1
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024:elae018. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [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: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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2
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Samidurai A, Olex AL, Ockaili R, Kraskauskas D, Roh SK, Kukreja RC, Das A. Integrated Analysis of lncRNA-miRNA-mRNA Regulatory Network in Rapamycin-Induced Cardioprotection against Ischemia/Reperfusion Injury in Diabetic Rabbits. Cells 2023; 12:2820. [PMID: 38132140 PMCID: PMC10742118 DOI: 10.3390/cells12242820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The inhibition of mammalian target of rapamycin (mTOR) with rapamycin (RAPA) provides protection against myocardial ischemia/reperfusion (I/R) injury in diabetes. Since interactions between transcripts, including long non-coding RNA (lncRNA), microRNA(miRNA) and mRNA, regulate the pathophysiology of disease, we performed unbiased miRarray profiling in the heart of diabetic rabbits following I/R injury with/without RAPA treatment to identify differentially expressed (DE) miRNAs and their predicted targets of lncRNAs/mRNAs. Results showed that among the total of 806 unique miRNAs targets, 194 miRNAs were DE after I/R in diabetic rabbits. Specifically, eight miRNAs, including miR-199a-5p, miR-154-5p, miR-543-3p, miR-379-3p, miR-379-5p, miR-299-5p, miR-140-3p, and miR-497-5p, were upregulated and 10 miRNAs, including miR-1-3p, miR-1b, miR-29b-3p, miR-29c-3p, miR-30e-3p, miR-133c, miR-196c-3p, miR-322-5p, miR-499-5p, and miR-672-5p, were significantly downregulated after I/R injury. Interestingly, RAPA treatment significantly reversed these changes in miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated the participation of miRNAs in the regulation of several signaling pathways related to I/R injury, including MAPK signaling and apoptosis. Furthermore, in diabetic hearts, the expression of lncRNAs, HOTAIR, and GAS5 were induced after I/R injury, but RAPA suppressed these lncRNAs. In contrast, MALAT1 was significantly reduced following I/R injury, with the increased expression of miR-199a-5p and suppression of its target, the anti-apoptotic protein Bcl-2. RAPA recovered MALAT1 expression with its sponging effect on miR-199-5p and restoration of Bcl-2 expression. The identification of novel targets from the transcriptome analysis in RAPA-treated diabetic hearts could potentially lead to the development of new therapeutic strategies for diabetic patients with myocardial infarction.
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Affiliation(s)
- Arun Samidurai
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Amy L. Olex
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Ramzi Ockaili
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Donatas Kraskauskas
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Sean K. Roh
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Rakesh C. Kukreja
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Anindita Das
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
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3
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Ataei A, Tahsili M, Hayadokht G, Daneshvar M, Mohammadi Nour S, Soofi A, Masoudi A, Kabiri M, Natami M. Targeting long noncoding RNAs in neuroblastoma: Progress and prospects. Chem Biol Drug Des 2023; 102:640-652. [PMID: 37291742 DOI: 10.1111/cbdd.14263] [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: 02/04/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 06/10/2023]
Abstract
Neuroblastoma (NB) is the third most prevalent tumor that mostly influences infants and young children. Although different treatments have been developed for the treatment of NB, high-risk patients have been reported to have low survival rates. Currently, long noncoding RNAs (lncRNAs) have shown an attractive potential in cancer research and a party of investigations have been performed to understand mechanisms underlying tumor development through lncRNA dysregulation. Researchers have just newly initiated to exhibit the involvement of lncRNAs in NB pathogenesis. In this review article, we tried to clarify the point we stand with respect to the involvement of lncRNAs in NB. Moreover, implications for the pathologic roles of lncRNAs in the development of NB have been discussed. It seems that some of these lncRNAs have promising potential to be applied as biomarkers for NB prognosis and treatment.
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Affiliation(s)
- Ali Ataei
- School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Golsa Hayadokht
- School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Alireza Masoudi
- Department of Laboratory Sciences, Faculty of Alied Medical Sciences, Qom University of Medical Sciences, Qom, Iran
| | - Maryam Kabiri
- Faculty of Medicine, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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4
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Feng YZ, Zhu QF, Xue J, Chen P, Yu Y. Shining in the dark: the big world of small peptides in plants. ABIOTECH 2023; 4:238-256. [PMID: 37970469 PMCID: PMC10638237 DOI: 10.1007/s42994-023-00100-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/24/2023] [Indexed: 11/17/2023]
Abstract
Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.
