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Identification of non-coding rnas Based on Alignment-Free Features in Crassostrea gigas(Pacific Oyster)Transcriptome

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Journal of Ocean University of China 2022年第6期21卷 1633-1640页

作者： CHAI Wenjing SONG Kai School of Mathematics and Statistics Qingdao UniversityQingdao 266071China

non-coding rnas(ncrnas)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and *** novel transcripts have been identified via high-throughput ***,identifying ncrnas among the transcripts of novel species using alignment-based features is ***,developing a fast and accurate method based on alignment-free features to identify ncrnas among novel transcripts is *** this study,we proposed a new approach,namely,coding potential prediction based on alignment-free features(CPAF),to identify ncrnas among a large number of *** used four types of features:Fickett score;Hexamer score;composition,transition,and distribution features;and modified *** the results,CPAF performed better than previous state-of-the-art methods in predicting ncrna transcripts,with particular reference to small ***,we applied CPAF to identify ncrnas in Pacific oyster *** approach identified more ncrnas than other previously used methods.

关键词： non-coding rna alignment-free k-mer transcripts

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Identification and characterization of moonlighting long non-coding rnas based on rna and protein interactome

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BIOINFORMATICS 2018年第20期34卷 3519-3528页

作者： Cheng, Lixin Leung, Kwong-Sak Chinese Univ Hong Kong Dept Comp Sci & Engn Shatin Hong Kong Peoples R China Shenzhen Univ Inst Translat Med Shenzhen Peoples Hosp 2 Affiliated Hosp 1 Shenzhen Peoples R China

Motivation: Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding rnas (lncrnas) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncrnas. MoonFinder is a statistical algorithm identifying moonlighting lncrnas without a priori knowledge through the integration of protein interactome, rna-protein interactions and functional annotation of proteins. Results: We identify 155 moonlighting lncrna candidates and uncover that they are a distinct class of lncrnas characterized by specific sequence and cellular localization features. The non-coding genes that transcript moonlighting lncrnas tend to have shorter but more exons and the moonlighting lncrnas have a variable localization pattern with a high chance of residing in the cytoplasmic compartment in comparison to the other lncrnas. Moreover, moonlighting lncrnas and moonlighting proteins are rather mutually exclusive in terms of both their direct interactions and interacting partners. Our results also shed light on how the moonlighting candidates and their interacting proteins implicated in the formation and development of cancers and other diseases.

关键词： non-coding rna rna-protein interactions EXONS (Genetics) MOLECULAR chaperones MACHINE learning

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Identification of novel non-coding rna-based negative feedback regulating the expression of the oncogenic transcription factor GLI1

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MOLECULAR ONCOLOGY 2014年第5期8卷 912-926页

作者： Villegas, Victoria E. Rahman, Mohammed Ferdous-Ur Fernandez-Barrena, Maite G. Diao, Yumei Liapi, Eleni Sonkoly, Eniko Stahle, Mona Pivarcsi, Andor Annaratone, Laura Sapino, Anna Ramirez Clavijo, Sandra Burglin, Thomas R. Shimokawa, Takashi Ramachandran, Saraswathi Kapranov, Philipp Fernandez-Zapico, Martin E. Zaphiropoulos, Peter G. Karolinska Inst Dept Biosci & Nutr Huddinge Sweden Univ Rosario Fac Nat Sci & Math Bogota Colombia Univ Rosario Doctoral Program Biomed Sci Bogota Colombia Mayo Clin Schulze Ctr Novel Therapeut Rochester MN USA Karolinska Inst Dept Med Unit Dermatol & Venereol Solna Sweden Univ Turin Dept Med Sci Turin Italy St Laurent Inst Cambridge MA USA

