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Development and characterization of non-coding rna-derived simple sequence repeat markers in coconut (Cocos nucifera L.)

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FUNCTIONAL & INTEGRATIVE GENOMICS 2022年第6期22卷 1243-1251页

作者： Sabana, A. A. Antony, Ginny Rajesh, M. K. Gangaraj, K. P. Niral, V Sudha, R. Jerard, B. A. Cent Univ Kerala Kasaragod 671320 Kerala India ICAR Cent Plantat Crops Res Inst ICAR CPCRI Kasaragod 671124 Kerala India ICAR Cent Isl Agr Res Inst ICAR CIARI Andaman & Nicobar Isl Port Blair 744101 India

non-coding rna (ncrna)-based SSR markers are highly useful in molecular breeding as ncrnas play a significant role in gene regulation. In the present study, for the first time in coconut, we have identified 597 ncrna-derived SSR markers, including 509 long non-coding rnaSSRs (lncrnaSSRs) and 88 micro rnaSSRs (mirnaSSRs). Of these, 20 primers (10 each from lncrna-SSR and mirna-SSR) were selected, screened on 6 coconut accessions, and 50% produced polymorphic fragments. These 10 polymorphic primers were used for genotyping 96 palms of 16 coconut accessions, comprising eight tall and dwarf accessions each. The number of alleles ranged from 2 to 9 per SSR marker, with an average of 4.6 alleles per locus. The average heterozygosity and Shannon index were 0.5 and 1.1, respectively, suggesting that ncrna-SSRs show high polymorphism level. Distance-based cluster analyses revealed that all the tall and dwarf accessions were differentiated and grouped in different clusters. The study demonstrates the usefulness of ncrna-based SSR markers for assessing genetic diversity and genetic improvement in coconut.

关键词： Coconut Genetic diversity lncrna mirna non-coding rna Polymorphic SSRs

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Targeting long non-coding rna to therapeutically upregulate gene expression

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NATURE REVIEWS DRUG DISCOVERY 2013年第6期12卷 433-446页

作者： Wahlestedt, Claes Univ Miami Sch Med Ctr Therapeut Innovat Miami FL 33136 USA Univ Miami Sch Med Dept Psychiat & Behav Sci Miami FL 33136 USA

The majority of currently available drugs and tool compounds exhibit an inhibitory mechanism of action and there is a relative lack of pharmaceutical agents that are capable of increasing the activity of effectors or pathways for therapeutic benefit. Indeed, the upregulation of many genes, including tumour suppressors, growth factors, transcription factors and genes that are deficient in various genetic diseases, would be desired in specific situations. Recently, key roles for regulatory long non-coding rnas (lncrnas) in the regulation of gene expression have begun to emerge. lncrnas can positively or negatively regulate gene expression and chromatin architecture. Here, we review the current understanding of the mechanisms of action of lncrnas and their roles in disease, focusing on recent work in the design of inhibitors of the natural antisense transcript (NAT) class of lncrnas, known as antagoNAT oligonucleotides, and the issues associated with their potential therapeutic application.

关键词： TUMOR suppressor proteins GROWTH factors TRANSCRIPTION factors GENETIC disorders non-coding rna GENE expression OLIGONUCLEOTIDES

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Current concepts of non-coding rna regulation of immune checkpoints in cancer

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MOLECULAR ASPECTS OF MEDICINE 2019年 70卷 117-126页

作者： Smolle, Maria Anna Prinz, Felix Calin, George Adrian Pichler, Martin Med Univ Graz Dept Orthopaed & Trauma Auenbruggerpl 5 A-8036 Graz Austria Med Univ Graz Div Oncol Res Unit Noncoding RNA & Genome Editing Canc Auenbruggerpl 15 A-8036 Graz Austria Univ Texas MD Anderson Canc Ctr Dept Expt Therapeut Unit 19501515 Holcombe Blvd Houston TX 77030 USA

The discovery of immune checkpoint molecules as important regulators of immune responses in healthy individuals as well as immune escape of malignant tumours has led to profound changes in understanding, research and treatment of human cancer. Especially the introduction of immune checkpoint inhibitors in cancer therapy has set anti-cancer therapy on a novel level. With increasing experience of approved CTLA-4 and PD1/PD-L1 inhibitors and the evolution of novel immune checkpoint molecules from pre-clinical models to clinical trials, mechanisms of the regulation of these immune system guiding factors, are of paramount importance to overcome mechanisms of resistance. non-protein coding rnas (i.e. non-coding rnas) such as short micrornas and long non-coding rnas are involved in regulating of various cellular processes and have attracted attention of cancer researchers and immunologists over the last years. In the present review, interactions between non coding rnas and immune checkpoint molecules, within the framework of human cancer, will be discussed and current and developing concepts between the immunological and non-coding rna world, will be elucidated.