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Affiliation(s)
- Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qing-Feng Zhu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Pei Chen
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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5
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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6
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Cancer-related micropeptides encoded by ncRNAs: Promising drug targets and prognostic biomarkers. Cancer Lett 2022; 547:215723. [DOI: 10.1016/j.canlet.2022.215723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023]
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7
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Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 2021; 37:110022. [PMID: 34788620 PMCID: PMC8609283 DOI: 10.1016/j.celrep.2021.110022] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/30/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community. There is widespread transcript diversity in the cortex and many novel transcripts Some genes display big differences in isoform number between human and mouse cortex There is evidence of differential transcript usage between human fetal and adult cortex There are many novel isoforms of genes associated with human brain disease
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Key Words
- isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing
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Affiliation(s)
| | | | - Isabel Castanho
- University of Exeter, Exeter, UK; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Connor Jops
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
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8
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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9
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Gao X, Zhang K, Zhou H, Zellmer L, Yuan C, Huang H, Liao DJ. At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms. Exp Ther Med 2021; 22:900. [PMID: 34257713 PMCID: PMC8243336 DOI: 10.3892/etm.2021.10332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/10/2021] [Indexed: 12/22/2022] Open
Abstract
Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro.
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Affiliation(s)
- Xia Gao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Keyin Zhang
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Haiyan Zhou
- Clinical Research Center, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Hai Huang
- Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
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10
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Tharakan R, Sawa A. Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods. Front Genet 2021; 12:651485. [PMID: 34025718 PMCID: PMC8136307 DOI: 10.3389/fgene.2021.651485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and conceptual challenges facing future micropeptide endeavors.
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Affiliation(s)
- Ravi Tharakan
- National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Akira Sawa
- Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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11
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Coellar JD, Long J, Danesh FR. Long Noncoding RNAs and Their Therapeutic Promise in Diabetic Nephropathy. Nephron Clin Pract 2021; 145:404-414. [PMID: 33853077 PMCID: PMC8266727 DOI: 10.1159/000515422] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/19/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in large-scale RNA sequencing and genome-wide profiling projects have unraveled a heterogeneous group of RNAs, collectively known as long noncoding RNAs (lncRNAs), which play central roles in many diverse biological processes. Importantly, an association between aberrant expression of lncRNAs and diverse human pathologies has been reported, including in a variety of kidney diseases. These observations have raised the possibility that lncRNAs may represent unexploited potential therapeutic targets for kidney diseases. Several important questions regarding the functionality of lncRNAs and their impact in kidney diseases, however, remain to be carefully addressed. Here, we provide an overview of the main functions and mechanisms of actions of lncRNAs, and their promise as therapeutic targets in kidney diseases, emphasizing on the role of some of the best-characterized lncRNAs implicated in the pathogenesis and progression of diabetic nephropathy.
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Affiliation(s)
- Juan D. Coellar
- Section of Nephrology, Division of Internal Medicine, The University of Texas at MD Anderson Cancer Center, Houston, TX 77030
| | - Jianyin Long
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030
| | - Farhad R. Danesh
- Section of Nephrology, Division of Internal Medicine, The University of Texas at MD Anderson Cancer Center, Houston, TX 77030
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030
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12
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Qing R, Tao F, Chatterjee P, Yang G, Han Q, Chung H, Ni J, Suter BP, Kubicek J, Maertens B, Schubert T, Blackburn C, Zhang S. Non-full-length Water-Soluble CXCR4 QTY and CCR5 QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors. iScience 2020; 23:101670. [PMID: 33376963 PMCID: PMC7756140 DOI: 10.1016/j.isci.2020.101670] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/12/2020] [Accepted: 10/08/2020] [Indexed: 01/06/2023] Open
Abstract
It was posited that functionalities of GPCRs require full-length sequences that are negated by residue deletions. Here we report that significantly truncated nfCCR5QTY and nfCXCR4QTY still bind native ligands. Receptor-ligand interactions were discovered from yeast 2-hybrid screening and confirmed by mating selection. Two nfCCR5QTY (SZ218a, SZ190b) and two nfCXCR4QTY (SZ158a, SZ146a) were expressed in E. coli. Synthesized receptors exhibited α-helical structures and bound respective ligands with reduced affinities. SZ190b and SZ158a were reconverted into non-QTY forms and expressed in HEK293T cells. Reconverted receptors localized on cell membranes and functioned as negative regulators for ligand-induced signaling when co-expressed with full-length receptors. CCR5-SZ190b individually can perform signaling at a reduced level with higher ligand concentration. Our findings provide insight into essential structural components for CCR5 and CXCR4 functionality, while raising the possibility that non-full-length receptors may be resulted from alternative splicing and that pseudo-genes in genomes may be present and functional in living organisms. Y2H screening reveals ligand interaction from truncated CXCR4 and CCR5 in QTY form Truncated CCR5QTY and CXCR4QTY can be produced in E. coli and bind native ligands Reconverted receptors localize on membranes and regulate cell signaling in HEK293 Our finding indicates potential presence and function for truncated receptors