non-coding rnas are a complex class of nucleic acids, with growing evidence supporting regulatory roles in gene expression. Here we identify a non-coding rna located head-to-head with the gene encoding the Glioma-associated oncogene 1 (GLI1), a transcriptional effector of multiple cancer-associated signaling pathways. The expression of this three-exon GLI1 antisense (GLI1AS) rna in cancer cells was concordant with GLI1 levels. sirnas knockdown of GLI1AS up-regulated GLI1 and increased cellular proliferation and tumor growth in a xenograft model system. Conversely, GLI1AS overexpression decreased the levels of GLI1, its target genes PTCH1 and PTCH2, and cellular proliferation. Additionally, we demonstrate that GLI1 knockdown reduced GLI1AS, while GLI1 overexpression increased GLI1AS, supporting the role of GLI1AS as a target gene of the GLI1 transcription factor. Activation of TGF beta and Hedgehog signaling, two known regulators of GLI1 expression, conferred a concordant up-regulation of GLI1 and GLI1AS in cancer cells. Finally, analysis of the mechanism underlying the interplay between GLI1 and GLI1AS indicates that the non-coding rna elicits a local alteration of chromatin structure by increasing the silencing mark H3K27me3 and decreasing the recruitment of rna polymerase II to this locus. Taken together, the data demonstrate the existence of a novel non-coding rna-based negative feedback loop controlling GLI1 levels, thus expanding the repertoire of mechanisms regulating the expression of this oncogenic transcription factor. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

关键词： non-coding rna Gene expression Transcription Chromatin GLI1 Cancer

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Small non-coding rna profiling and the role of pirna pathway genes in the protection of chicken primordial germ cells

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BMC GENOMICS 2014年第1期15卷 1-15页

作者： Rengaraj, Deivendran Lee, Sang In Park, Tae Sub Lee, Hong Jo Kim, Young Min Sohn, Yoon Ah Jung, Myunghee Noh, Seung-Jae Jung, Hojin Han, Jae Yong Seoul Natl Univ Dept Agr Biotechnol Coll Agr & Life Sci Seoul 151921 South Korea Seoul Natl Univ Res Inst Agr & Life Sci Coll Agr & Life Sci Seoul 151921 South Korea Chung Ang Univ Dept Anim Sci & Technol Anseong 456756 South Korea Seoul Natl Univ Grad Sch Int Agr Technol Pyeongchang Gun 232916 Gangwon Do South Korea Seoul Natl Univ Inst Green Bio Sci & Technol Pyeongchang Gun 232916 Gangwon Do South Korea Insilicogen Inc Codes Div Suwon 441813 South Korea

Background: Genes, rnas, and proteins play important roles during germline development. However, the functions of non-coding rnas (ncrnas) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncrnas, including micro rnas (mirnas), small-interfering rnas (sirnas), and PIWI-interacting rnas (pirnas). These ncrnas are functionally important in the genome, however, the identification and annotation of ncrnas in a genome is challenging. The aim of this study was to identify different types of small ncrnas particularly pirnas, and the role of pirna pathway genes in the protection of chicken primordial germ cells (PGCs). Results: At first, we performed next-generation sequencing to identify ncrnas in chicken PGCs, and we performed ab initio predictive analysis to identify putative pirnas in PGCs. Then, we examined the expression of three repetitive sequence-linked pirnas and 14 genic-transcript-linked pirnas along with their linked genes using real-time PCR. All pirnas and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known pirna pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using sirnas. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative pirna-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs. Conclusions: Our results increase the understanding of PGC-expressed pirnas and the role of pirna pathway genes in the protection of germ cells.