关键词： Immune checkpoint molecule non-coding rna Cancer

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Representation of non-coding rna-mediated regulation of gene expression using the Gene Ontology

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rna BIOLOGY 2024年第1期21卷 36-48页

作者： Antonazzo, Giulia Gaudet, Pascale Lovering, Ruth C. Attrill, Helen Univ Cambridge Dept Physiol Dev & Neurosci Downing St Cambridge CB2 3DY England SIB Swiss Inst Bioinformat Swiss Prot Grp Geneva Switzerland UCL Inst Cardiovasc Sci Funct Gene Annotat London England

Regulatory non-coding rnas (ncrnas) are increasingly recognized as integral to the control of biological processes. This is often through the targeted regulation of mrna expression, but this is by no means the only mechanism through which regulatory ncrnas act. The Gene Ontology (GO) has long been used for the systematic annotation of protein-coding and ncrna gene function, but rapid progress in the understanding of ncrnas meant that the ontology needed to be revised to accurately reflect current knowledge. Here, a targeted effort to revise GO terms used for the annotation of regulatory ncrnas is described, focusing on micrornas (mirnas), long non-coding rnas (lncrnas), small interfering rnas (sirnas) and PIWI-interacting rnas (pirnas). This paper provides guidance to biocurators annotating ncrna-mediated processes using the GO and serves as background for researchers wishing to make use of the GO in their studies of ncrnas and the biological processes they regulate.

关键词： Gene Ontology non-coding rna bioinformatics biocuration gene silencing guidelines

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A novel variable exonic region and differential expression of LINC00663 non-coding rna in various cancer cell lines and normal human tissue samples

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TUMOR BIOLOGY 2016年第7期37卷 8791-8798页

作者： Bozgeyik, Esra Igci, Yusuf Ziya Jacksi, Mevan F. Sami Arman, Kaifee Gurses, Serdar A. Bozgeyik, Ibrahim Pala, Elif Yumrutas, Onder Temiz, Ebru Igci, Mehri Gaziantep Univ Dept Med Biol Fac Med Gaziantep Turkey Zirve Univ Dept Med Biol Fac Med Gaziantep Turkey Adiyaman Univ Dept Med Biol Adiyaman Turkey Sanko Univ Dept Med Biol Gaziantep Turkey

Long non-coding rnas (lncrnas) are found to play crucial roles in several biological processes and have been associated with many complex human diseases including cancers. Several lines of evidences indicate that lncrnas deregulated in many cancer tissues. In this particular study, differential expression of long intergenic non-coding rna 663 (LINC00663) was demonstrated in various cancer cell lines and healthy human tissues by using RT-PCR and qPCR methods. While expression level of LINC00663 was most prominent in thyroid gland and uterus, it is least expressed in skeletal muscle tissues. Moreover, LINC00663 was found to be differentially expressed in various cancer cells. Particularly, its expression was highly diminished in DU-145, PC3, HGC-27, CRL-1469, A549, MCF7, and BCPAP cancer cells. Also, LINC00663 expression was most prominent in A172 glioblastoma cells. Additionally, a novel splice variant of LINC00663 rna was also detected. The sequence and Basic Local Alignment Search Tool (BLAST) analysis results revealed the presence of a novel exonic region between exons 2 and 3. Subsequently, five potential splice variants showing high level of variation have been identified. Secondary structures of these variants with minimum free energy were also demonstrated. Furthermore, putative microrna (mirna) binding sites to these variants have been shown. In conclusion, LINC00663 was shown to be differentially expressed in various human tissues and cancer cell lines. Also, LINC00663 undergoes alternative splicing and the novel exonic region alters its secondary structure and its interactions with potential targeting mirnas. The role of LINC00663 in cancer formation further needs to be investigated with a wide range of studies.

关键词： Cancer non-coding rna LINC00663 lncrna mirna

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Definition and annotation of (myco)bacterial non-coding rna

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TUBERCULOSIS 2013年第1期93卷 26-29页

作者： Lamichhane, Gyanu Arnvig, Kristine B. McDonough, Kathleen A. Johns Hopkins Univ Sch Med Ctr TB Res Baltimore MD 21231 USA Natl Inst Med Res MRC Div Mycobacterial Res London NW7 1AA England New York State Dept Hlth Wadsworth Ctr Albany NY 12201 USA SUNY Albany Sch Publ Hlth Albany NY 12201 USA

rna in bacteria may be broadly classified into coding and non-coding types. The prior, also known as messenger rna, encode proteins as their final product. The non-coding rna include all rnas that are not translated into a protein. Examples of extensively studied and therefore prominent non-coding rnas include rrna, trna, tmrna, whose designations reflect the functions performed by these rnas. Discoveries of non-coding rnas in mycobacteria have been reported in the recent years. At this early stage of this discipline of mycobacterial research, there is an opportunity for the scientific community to establish a consistent, systematic and objective approach to annotation of these rnas. We are providing recommendations for this systematic annotation that we hope will be adopted by the mycobacterial research community. These may also serve as templates for annotation of non-coding rnas in other bacteria. (C) 2012 Elsevier Ltd. All rights reserved.

