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      Systematic identification and characterization of Aedes aegypti long noncoding RNAs (lncRNAs)

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          Abstract

          Long noncoding RNAs (lncRNAs) play diverse roles in biological processes. Aedes aegypti ( Ae. aegypti), a blood-sucking mosquito, is the principal vector responsible for replication and transmission of arboviruses including dengue, Zika, and Chikungunya virus. Systematic identification and developmental characterisation of Ae. aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs, followed by developmental profiling of lncRNA in Ae. aegypti. We identified a total of 4,689 novel lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense respectively. Ae. aegypti lncRNAs share many characteristics with other species including low expression, low GC content, short in length, and low conservation. Besides, the expression of Ae. aegypti lncRNAs tend to be correlated with neighbouring and antisense protein-coding genes. A subset of lncRNAs shows evidence of maternal inheritance; hence, suggesting potential role of lncRNAs in early-stage embryos. Additionally, lncRNAs show higher tendency to be expressed in developmental and temporal specific manner. The results from this study provide foundation for future investigation on the function of Ae. aegypti lncRNAs.

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          Long noncoding RNA as modular scaffold of histone modification complexes.

          Miao-Chih Tsai, Ohad Manor, Yue Wan … (2010)
          Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here, we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5' domain of HOTAIR binds polycomb repressive complex 2 (PRC2), whereas a 3' domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1 and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes.
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            RNA maps reveal new RNA classes and a possible function for pervasive transcription.

            Philipp Kapranov, Jill Cheng, Sujit Dike … (2007)
            Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a novel role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome.
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              A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

              Laura Poliseno, Leonardo Salmena, JiangWen Zhang … (2010)
              The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs possess a biological role in cancer cells that relies upon their ability to compete for microRNA binding and is independent of their protein-coding function. As a paradigm for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene (PTENP1) and the critical consequences of this interaction. We find that PTENP1 is biologically active as determined by its ability to regulate cellular levels of PTEN, and that it can exert a growth-suppressive role. We also show that PTENP1 locus is selectively lost in human cancer. We extend our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. Further, we demonstrate that the transcripts of protein coding genes such as PTEN are also biologically active. Together, these findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.
              Article 0 comments Cited 978 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Ghows Azzam:
                ORCID: http://orcid.org/0000-0001-5352-8675
                ghows@usm.my
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 21 August 2019
                Publication date PMC-release: 21 August 2019
                Publication date Collection: 2019
                Volume: 9
                Electronic Location Identifier: 12147
                Affiliations
                [1 ]ISNI 0000 0001 2294 3534, GRID grid.11875.3a, School of Biological Sciences, , Universiti Sains Malaysia, ; 11800 Penang, Malaysia
                [2 ]ISNI 0000 0001 2294 3534, GRID grid.11875.3a, Infectomics Cluster, Advanced Medical & Dental Institute, , Universiti Sains Malaysia, Bertam, ; 13200 Kepala Batas, Penang Malaysia
                Author information
                http://orcid.org/0000-0001-5352-8675
                Article
                Publisher ID: 47506
                DOI: 10.1038/s41598-019-47506-9
                PMC ID: 6704130
                PubMed ID: 30626917
                SO-VID: 31c5b53a-870d-463d-8e47-3b45ff1e5aeb
                Copyright © © The Author(s) 2019
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 13 January 2019
                Date accepted : 18 July 2019
                Funding
                Funded by: MOSTI ScienceFund (305/PBIOLOGI/613238) USM Research University Grant (1001/PBIOLOGI/811320)
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2019

                ScienceOpen disciplines: Uncategorized
                Keywords: long non-coding rnas,transcriptomics,gene regulatory networks
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: long non-coding rnas, transcriptomics, gene regulatory networks

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