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Affiliation(s)
- Rui Qing
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fei Tao
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Pranam Chatterjee
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gaojie Yang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiuyi Han
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Haeyoon Chung
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jun Ni
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Bernhard P Suter
- Next Interactions, Inc., 2600 Hilltop Drive, Building B, C332, Richmond, CA 94806, USA
| | - Jan Kubicek
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | - Barbara Maertens
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | | | - Camron Blackburn
- The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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13
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Li J, Liu C. Coding or Noncoding, the Converging Concepts of RNAs. Front Genet 2019; 10:496. [PMID: 31178900 PMCID: PMC6538810 DOI: 10.3389/fgene.2019.00496] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of RNA. In this review, we summarize current evidence pointing to dual roles of RNA molecules defined by their coding and non-coding potentials. We also discuss how the emerging roles of RNA transform our understanding of gene expression and evolution.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
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14
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Hubé F, Francastel C. Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred. Front Genet 2018; 9:140. [PMID: 29720998 PMCID: PMC5915474 DOI: 10.3389/fgene.2018.00140] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Florent Hubé
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, Centre National de la Recherche Scientifique UMR7216, Paris, France
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, Centre National de la Recherche Scientifique UMR7216, Paris, France
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15
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He Y, Yuan C, Chen L, Lei M, Zellmer L, Huang H, Liao DJ. Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs. Genes (Basel) 2018; 9:E40. [PMID: 29337901 PMCID: PMC5793191 DOI: 10.3390/genes9010040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/29/2017] [Accepted: 01/07/2018] [Indexed: 02/06/2023] Open
Abstract
Tens of thousands of chimeric RNAs, i.e., RNAs with sequences of two genes, have been identified in human cells. Most of them are formed by two neighboring genes on the same chromosome and are considered to be derived via transcriptional readthrough, but a true readthrough event still awaits more evidence and trans-splicing that joins two transcripts together remains as a possible mechanism. We regard those genomic loci that are transcriptionally read through as unannotated genes, because their transcriptional and posttranscriptional regulations are the same as those of already-annotated genes, including fusion genes formed due to genetic alterations. Therefore, readthrough RNAs and fusion-gene-derived RNAs are not chimeras. Only those two-gene RNAs formed at the RNA level, likely via trans-splicing, without corresponding genes as genomic parents, should be regarded as authentic chimeric RNAs. However, since in human cells, procedural and mechanistic details of trans-splicing have never been disclosed, we doubt the existence of trans-splicing. Therefore, there are probably no authentic chimeras in humans, after readthrough and fusion-gene derived RNAs are all put back into the group of ordinary RNAs. Therefore, it should be further determined whether in human cells all two-neighboring-gene RNAs are derived from transcriptional readthrough and whether trans-splicing truly exists.
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Affiliation(s)
- Yan He
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang City 443002, Hubei, China.
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Mingjuan Lei
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, 435 E. River Road, Minneapolis, MN 55455, USA.
| | - Hai Huang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
- Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, Guizhou, China.
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16
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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17
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Abstract
The dynamic structure and functions of genomes are being revealed simultaneously with the progress of technologies and researches in genomics. Evidence indicating genome regional characteristics (genome annotations in a broad sense) provide the basis for further analyses. Target listing and screening can be effectively performed in silico using such data. Here, we describe steps to obtain publicly available genome annotations or to construct new annotations based on your own analyses, as well as an overview of the types of available genome annotations and corresponding resources.
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Affiliation(s)
- Imad Abugessaisa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan. .,Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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18
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Abstract
Every ribonucleic acid begins its cellular life as a transcript. If the transcript or its processing product has a function it should be regarded an RNA. Nonfunctional transcripts, by-products from processing, degradation intermediates, even those originating from (functional) RNAs, and non-functional products of transcriptional gene regulation accomplished via the act of transcription, as well as stochastic (co)transcripts could simply be addressed as transcripts (class 0). The copious functional RNAs (class I), often maturing after one or more processing steps, already are systematized into ever expanding sub-classifications ranging from micro RNAs to rRNAs. Established sub-classifications addressing a wide functional diversity remain unaffected. mRNAs (class II) are distinct from any other RNA by virtue of their potential to be translated into (poly)peptide(s) on ribosomes. We are not proposing a novel RNA classification, but wish to add a basic concept with existing terminology (transcript, RNA, and mRNA) that should serve as an additional framework for carefully delineating RNA function from an avalanche of RNA sequencing data. At the same time, this top level hierarchical model should illuminate important principles of RNA evolution and biology thus heightening our awareness that in biology boundaries and categorizations are typically fuzzy.