关键词： Aves non-coding rna pirna Primordial Germ Cells

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Expression of a non-coding rna in ectromelia virus is required for normal plaque formation

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VIRUS GENES 2014年第1期48卷 38-47页

作者： Esteban, David J. Upton, Chris Bartow-McKenney, Casey Buller, R. Mark L. Chen, Nanhai G. Schriewer, Jill Lefkowitz, Elliot J. Wang, Chunlin Vassar Coll Dept Biol Poughkeepsie NY 12601 USA Univ Victoria Dept Biochem & Microbiol Victoria BC Canada St Louis Univ Dept Mol Microbiol & Immunol St Louis MO 63103 USA Genelux Corp San Diego Sci Ctr San Diego CA USA Univ Alabama Birmingham Dept Microbiol Birmingham AL 35294 USA

Poxviruses are dsDNA viruses with large genomes. Many genes in the genome remain uncharacterized, and recent studies have demonstrated that the poxvirus transcriptome includes numerous so-called anomalous transcripts not associated with open reading frames. Here, we characterize the expression and role of an apparently non-coding rna in orthopoxviruses, which we call viral hairpin rna (vhrna). Using a bioinformatics approach, we predicted expression of a transcript not associated with an open reading frame that is likely to form a stem-loop structure due to the presence of a 21 nt palindromic sequence. Expression of the transcript as early as 2 h post-infection was confirmed by northern blot and analysis of publicly available vaccinia virus infected cell transcriptomes. The transcription start site was determined by RACE PCE and transcriptome analysis, and early and late promoter sequences were identified. Finally, to test the function of the transcript we generated an ectromelia virus knockout, which failed to form plaques in cell culture. The important role of the transcript in viral replication was further demonstrated using sirna. Although the function of the transcript remains unknown, our work contributes to evidence of an increasingly complex poxvirus transcriptome, suggesting that transcripts such as vhrna not associated with an annotated open reading frame can play an important role in viral replication.

关键词： Ectromelia virus Vaccinia virus non-coding rna Stem-loop Plaques

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Characteristics of long non-coding rna and its relation to hepatocellular carcinoma

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CARCINOGENESIS 2014年第3期35卷 507-514页

作者： Huang, Jin-Lan Zheng, Lei Hu, Yan-Wei Wang, Qian Southern Med Univ Nanfang Hosp Lab Med Ctr Guangzhou 510515 Guangdong Peoples R China

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide with high prevalence and lethality. However, the underlying mechanism for HCC has not been entirely elucidated. Recent studies have highlighted the roles of long non-coding rnas (lncrnas) in carcinogenesis, and it is suggested that they might play critical roles in HCC progression. Here, we will briefly introduce the biology of lncrnas, emphasizing the mechanisms and emerging roles of HCC-related lncrnas. To date, HCC-related lncrnas are demonstrated to influence the life cycle of genes by various means including epigenetic silencing, splicing regulation, lncrnamirna interaction, lncrnaprotein interaction and genetic variation. Moreover, they can participate in diverse biological processes involved in HCC progression through impacts upon cell proliferation, apoptosis, invasion and metastasis and angiogenesis. Since lncrna can present in body fluid and have good specificity and accessibility, some HCC-related lncrnas are suggested to be useful as novel potential biomarkers for HCC diagnosis, prognosis and prediction of response to therapy. Those HCC-related lncrnas may provide potential novel therapeutic targets for HCC and other diseases.

关键词： non-coding rna LIVER -- Cancer GENE silencing APOPTOSIS CELL proliferation EPIGENETICS

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Targeted next-generation sequencing and non-coding rna expression analysis of clear cell papillary renal cell carcinoma suggests distinct pathological mechanisms from other renal tumour subtypes

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JOUrnaL OF PATHOLOGY 2014年第1期232卷 32-42页

作者： Lawrie, Charles H. Larrea, Erika Larrinaga, Gorka Goicoechea, Ibai Arestin, Maria Fernandez-Mercado, Marta Hes, Ondrej Caceres, Francisco Manterola, Lorea Lopez, Jose I. Biodonostia Res Inst Oncol Area San Sebastian 20014 Spain Univ Oxford Nuffield Dept Clin Lab Sci Oxford OX1 2JD England Basque Fdn Sci IKERBASQUE Bilbao Spain Univ Basque Country UPV EHU Sch Nursing Leioa Bizkaia Spain Charles Univ Hosp Dept Pathol Plzen Czech Republic Cruces Univ Hosp Dept Urol Baracaldo Bizkaia Spain Univ Basque Country UPV EHU BioCruces Res Inst Cruces Univ Hosp Dept Pathol Baracaldo Bizkaia Spain

