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Lee DH, Park EG, Kim JM, Shin HJ, Lee YJ, Jeong HS, Roh HY, Kim WR, Ha H, Kim SW, Choi YH, Kim HS. Genomic analyses of intricate interaction of TE-lncRNA overlapping genes with miRNAs in human diseases. Genes Genomics 2024:10.1007/s13258-024-01547-1. [PMID: 39215947 DOI: 10.1007/s13258-024-01547-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/09/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Transposable elements (TEs) are known to be inserted into genome to create transcript isoforms or to generate long non-coding RNA (lncRNA) sequences. The insertion of TEs generates a gene protein sequence within the genome, but also provides a microRNA (miRNA) regulatory region. OBJECTIVE To determine the effect of gene sequence changes caused by TE insertion on miRNA binding and to investigate the formation of an overlapping lncRNA that represses it. METHODS The distribution of overlapping regions between exons and TE regions with lncRNA was examined using the Bedtools. miRNAs that can bind to those overlapping regions were identified through the miRDB web program. For TE-lncRNA overlapping genes, bioinformatic analysis was conducted using DAVID web database. Differential expression analysis was conducted using data from the GEO dataset and TCGA. RESULTS Most TEs were distributed more frequently in untranslated regions than open reading frames. There were 30 annotated TE-lncRNA overlapping genes with same strand that could bind to the same miRNA. As a result of identifying the association between these 30 genes and diseases, TGFB2, FCGR2A, DCTN5, and IFI6 were associated with breast cancer, and HMGCS1, FRMD4A, EDNRB, and SNCA were associated with Alzheimer's disease. Analysis of the GEO and TCGA data showed that the relevant expression of miR-891a and miR-28, which bind to the TE overlapping region of DCTN5 and HMGCS1, decreased. CONCLUSION This study indicates that the interaction between TE-lncRNA overlapping genes and miRNAs can affect disease progression.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jung-Min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyeon-Su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hongseok Ha
- Institute of Endemic Disease, Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea
| | - Sang-Woo Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dong-Eui University, Busan, 47227, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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2
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Park EG, Lee DH, Kim WR, Lee YJ, Bae WH, Kim JM, Shin HJ, Ha H, Yi JM, Cho SG, Choi YH, Leem SH, Cha HJ, Kim SW, Kim HS. Human Endogenous Retrovirus-H-Derived miR-4454 Inhibits the Expression of DNAJB4 and SASH1 in Non-Muscle-Invasive Bladder Cancer. Genes (Basel) 2023; 14:1410. [PMID: 37510314 PMCID: PMC10379226 DOI: 10.3390/genes14071410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Although most human endogenous retroviruses (HERVs) have been silenced and lost their ability to translocate because of accumulated mutations during evolution, they still play important roles in human biology. Several studies have demonstrated that HERVs play pathological roles in numerous human diseases, especially cancer. A few studies have revealed that long non-coding RNAs that are transcribed from HERV sequences affect cancer progression. However, there is no study on microRNAs derived from HERVs related to cancer. In this study, we identified 29 microRNAs (miRNAs) derived from HERV sequences in the human genome. In particular, we discovered that miR-4454, which is HERV-H-derived miRNA, was upregulated in non-muscle-invasive bladder cancer (NMIBC) cells. To figure out the effects of upregulated miR-4454 in NMIBC, genes whose expression was downregulated in NMIBC, as well as tumor suppressor genes, were selected as putative target genes of miR-4454. The dual-luciferase assay was used to determine the negative relationship between miR-4454 and its target genes, DNAJB4 and SASH1, and they were confirmed to be promising target genes of miR-4454. Taken together, this study suggests that the upregulation of miR-4454 derived from HERV-H in NMIBC reduces the expression of the tumor suppressor genes, DNAJB4 and SASH1, to promote NMIBC progression.