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Affiliation(s)
- Jürgen Brosius
- a Institute of Experimental Pathology, ZMBE, University of Münster , Von-Esmarch-Str. 56, 48149 ; Münster , Germany.,b Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB) , Fehrbelliner Str. 38, 16816 ; Germany
| | - Carsten A Raabe
- a Institute of Experimental Pathology, ZMBE, University of Münster , Von-Esmarch-Str. 56, 48149 ; Münster , Germany.,b Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB) , Fehrbelliner Str. 38, 16816 ; Germany
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19
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Li H, Hu C, Bai L, Li H, Li M, Zhao X, Czajkowsky DM, Shao Z. Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. DNA Res 2016; 23:571-580. [PMID: 27559081 PMCID: PMC5144680 DOI: 10.1093/dnares/dsw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.
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Affiliation(s)
- Hongmei Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingfa Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Zhao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Deepthi V, V. I. Nair V, Thomas V, Raj N, P. Ramakrishnan S, Khan J, Kaushik M, K. Dhar P, S. Nair A. Function annotation of peptides generated from the non-coding regions of D. melanogaster genome. Bioinformation 2016; 12:202-208. [PMID: 28149056 PMCID: PMC5267965 DOI: 10.6026/97320630012202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/25/2016] [Accepted: 05/25/2016] [Indexed: 11/23/2022] Open
Abstract
De novo emergence of genes is the most fundamental form of genetic diversity that is attracting the attention of the scientific community. Identification of short open reading frames (sORFs) from the non-coding regions of different genomes has been leading this thought recently. The coding potential of these newly identified sORFs have been investigated through experimental and computational approaches in recent studies. In the present work we have tried to make peptides from intergenic sequences of D. melanogaster genome leading to therapeutic applications. Towards this goal of making novel peptides from non-coding genome, we have found strong computational evidence of 145 peptides with conformational stability from the intergenic sequences of D. melanogaster. The structure of these completely unique peptides was predicted using ab initio method. The function annotation of these peptides was carried out using this structural information. The newly generated proteins were categorised as DNA/Protein/ion binding proteins, electron transporters and a very few as enzymes too. Experimental studies can certainly provide validations to these preliminary findings. This work provides further evidence of untapped potential of non-coding genome.
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Affiliation(s)
- Varughese Deepthi
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
| | - Vineetha V. I. Nair
- Indian Institute of Information Technology and Management, Kerala,Technopark, Trivandrum, India
| | - Vipin Thomas
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
| | - Navya Raj
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
| | - Shidhi P. Ramakrishnan
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
| | - Juveria Khan
- School of Biotechnology,Jawaharlal Nehru University, New Delhi 110067
| | - Monika Kaushik
- School of Biotechnology,Jawaharlal Nehru University, New Delhi 110067
| | - Pawan K. Dhar
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
- School of Biotechnology,Jawaharlal Nehru University, New Delhi 110067
| | - Achuthsankar S. Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom, Trivandrum
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21
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Herrera VLM, Steffen M, Moran AM, Tan GA, Pasion KA, Rivera K, Pappin DJ, Ruiz-Opazo N. Confirmation of translatability and functionality certifies the dual endothelin1/VEGFsp receptor (DEspR) protein. BMC Mol Biol 2016; 17:15. [PMID: 27301377 PMCID: PMC4906906 DOI: 10.1186/s12867-016-0066-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Background In contrast to rat and mouse databases, the NCBI gene database lists the human dual-endothelin1/VEGFsp receptor (DEspR, formerly Dear) as a unitary transcribed pseudogene due to a stop [TGA]-codon at codon#14 in automated DNA and RNA sequences. However, re-analysis is needed given prior single gene studies detected a tryptophan [TGG]-codon#14 by manual Sanger sequencing, demonstrated DEspR translatability and functionality, and since the demonstration of actual non-translatability through expression studies, the standard-of-excellence for pseudogene designation, has not been performed. Re-analysis must meet UNIPROT criteria for demonstration of a protein’s existence at the highest (protein) level, which a priori, would override DNA- or RNA-based deductions. Methods To dissect the nucleotide sequence discrepancy, we performed Maxam–Gilbert sequencing and reviewed 727 RNA-seq entries. To comply with the highest level multiple UNIPROT criteria for determining DEspR’s existence, we