all subtelomeric lncrnas, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mrnas, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circrnas, which is notable given the lack of rna interference in the organism, and discovered that a highly expressed, five-exon antisense rna is poised

关键词： rna sequencing non-coding rna lncrna Antisense rna circrna microrna Malaria Plasmodium Transcriptome Gene regulation Extreme genome PfGDV1

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：