Clear cell tubulopapillary renal cell carcinoma (CCPRCC) is a recently described rare renal malignancy that displays characteristic gross, microscopic and immunohistochemical differences from other renal tumour types. However, CCPRCC remains a very poorly understood entity. We therefore sought to elucidate some of the molecular mechanisms involved in this neoplasm by carrying out targeted next-generation sequencing (NGS) to identify associated mutations, and in addition examined the expression of non-coding (nc) rnas. We identified multiple somatic mutations in CCPRCC cases, including a recurrent [3/14 cases (21%)] non-synonymous T992I mutation in the MET proto-oncogene, a gene associated with epithelial-to-mesenchymal transition (EMT). Using a microarray approach, we found that the expression of mature (n = 1105) and pre-mirnas (n = 1105), as well as snorna and scarnas (n = 2214), in CCPRCC cases differed from that of clear cell renal cell carcinoma (CCRCC) or papillary renal cell carcinoma (PRCC) tumours. Surprisingly, and unlike other renal tumour subtypes, we found that all five members of the miR-200 family were over-expressed in CCPRCC cases. As these mirnas are intimately involved with EMT, we stained CCPRCC cases for E-cadherin, vimentin and -catenin and found that the tumour cells of all cases were positive for all three markers, a combination rarely reported in other renal tumours that could have diagnostic implications. Taken together with the mutational analysis, these data suggest that EMT in CCPRCC tumour cells is incomplete or blocked, consistent with the indolent clinical course typical of this malignancy. In summary, as well as describing a novel pathological mechanism in renal carcinomas, this study adds to the mounting evidence that CCPRCC should be formally considered a distinct entity. Microarray data have been deposited in the GEO database [GEO accession number (GSE51554)]. Copyright (c) 2013 Pathological Society of Great Britain and Ireland. P

关键词： mirna non-coding rna EMT renal carcinoma clear cell papillary renal cell carcinoma

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NrsZ: a novel, processed, nitrogen-dependent, small non-coding rna that regulates Pseudomonas aeruginosa PAO1 virulence

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ENVIRONMENTAL MICROBIOLOGY 2014年第4期16卷 1053-1068页

作者： Wenner, Nicolas Maes, Alexandre Cotado-Sampayo, Marta Lapouge, Karine Univ Lausanne Dept Fundamental Microbiol CH-1015 Lausanne Switzerland Fasteris SA CH-1228 Plan Les Ouates Switzerland

The opportunistic pathogen Pseudomonas aeruginosa PAO1 has a remarkable capacity to adapt to various environments and to survive with limited nutrients. Here, we report the discovery and characterization of a novel small non-coding rna: NrsZ (nitrogen-regulated srna). We show that under nitrogen limitation, NrsZ is induced by the NtrB/C two-component system, an important regulator of nitrogen assimilation and P. aeruginosa's swarming motility, in concert with the alternative sigma factor RpoN. Furthermore, we demonstrate that NrsZ modulates P. aeruginosa motility by controlling the production of rhamnolipid surfactants, virulence factors notably needed for swarming motility. This regulation takes place through the post-transcriptional control of rhlA, a gene essential for rhamnolipids synthesis. Interestingly, we also observed that NrsZ is processed in three similar short modules, and that the first short module encompassing the first 60 nucleotides is sufficient for NrsZ regulatory functions.