performed various experiments using multiple anti-DEspR monoclonal antibodies (mAbs) targeting distinct DEspR epitopes with one spanning the contested tryptophan [TGG]-codon#14, assessing: (a) DEspR protein expression, (b) predicted full-length protein size, (c) sequence-predicted protein-specific properties beyond codon#14: receptor glycosylation and internalization, (d) protein-partner interactions, and (e) DEspR functionality via DEspR-inhibition effects. Results Maxam–Gilbert sequencing and some RNA-seq entries demonstrate two guanines, hence a tryptophan [TGG]-codon#14 within a compression site spanning an error-prone compression sequence motif. Western blot analysis using anti-DEspR mAbs targeting distinct DEspR epitopes detect the identical glycosylated 17.5 kDa pull-down protein. Decrease in DEspR-protein size after PNGase-F digest demonstrates post-translational glycosylation, concordant with the consensus-glycosylation site beyond codon#14. Like other small single-transmembrane proteins, mass spectrometry analysis of anti-DEspR mAb pull-down proteins do not detect DEspR, but detect DEspR-protein interactions with proteins implicated in intracellular trafficking and cancer. FACS analyses also detect DEspR-protein in different human cancer stem-like cells (CSCs). DEspR-inhibition studies identify DEspR-roles in CSC survival and growth. Live cell imaging detects fluorescently-labeled anti-DEspR mAb targeted-receptor internalization, concordant with the single internalization-recognition sequence also located beyond codon#14. Conclusions Data confirm translatability of DEspR, the full-length DEspR protein beyond codon#14, and elucidate DEspR-specific functionality. Along with detection of the tryptophan [TGG]-codon#14 within an error-prone compression site, cumulative data demonstrating DEspR protein existence fulfill multiple UNIPROT criteria, thus refuting its pseudogene designation. Electronic supplementary material The online version of this article (doi:10.1186/s12867-016-0066-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Victoria L M Herrera
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Martin Steffen
- Department of Pathology and Biomedical Engineering, Boston University, Boston, USA
| | - Ann Marie Moran
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Glaiza A Tan
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Khristine A Pasion
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA
| | - Keith Rivera
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Nelson Ruiz-Opazo
- Whitaker Cardiovascular Institute, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA. .,Department of Medicine, Boston University School of Medicine, 700 Albany Street, Boston, MA, 02118, USA.
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22
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Tatarinova TV, Lysnyansky I, Nikolsky YV, Bolshoy A. The mysterious orphans of Mycoplasmataceae. Biol Direct 2016; 11:2. [PMID: 26747447 PMCID: PMC4706650 DOI: 10.1186/s13062-015-0104-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/30/2015] [Indexed: 01/08/2023] Open
Abstract
Background The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in the bacterium Escherichia coli and in the archaeon Archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (BMC Evol Biol 2:20, 2002). It is now generally accepted that in bacterial and archaeal genomes the distributions of protein length are different between sequences with and without homologs. In this study, we examine this postulate by conducting a comprehensive analysis of all annotated prokaryotic genomes and by focusing on certain exceptions. Results We compared the distribution of lengths of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently completely sequenced and COG-annotated prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes of Mycoplasma and Ureaplasma have atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80 % of atypical genomes. Conclusions We confirmed on a ubiquitous set of genomes that the previous observation of HHPs and ORFans have different gene length distributions. We also showed that Mycoplasmataceae genomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon, such as an adaptation to Mycoplasmataceae’s ecological niche, specifically its “quiet” co-existence with host organisms, resulting in long ABC transporters. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0104-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatiana V Tatarinova
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, 90027, CA, USA. .,Spatial Sciences Institute, University of Southern California, Los Angeles, 90089, CA, USA.
| | - Inna Lysnyansky
- Mycoplasma Unit, Division of Avian and Aquatic Diseases, Kimron Veterinary Institute, POB 12, Beit Dagan, 50250, Israel.
| | - Yuri V Nikolsky
- School of Systems Biology, George Mason University, 10900 University Blvd, MSN 5B3, Manassas, VA, 20110, USA. .,Prosapia Genetics, LLC, 534 San Andres Dr., Solana Beach, CA, 92075, USA. .,Vavilov Institute of General Genetics, Moscow, Russian Federation.
| | - Alexander Bolshoy
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel.