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Affiliation(s)
- Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (E.G.P.); (D.H.L.); (W.R.K.); (Y.J.L.); (W.H.B.); (J.-m.K.); (H.J.S.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Hongseok Ha
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, Inje University College of Medicine, Busan 47392, Republic of Korea;
| | - Ssang Goo Cho
- Department of Stem Cell & Regenerative Biotechnology, Institute of Advanced Regenerative Science, Konkuk University, Seoul 05029, Republic of Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Korean Medicine, Dong-Eui University, Busan 47227, Republic of Korea;
| | - Sun Hee Leem
- Department of Biological Science, Dong-A University, Busan 49315, Republic of Korea;
| | - Hee Jae Cha
- Department of Parasitology and Genetics, College of Medicine, Kosin University, Busan 49104, Republic of Korea;
| | - Sang Woo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea;
| | - Heui Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea;
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3
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Shapiro JA. Repetitive DNA is Functional and Encodes Parts of the Non-Coding RNA Repertoire. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200026. [PMID: 36911293 PMCID: PMC9993471 DOI: 10.1002/ggn2.202200026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 11/28/2022]
Abstract
This is a commentary on the article by Eviatar Nevo and Kexin Li entitled "Sympatric Speciation in Mole Rats and Wild Barley and Their Genome Repeatome Evolution: A Commentary", published recently in Advanced Genetics.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIL60637USA
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4
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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5
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Chromosomal Heteromorphisms and Cancer Susceptibility Revisited. Cells 2022; 11:cells11203239. [PMID: 36291106 PMCID: PMC9600968 DOI: 10.3390/cells11203239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/21/2022] Open
Abstract
Chromosomal heteromorphisms (CHs) are a part of genetic variation in man. The past literature largely posited whether CHs could be correlated with the development of malignancies. While this possibility seemed closed by end of the 1990s, recent data have raised the question again on the potential influences of repetitive DNA elements, the main components of CHs, in cancer susceptibility. Such new evidence for a potential role of CHs in cancer can be found in the following observations: (i) amplification and/or epigenetic alterations of CHs are routinely reported in tumors; (ii) the expression of CH-derived RNA in embryonal and other cells under stress, including cancer cells; (iii) the expression of parts of CH-DNA as long noncoding RNAs; plus (iv) theories that suggest a possible application of the “two-hit model” for euchromatic copy number variants (CNVs). Herein, these points are discussed in detail, which leads to the conclusion that CHs are by far not given sufficient consideration in routine cytogenetic analysis, e.g., leukemias and lymphomas, and need more attention in future research settings including solid tumors. This heightened focus may only be achieved by approaches other than standard sequencing or chromosomal microarrays, as these techniques are at a minimum impaired in their ability to detect, if not blind to, (highly) repetitive DNA sequences.
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2021; 12:3297. [PMID: 34078885 PMCID: PMC8172540 DOI: 10.1038/s41467-021-23143-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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7
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Liehr T. Repetitive Elements in Humans. Int J Mol Sci 2021; 22:ijms22042072. [PMID: 33669810 PMCID: PMC7922087 DOI: 10.3390/ijms22042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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8
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Zhong Z, Hong M, Chen X, Xi Y, Xu Y, Kong D, Deng J, Li Y, Hu R, Sun C, Liang J. Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma. BMC Med Genomics 2020; 13:57. [PMID: 32228580 PMCID: PMC7104528 DOI: 10.1186/s12920-020-0707-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/19/2020] [Indexed: 12/11/2022] Open
Abstract
Background As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during the advanced stage of the disease and exhibits a low five-year survival rate. The importance of tumor microenvironment (TME) in tumor initiation and metastasis is widely recognized. In addition, accumulating evidence indicates that long non-coding RNA (lncRNA) is involved in crosstalk between TME and tumor cells. However, the lncRNA-associated regulators modulating the HNSCC microenvironment and progression remain largely unknown. Methods The publicly available transcriptome data and matched clinical HNSCC data were collected from The Cancer Genome Atlas (TCGA). Immune scores (ISs) and stromal scores (SSs) of HNSCC TME were calculated using ESTIMATE algorithm. Weighted gene co-expression network analysis (WGCNA) was conducted to determine the co-expressed lncRNAs and protein-coding mRNAs. Results Results showed that the high IS HNSCC male patient subgroup exhibited improved survival. Additionally, we identified 169 lncRNAs and 825 protein-coding mRNAs that were differentially expressed in high IS HNSCC samples, with the up-regulated mRNAs displaying enrichment in immune-related biological processes. Notably, we identified a high co-expression lncRNA-mRNA module (i.e., purple module) that showed strong correlation with ISs. This module contained 79 lncRNAs and 442 mRNAs, including 26 lncRNAs and 215 mRNAs showing association between expression and male HNSCC survival. Consistently, 207 of the 215 mRNAs were up-regulated in high IS HNSCC group and were enriched in immune-related signaling pathways. Based on bioinformatics analyses and previous functional assays, certain lncRNAs (e.g., AL365361.1 and PCED1B-AS1) in the purple module likely contributed to the modification of tumor immune microenvironment (TIME) in the high IS HNSCC patients, achieved by regulating transcription of abundant immune-related genes (e.g., CCR7 and TLR8). Conclusions In summary, we ascertained a HNSCC male patient subgroup that displayed high ISs and good survival probability. We identified hundreds of genes with specific expression patterns in this HNSCC subgroup as well as a highly co-expressed lncRNA-mRNA module with great potential for the modulation of TIME of HNSCC. Our study provides evidence of a link between the lncRNA-associated gene network, TIME, and HNSCC progression, and highlights potential therapeutic targets for this disease.