关键词： non-coding rna Annotation srna

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The Long non-coding rna-RoR Promotes the Tumorigenesis of Human Colorectal Cancer by Targeting miR-6833-3p Through SMC4

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ONCOTARGETS AND THERAPY 2020年 13卷 2573-2581页

作者： Li, Xinyu Chen, Wen Jia, Jing You, Zhicheng Hu, Changjin Zhuang, Yihuang Lin, Zhibin Liu, Yan Yang, Chunkang Xu, Rongyu Quanzhou First Hosp Quanzhou Fujian Peoples R China Fujian Med Univ Affiliated Hosp 2 Quanzhou Fujian Peoples R China Yongchun Cty Hosp Quanzhou Fujian Peoples R China Fujian Univ Tradit Chinese Med Jinjiang Hosp Tradit Chinese Med Jinjiang Fujian Peoples R China Fujian Tumor Hosp Fuzhou Fujian Peoples R China

Background: Long non-coding rna regulator of reprogramming (LINC-RoR) has shown different expressions in a variety of tumors as a stem cell inducer through reprogramming regulation. However, its role and regulation mechanisms in colorectal cancer (CRC) are still unclear. Materials and Methods: Quantitative real-time PCR and Western blot were performed to examine LINC-RoR expression in paired CRC samples and cell lines. The relationship of LINC-RoR expression with clinicopathological characteristics and clinical outcomes was analyzed. The biological functions of LINC-RoR were studied by MTS and colony formation in vitro. Cell apoptosis was analysed by the flow cytometry. The Dual-luciferase reporter assays and RIP assays were performed to explore the regulatory relationship of LINC-RoR. Results: In this study, we found that LINC-RoR was upregulated in CRC cell lines and tissues. High expression of LINC-RoR was associated with poorer survival time and multivariate analysis results showed that LINC-RoR was an independent risk factor of tumor malignancy progression. Overexpression of LINC-RoR promoted the cell proliferation and knocked down it can reverse the effect in vitro. The regulatory network of LINC-ROR/miR-6833-3p/SMC4 was predicted with bioinformatics analysis tools and validated via dual-luciferase reporter assays and RIP. Further study revealed that in overexpression LINC-RoR cell lines the expression of miR-6833-3p was downregulated and miR-6833-3p can inhibit its target gene SMC4, the apoptosis-related protein. Conclusion: We concluded that LINC-RoR functions as an oncogene in CRC through the miR-6833-3p/SMC4 pathway.

关键词： LINC-RoR colorectal cancer miR-6833-3p SMC4 non-coding rna apoptosis

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NEAT1: A novel cancer-related long non-coding rna

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CELL PROLIFERATION 2017年第2期50卷 1-6页

作者： Yu, Xin Li, Zheng Zheng, Heyi Chan, Matthew T. V. Wu, William Ka Kei Chinese Acad Med Sci Peking Union Med Coll Hosp Peking Union Med Coll Dept Dermatol Beijing Peoples R China Chinese Acad Med Sci Peking Union Med Coll Hosp Peking Union Med Coll Dept Orthoped Surg Beijing Peoples R China Chinese Univ Hong Kong Dept Anaesthesia & Intens Care Hong Kong Peoples R China Chinese Univ Hong Kong LKS Inst Hlth Sci State key Lab Digest Dis Hong Kong Peoples R China

Aberrant overexpression of the long non-coding rna NEAT1 (nuclear paraspeckle assembly transcript 1) has been documented in different types of solid tumours, such as lung cancer, oesophageal cancer, colorectal cancer and hepatocellular carcinoma, in which its high levels are associated with poor prognosis. In contrast, NEAT1 is down-regulated in acute promyelocytic leukaemia where it promotes leucocyte differentiation. In this review, we provide an overview of current evidence concerning the oncogenic role and potential clinical utilities of NEAT1. Further investigations are warranted to elucidate the upstream and downstream mechanisms of NEAT1 overexpression.

