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      Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA

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          Abstract

          Non-coding RNAs do not encode proteins and regulate various oncological processes. They are also important potential cancer diagnostic and prognostic biomarkers. Bioinformatics and translation omics have begun to elucidate the roles and modes of action of the functional peptides encoded by ncRNA. Here, recent advances in long non-coding RNA (lncRNA) and circular RNA (circRNA)-encoded small peptides are compiled and synthesized. We introduce both the computational and analytical methods used to forecast prospective ncRNAs encoding oncologically functional oligopeptides. We also present numerous specific lncRNA and circRNA-encoded proteins and their cancer-promoting or cancer-inhibiting molecular mechanisms. This information may expedite the discovery, development, and optimization of novel and efficacious cancer diagnostic, therapeutic, and prognostic protein-based tools derived from non-coding RNAs. The role of ncRNA-encoding functional peptides has promising application perspectives and potential challenges in cancer research. The aim of this review is to provide a theoretical basis and relevant references, which may promote the discovery of more functional peptides encoded by ncRNAs, and further develop novel anticancer therapeutic targets, as well as diagnostic and prognostic cancer markers.

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          This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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            Origin, biogenesis, and activity of plant microRNAs.

            MicroRNAs (miRNAs) are key posttranscriptional regulators of eukaryotic gene expression. Plants use highly conserved as well as more recently evolved, species-specific miRNAs to control a vast array of biological processes. This Review discusses current advances in our understanding of the origin, biogenesis, and mode of action of plant miRNAs and draws comparisons with their metazoan counterparts.
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              Clustal Omega for making accurate alignments of many protein sequences.

              Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk.
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                Author and article information

                Contributors
                xiongwei@csu.edu.cn
                Journal
                Mol Cancer
                Mol. Cancer
                Molecular Cancer
                BioMed Central (London )
                1476-4598
                4 February 2020
                4 February 2020
                2020
                : 19
                : 22
                Affiliations
                [1 ]GRID grid.216417.7, ISNI 0000 0001 0379 7164, NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, , Central South University, ; Changsha, Hunan China
                [2 ]GRID grid.216417.7, ISNI 0000 0001 0379 7164, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, , Central South University, ; Changsha, Hunan China
                [3 ]GRID grid.216417.7, ISNI 0000 0001 0379 7164, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, the Third Xiangya Hospital, , Central South University, ; Changsha, Hunan China
                [4 ]GRID grid.39382.33, ISNI 0000 0001 2160 926X, Department of Medicine, Dan L Duncan Comprehensive Cancer Center, , Baylor College of Medicine, ; Houston, Texas USA
                Author information
                http://orcid.org/0000-0003-1635-8173
                Article
                1147
                10.1186/s12943-020-1147-3
                6998289
                32019587
                6a92c49f-ad4e-453f-8b42-4c03fb39049c
                © The Author(s). 2020

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 19 November 2019
                : 28 January 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81903138
                Award ID: 81803025
                Award ID: 81772928
                Award ID: 81702907
                Award ID: 81772901
                Award ID: 81672993
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004735, Natural Science Foundation of Hunan Province;
                Award ID: 2019JJ50778
                Award ID: 2018SK21210
                Award ID: 2018SK21211
                Award ID: 2018JJ3704
                Award ID: 2018JJ3815
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100010083, Hunan Provincial Innovation Foundation for Postgraduate;
                Award ID: CX20190234
                Award ID: CX20190235
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100012476, Fundamental Research Funds for Central Universities of the Central South University;
                Award ID: 2019zzts890
                Award ID: 2019zzts178
                Award ID: 2019zzts179
                Award Recipient :
                Categories
                Review
                Custom metadata
                © The Author(s) 2020

                Oncology & Radiotherapy
                cancer,circrna,lncrna,peptide
                Oncology & Radiotherapy
                cancer, circrna, lncrna, peptide

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