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Affiliation(s)
- Zhaoming Zhong
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Min Hong
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Xiao Chen
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Yan Xi
- Department of Head and Neck Surgery Section II, Third Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Yuanyuan Xu
- Department of Oncology, First People's Hospital of Kunming, Kunming, China
| | - Deyu Kong
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Jun Deng
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Yun Li
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Rui Hu
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Chuanzheng Sun
- Department of Head and Neck Surgery Section II, Third Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.
| | - Jin Liang
- Department of Medical Oncology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.
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9
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Mustafin RN, Khusnutdinova EK. The Role of Transposons in Epigenetic Regulation of Ontogenesis. Russ J Dev Biol 2018. [DOI: 10.1134/s1062360418020066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Benway CJ, Iacomini J. Defining a microRNA-mRNA interaction map for calcineurin inhibitor induced nephrotoxicity. Am J Transplant 2018; 18:796-809. [PMID: 28925592 DOI: 10.1111/ajt.14503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/21/2017] [Accepted: 09/04/2017] [Indexed: 02/06/2023]
Abstract
Calcineurin inhibitors induce nephrotoxicity through poorly understood mechanisms thereby limiting their use in transplantation and other diseases. Here we define a microRNA (miRNA)-messenger RNA (mRNA) interaction map that facilitates exploration into the role of miRNAs in cyclosporine-induced nephrotoxicity (CIN) and the gene pathways they regulate. Using photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP), we isolated RNAs associated with Argonaute 2 in the RNA-induced silencing complex (RISC) of cyclosporine A (CsA) treated and control human proximal tubule cells and identified mRNAs undergoing active targeting by miRNAs. CsA causes specific changes in miRNAs and mRNAs associated with RISC, thereby altering post-transcriptional regulation of gene expression. Pathway enrichment analysis identified canonical pathways regulated by miRNAs specifically following CsA treatment. RNA-seq performed on total RNA indicated that only a fraction of total miRNAs and mRNAs are actively targeted in the RISC, indicating that PAR-CLIP more accurately defines meaningful targeting interactions. Our data also revealed a role for miRNAs in calcineurin-independent regulation of JNK and p38 MAPKs caused by targeting of MAP3K1. Together, our data provide a novel resource and unique insights into molecular pathways regulated by miRNAs in CIN. The gene pathways and miRNAs defined may represent novel targets to reduce calcineurin induced nephrotoxicity.
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Affiliation(s)
- Christopher J Benway
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - John Iacomini
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA.,Graduate Program in Immunology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA.,Tufts University School of Medicine, Boston, MA, USA
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11
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Frías-Lasserre D, Villagra CA. The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution. Front Microbiol 2017; 8:2483. [PMID: 29312192 PMCID: PMC5744636 DOI: 10.3389/fmicb.2017.02483] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.
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Affiliation(s)
- Daniel Frías-Lasserre
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
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12
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Abstract
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci. Parsing and characterizing the functions of noncoding RNAs-lncRNAs in particular-is one of the great challenges of modern genome biology. Here we discuss concepts and computational methods for the identification of structural domains in lncRNAs from genomic and transcriptomic data. In the first part, we briefly review how to identify RNA structural motifs in individual lncRNAs. In the second part, we describe how to leverage the evolutionary dynamics of structured RNAs in a computationally efficient screen to detect putative functional lncRNA motifs using comparative genomics.
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Affiliation(s)
- Martin A Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia. .,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia.
| | - John S Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia
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13
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Villarreal LP. Viruses and the placenta: the essential virus first view. APMIS 2016; 124:20-30. [PMID: 26818259 DOI: 10.1111/apm.12485] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/26/2015] [Indexed: 01/05/2023]
Abstract
A virus first perspective is presented as an alternative hypothesis to explain the role of various endogenized retroviruses in the origin of the mammalian placenta. It is argued that virus-host persistence is a key determinant of host survival and the various ERVs involved have directly affected virus-host persistence.
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Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
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14
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Weirick T, Militello G, Müller R, John D, Dimmeler S, Uchida S. The identification and characterization of novel transcripts from RNA-seq data. Brief Bioinform 2015; 17:678-85. [PMID: 26283677 DOI: 10.1093/bib/bbv067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Indexed: 11/12/2022] Open
Abstract
Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques 'RNA sequencing (RNA-seq)' is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called 'noncoding RNAs (ncRNAs)'. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.
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