关键词： non-coding rna CANCER prognosis CANCER cell differentiation OVEREXPRESSION (Genetics) DOWN-regulation (Biology)

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HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small non-coding rna

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MOLECULAR CELL 2018年第2期71卷 256-+页

作者： Tebaldi, Toma Zuccotti, Paola Peroni, Daniele Koehn, Marcel Gasperini, Lisa Potrich, Valentina Bonazza, Veronica Dudnakova, Tatiana Rossi, Annalisa Sanguinetti, Guido Conti, Luciano Macchi, Paolo D'Agostino, Vito Viero, Gabriella Tollervey, David Huettelmaier, Stefan Quattrone, Alessandro Univ Trento Ctr Integrat Biol Lab Translat Genom I-38123 Trento Italy Martin Luther Univ Halle Wittenberg Inst Mol Med D-06120 Halle Germany Martin Luther Univ Halle Wittenberg Julius Bernstein Inst Physiol D-06097 Halle Germany Univ Trento Ctr Integrat Biol Lab Mol & Cellular Neurobiol I-38123 Trento Italy Univ Edinburgh Wellcome Trust Ctr Cell Biol Edinburgh EH9 3BF Midlothian Scotland Univ Edinburgh Sch Informat Edinburgh EH8 9AB Midlothian Scotland Univ Trento Ctr Integrat Biol Lab Stem Cell Biol I-38123 Trento Italy Univ Trento Ctr Integrat Biol I-38123 Trento Italy CNR Unit Trento Inst Biophys I-38123 Trento Italy Yale Univ Sch Med Yale Canc Ctr New Haven CT 06520 USA

The rna-binding protein HuD promotes neurogenesis and favors recovery from peripheral axon injury. HuD interacts with many mrnas, altering both stability and translation efficiency. We generated a nucleotide resolution map of the HuD rna interactome in motor neuron-like cells, identifying HuD target sites in 1,304 mrnas, almost exclusively in the 3' UTR. HuD binds many mrnas encoding mTORC1-responsive ribosomal proteins and translation factors. Altered HuD expression correlates with the translation efficiency of these mrnas and overall protein synthesis, in a mTORC1-independent fashion. The predominant HuD target is the abundant, small non-coding rna Y3, amounting to 70% of the HuD interaction signal. Y3 functions as a molecular sponge for HuD, dynamically limiting its recruitment to polysomes and its activity as a translation and neuron differentiation enhancer. These findings uncover an alternative route to the mTORC1 pathway for translational control in motor neurons that is tunable by a small non-coding rna.

关键词： HuD ELAVL4 rna binding protein NSC-34 neuron differentiation translation polysomes mTORC1 Y3 Rny3 Y rna non-coding rna

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Core competing endogenous rna network based on mrna and non-coding rna expression profiles in chicken fatty liver

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ANIMAL GENETICS 2024年第5期55卷 772-778页

作者： Xiao, Qingxing Zhang, Yonghong Ni, Hongyu Yin, Yijing Gao, Anchong Cui, Benhai Zhang, Wei Li, Yumei Yang, Yuwei Jilin Univ Coll Anim Sci Changchun 130062 Peoples R China Jiuzhou Flying Goose Husb & Technol Co Ltd Baicheng Peoples R China Anim Dis Prevent & Control Ctr Baicheng Peoples R China

Fatty liver disease is a common metabolic disease in chickens. This disease can lead to a decrease in egg production and increase the risk of death in chickens. Long non-coding rnas (lncrnas) are involved in fatty liver formation by directly targeting genes or regulating gene expression by competitively binding micrornas. However, a large proportion of competing endogenous rna (cerna) networks in fatty liver diseases are still unclear. The total of 300 Jingxing-Huang chickens were used for fatty liver model construction. Then, differentially expressed (DE) genes (DEGs) identified through whole-transcriptome sequencing from four chickens with fatty liver and four chickens without fatty liver were chosen from the F1 generation. A total of 953 DEGs were identified between the fatty liver group and the control group, including 26 DE micro (mi)rnas and 56 DE lncrnas. Differential expression heatmaps and volcano plots were obtained after clustering expression analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that these DEGs were involved in many biological processes and signaling pathways related to fatty acid metabolism and lipid synthesis. Furthermore, cytoscape was used to construct a cerna network of the DE mirnas, DE mrnas, and DE lncrnas. Eleven DE lncrnas, seven DE mirnas, and 13 DE mrnas were found to be associated with the pathogenesis of fatty liver disease. An lncrna-mirna-mrna cerna network was constructed to elucidate the mechanisms of fatty liver diseases, and the ENSGALT00000079786-miR-140/miR-143/miR-1a/miR-22/miR-375 network was identified. These results provide a valuable resource for further elucidating the posttranscriptional regulatory mechanisms of chicken liver and adipose fat development or deposition.

关键词： cerna network chicken fatty liver non-coding rna

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