关键词： non-coding rna PSEUDOMONAS aeruginosa VIRULENCE (Microbiology) RHAMNOLIPIDS GLYCOLIPIDS BACTERIA -- Swarming

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Exosomal non-coding rnas: Emerging roles in bilateral communication between cancer cells and macrophages

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MOLECULAR THERAPY 2022年第3期30卷 1036-1053页

作者： Li, Wenhao Wang, Xiaolong Li, Chen Chen, Tong Yang, Qifeng Shandong Univ Qilu Hosp Cheeloo Coll Med Dept Breast SurgGen Surg Jinan 250012 Shandong Peoples R China Shandong Univ Qilu Hosp Cheeloo Coll Med Dept Pathol Tissue Bank Jinan 250012 Shandong Peoples R China Shandong Univ Res Inst Breast Canc Jinan 250012 Shandong Peoples R China

The tumor microenvironment (TME) is a dynamic network of cellular organization that comprises diverse cell types and significantly contributes to cancer development. As pivotal immune stromal cells in the TME, macrophages are extensively heterogeneous and exert both antitumor and protumor functions. Exosomes are nanosized extracellular membranous vesicles with diameters between 30 and 150 nm. By transferring multiple bioactive substances such as proteins, lipids, and nucleic acids, exosomes play an important role in the communication between cells. Recently, growing evidence has demonstrated that non coding rnas (ncrnas) are enriched in exosomes and that exosomal ncrnas are involved in the crosstalk between cancer cells and macrophages. Furthermore, circulating exosomal ncrnas can be detected in biofluids, serving as promising noninvasive biomarkers for the early diagnosis and prognostic prediction of cancer. Exosome-based therapies are emerging as potent strategies that can be utilized to alleviate tumor progression. Herein, the present knowledge of exosomal ncrnas and their vital roles in regulating the interplay between cancer cells and macrophages, as well as their clinical applications are summarized.

关键词： cancer macrophage exosome non-coding rna crosstalk

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Advances in research regarding the roles of non-coding rnas in non-syndromic cleft lip with or without cleft palate: A systematic review

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ARCHIVES OF ORAL BIOLOGY 2022年 134卷 105319-105319页

作者： Wei, Yuanyuan Tian, Yu Yu, Xin Miao, Ziyue Xu, Yan Pan, Yongchu Nanjing Med Univ Dept Orthodont Affiliated Stomatol Hosp Nanjing Peoples R China Jiangsu Prov Key Lab Oral Dis Beijing Peoples R China Jiangsu Prov Engn Res Ctr Stomatol Translat Med Zhenjiang Peoples R China Fudan Univ Shanghai Stomatol Hosp Dept Orthodont Shanghai Peoples R China Fudan Univ Shanghai key Lab Craniomaxillofacial Dev & Dis Shanghai Peoples R China

Objective: To investigate by means of a literature review, what non-coding rnas engage in non-syndromic cleft lip with or without cleft palate (NSCL/P) and how they lead to the occurrence of this ***: A literature search of online databases (Medline via PubMed, Web of Science, Scopus, and Embase) was performed using appropriate keywords (e.g. non-coding rna, mirna, lncrna, NSCL/P, non-syndromic cleft lip only, and non-syndromic orofacial cleft). The risk of bias in the included studies was then assessed, and a comprehensive review of reported non-coding rnas associated with NSCL/P was ***: The initial search retrieved 133 studies reporting non-coding rnas associated with NSCL/P;after excluding 18 replicates and 77 ineligible studies, 35 remained. Of these, 16 studies fulfilled all the criteria and were included in the systematic review. These studies established the roles of non-coding rnas in the development of craniofacial structures. The differential expression of these non-coding rnas could lead to orofacial clefts, indicating their significance in NSCL/P and their profound research value. Conclusion: There is evidence that non-coding rnas are involved in the formation of NSCL/P. Specifically, they play significant roles in the regulation of genes and signalling pathways related to NSCL/P.

关键词： non-syndromic cleft lip with or without cleft palate non-coding rna Mirna Lncrna Congenital craniomaxillofacial malformations Cleft development

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