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23
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Thomas V, Raj N, Varughese D, Kumar N, Sehrawat S, Grover A, Singh S, Dhar PK, Nair AS. Predicting stable functional peptides from the intergenic space of E. coli. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:135-140. [PMID: 28392846 DOI: 10.1007/s11693-015-9172-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022]
Abstract
Expression of synthetic proteins from intergenic regions of E. coli and their functional association was recently demonstrated (Dhar et al. in J Biol Eng 3:2, 2009. doi:10.1186/1754-1611-3-2). This gave birth to the question: if one can make 'user-defined' genes from non-coding genome-how big is the artificially translatable genome? (Dinger et al. in PLoS Comput Biol 4, 2008; Frith et al. in RNA Biol 3(1):40-48, 2006a; Frith et al. in PLoS Genet 2(4):e52, 2006b). To answer this question, we performed a bioinformatics study of all reported E. coli intergenic sequences, in search of novel peptides and proteins, unexpressed by nature. Overall, 2500 E. coli intergenic sequences were computationally translated into 'protein sequence equivalents' and matched against all known proteins. Sequences that did not show any resemblance were used for building a comprehensive profile in terms of their structure, function, localization, interactions, stability so on. A total of 362 protein sequences showed evidence of stable tertiary conformations encoded by the intergenic sequences of E. coli genome. Experimental studies are underway to confirm some of the key predictions. This study points to a vast untapped repository of functional molecules lying undiscovered in the non-expressed genome of various organisms.
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Affiliation(s)
- Vipin Thomas
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India
| | - Navya Raj
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India
| | - Deepthi Varughese
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India
| | - Naveen Kumar
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India
| | - Seema Sehrawat
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, 201316 U.P. India
| | - Pawan K Dhar
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India.,School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Achuthsankar S Nair
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, 695581 Kerala India
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24
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Jia Y, Chen L, Ma Y, Zhang J, Xu N, Liao DJ. To Know How a Gene Works, We Need to Redefine It First but then, More Importantly, to Let the Cell Itself Decide How to Transcribe and Process Its RNAs. Int J Biol Sci 2015; 11:1413-23. [PMID: 26681921 PMCID: PMC4671999 DOI: 10.7150/ijbs.13436] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Recent genomic and ribonomic research reveals that our genome produces a stupendous amount of non-coding RNAs (ncRNAs), including antisense RNAs, and that many genes contain other gene(s) in their introns. Since ncRNAs either regulate the transcription, translation or stability of mRNAs or directly exert cellular functions, they should be regarded as the fourth category of RNAs, after ribosomal, messenger and transfer RNAs. These and other research advances challenge the current concept of gene and raise a question as to how we should redefine gene. We can either consider each tiny part of the classically-defined gene, such as each mRNA variant, as a “gene”, or, alternatively and oppositely, regard a whole genomic locus as a “gene” that may contain intron-embedded genes and produce different types of RNAs and proteins. Each of the two ways to redefine gene not only has its strengths and weaknesses but also has its particular concern on the methodology for the determination of the gene's function: Ectopic expression of complementary DNA (cDNA) in cells has in the past decades provided us with great deal of detail about the functions of individual mRNA variants, and will make the data less conflicting with each other if just a small part of a classically-defined gene is considered as a “gene”. On the other hand, genomic DNA (gDNA) will better help us in understanding the collective function of a genomic locus. In our opinion, we need to be more cautious in the use of cDNA and in the explanation of data resulting from cDNA, and, instead, should make delivery of gDNA into cells routine in determination of genes' functions, although this demands some technology renovation.
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Affiliation(s)
- Yuping Jia
- 1. Shandong Academy of Pharmaceutical Sciences, Ji'nan, Shandong, 250101, P.R. China
| | - Lichan Chen
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yukui Ma
- 1. Shandong Academy of Pharmaceutical Sciences, Ji'nan, Shandong, 250101, P.R. China
| | - Jian Zhang
- 3. Center for Translational Medicine, Pharmacology and Biomedical Sciences Building, Guangxi Medical University, 22 Shuangyong Road, Nanning, Guangxi 530021, P.R. China
| | - Ningzhi Xu
- 4. Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P.R. China
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25
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Xing GL, Tian SH, Xie XL, Fu J. HS-4, a highly potent inhibitor of cell proliferation of human cancer cell. ASIAN PAC J TROP MED 2015; 8:417-20. [PMID: 26003604 DOI: 10.1016/s1995-7645(14)60354-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To investigate the antitumor activity of the compound HS-4 and the action mechanism. METHODS MTT method was used to test in vitro antitumor activity of the compound HS-4. Orthotopic xenotransplantation tumor model of liver cancer was established in nude mice, and, in vivo antitumor activity of compound HS-4 was tested with a small animal in-vivo imaging system. Sequencing of small RNA library and RNA library was performed in HS-4 treated tumor cell group and control group to investigate the anti-cancer mechanism of HS-4 at level of functional genomics, using high-throughput sequencing technology. RESULTS HS-4 was found to have relatively high in-vitro antitumor activity against liver cancer cells, gastric cancer cells, renal cancer cells, lung cancer cells, breast cancer cells and colon cancer cells. The IC50 values against SMMC-7721 and Bel-7402 of liver cancer cells were 0.14 and 0.13 nmol/L respectively, while the IC50 values against MGC-803 and SGC-7901 of gastric cancer cells were 0.19 and 0.21 nmol/L, respectively. It was demonstrated that HS-4 possessed a better therapeutic effect in liver cancer. CONCLUSIONS A new reliable orthotopic xenotransplantation tumor model of liver cancer in nude mice is established. The new compounds HS-4 was found to possess relatively high in vivo and in vitro antitumor activity against liver cancer cells.
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Affiliation(s)
- Gui-Lan Xing
- Hainan Province Drug Safety Evaluation and Research Center, Hainan Medical College, Haikou, 571199, China
| | - Shu-Hong Tian
- Hainan Province Drug Safety Evaluation and Research Center, Hainan Medical College, Haikou, 571199, China
| | - Xue-Li Xie
- Hainan Province Drug Safety Evaluation and Research Center, Hainan Medical College, Haikou, 571199, China.
| | - Jian Fu
- Hainan Province Drug Safety Evaluation and Research Center, Hainan Medical College, Haikou, 571199, China.
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In silico study of peptide inhibitors against BACE 1. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:67-72. [PMID: 25972990 DOI: 10.1007/s11693-015-9169-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
Abstract
Peptides are increasingly used as inhibitors of various disease specific targets. Several naturally occurring and synthetically developed peptides are undergoing clinical trials. Our work explores the possibility of reusing the non-expressing DNA sequences to predict potential drug-target specific peptides. Recently, we experimentally demonstrated the artificial synthesis of novel proteins from non-coding regions of Escherichia coli genome. In this study, a library of synthetic peptides (Synpeps) was constructed from 2500 intergenic E. coli sequences and screened against Beta-secretase 1 protein, a known drug target for Alzheimer's disease (AD). Secondary and tertiary protein structure predictions followed by protein-protein docking studies were performed to identify the most promising enzyme inhibitors. Interacting residues and favorable binding poses of lead peptide inhibitors were studied. Though initial results are encouraging, experimental validation is required in future to develop efficient target specific inhibitors against AD.
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Legeai F, Derrien T. Identification of long non-coding RNAs in insects genomes. CURRENT OPINION IN INSECT SCIENCE 2015; 7:37-44. [PMID: 32846672 DOI: 10.1016/j.cois.2015.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 06/11/2023]
Abstract
The development of high throughput sequencing technologies (HTS) has allowed researchers to better assess the complexity and diversity of the transcriptome. Among the many classes of non-coding RNAs (ncRNAs) identified the last decade, long non-coding RNAs (lncRNAs) represent a diverse and numerous repertoire of important ncRNAs, reinforcing the view that they are of central importance to the cell machinery in all branches of life. Although lncRNAs have been involved in essential biological processes such as imprinting, gene regulation or dosage compensation especially in mammals, the repertoire of lncRNAs is poorly characterized for many non-model organisms. In this review, we first focus on what is known about experimentally validated lncRNAs in insects and then review bioinformatic methods to annotate lncRNAs in the genomes of hexapods.
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Affiliation(s)
- Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, BP35327, 35653 Le Rheu cedex, France; IRISA/INRIA GenScale, Campus Beaulieu, 35000 Rennes, France.
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
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Yang G, Lu X, Yuan L. LncRNA: a link between RNA and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1097-109. [PMID: 25159663 DOI: 10.1016/j.bbagrm.2014.08.012] [Citation(s) in RCA: 787] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
Unraveling the gene expression networks governing cancer initiation and development is essential while remains largely uncompleted. With the innovations in RNA-seq technologies and computational biology, long noncoding RNAs (lncRNAs) are being identified and characterized at a rapid pace. Recent findings reveal that lncRNAs are implicated in serial steps of cancer development. These lncRNAs interact with DNA, RNA, protein molecules and/or their combinations, acting as an essential regulator in chromatin organization, and transcriptional and post-transcriptional regulation. Their misexpression confers the cancer cell capacities for tumor initiation, growth, and metastasis. The review here will emphasize their aberrant expression and function in cancer, and the roles in cancer diagnosis and therapy will be also discussed.
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Affiliation(s)
- Guodong Yang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an 710032, PR China.
| | - Xiaozhao Lu
- Department of Nephrology, 323 Hospital of PLA, Xi'an 710054, PR China
| | - Lijun Yuan
- Department of Ultrasound, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, PR China.
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29
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Zhang J, Lou X, Shen H, Zellmer L, Sun Y, Liu S, Xu N, Liao DJ. Isoforms of wild type proteins often appear as low molecular weight bands on SDS-PAGE. Biotechnol J 2014; 9:1044-54. [PMID: 24906056 DOI: 10.1002/biot.201400072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 11/08/2022]
Abstract
Immunoblotting, after polyacrylamide gel electrophoresis with sodium dodecyl sulfate (SDS-PAGE), is a technique commonly used to detect specific proteins. SDS-PAGE often results in the visualization of protein band(s) in addition to the one expected based on the theoretical molecular mass (TMM) of the protein of interest. To determine the likelihood of additional band(s) being nonspecific, we used liquid chromatography - mass spectrometry to identify proteins that were extracted from bands with the apparent molecular mass (MM) of 40 and 26 kD, originating from protein extracts derived from non-malignant HEK293 and cancerous MDA-MB231 (MB231) cells separated using SDS-PAGE. In total, approximately 57% and 21% of the MS/MS spectra were annotated as peptides in the two cell samples, respectively. Moreover, approximately 24% and 36.2% of the identified proteins from HEK293 and MB231 cells matched their TMMs. Of the identified proteins, 8% from HEK293 and 26% from MB231 had apparent MMs that were larger than predicted, and 67% from HEK293 and 37% from MB231 exhibited smaller MM values than predicted. These revelations suggest that interpretation of the positive bands of immunoblots should be conducted with caution. This study also shows that protein identification performed by mass spectrometry on bands excised from SDS-PAGE gels could make valuable contributions to the identification of cancer biomarkers, and to cancer-therapy studies.
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Affiliation(s)
- Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P. R. China
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Crappé J, Van Criekinge W, Menschaert G. Little things make big things happen: A summary of micropeptide encoding genes. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Lou X, Zhang J, Liu S, Xu N, Liao DJ. The other side of the coin: the tumor-suppressive aspect of oncogenes and the oncogenic aspect of tumor-suppressive genes, such as those along the CCND-CDK4/6-RB axis. Cell Cycle 2014; 13:1677-93. [PMID: 24799665 DOI: 10.4161/cc.29082] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although cancer-regulatory genes are dichotomized to oncogenes and tumor-suppressor gene s, in reality they can be oncogenic in one situation but tumor-suppressive in another. This dual-function nature, which sometimes hampers our understanding of tumor biology, has several manifestations: (1) Most canonically defined genes have multiple mRNAs, regulatory RNAs, protein isoforms, and posttranslational modifications; (2) Genes may interact at different levels, such as by forming chimeric RNAs or by forming different protein complexes; (3) Increased levels of tumor-suppressive genes in normal cells drive proliferation of cancer progenitor cells in the same organ or tissue by imposing compensatory proliferation pressure, which presents the dual-function nature as a cell-cell interaction. All these manifestations of dual functions can find examples in the genes along the CCND-CDK4/6-RB axis. The dual-function nature also underlies the heterogeneity of cancer cells. Gene-targeting chemotherapies, including that targets CDK4, are effective to some cancer cells but in the meantime may promote growth or progression of some others in the same patient. Redefining "gene" by considering each mRNA, regulatory RNA, protein isoform, and posttranslational modification from the same genomic locus as a "gene" may help in better understanding tumor biology and better selecting targets for different sub-populations of cancer cells in individual patients for personalized therapy.
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Affiliation(s)
- Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing, PR China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology; Cancer Institute; Chinese Academy of Medical Science; Beijing, PR China
| | - D Joshua Liao
- Hormel Institute; University of Minnesota; Austin, MN USA
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32
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Ericson M, Janes MA, Butter F, Mann M, Ullu E, Tschudi C. On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei. BMC Biol 2014; 12:14. [PMID: 24552149 PMCID: PMC3942054 DOI: 10.1186/1741-7007-12-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/06/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. RESULTS Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. CONCLUSIONS Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host.
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Affiliation(s)
- Megan Ericson
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Michael A Janes
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
- Current address: San Francisco General Hospital, Pulmonary & Critical Care, San Francisco, CA, USA
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Current address: Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elisabetta Ullu
- Department of Cell Biology and Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
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33
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Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 2014; 15:193-204. [PMID: 24514441 DOI: 10.1038/nrg3520] [Citation(s) in RCA: 382] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Short open reading frames (sORFs) are a common feature of all genomes, but their coding potential has mostly been disregarded, partly because of the difficulty in determining whether these sequences are translated. Recent innovations in computing, proteomics and high-throughput analyses of translation start sites have begun to address this challenge and have identified hundreds of putative coding sORFs. The translation of some of these has been confirmed, although the contribution of their peptide products to cellular functions remains largely unknown. This Review examines this hitherto overlooked component of the proteome and considers potential roles for sORF-encoded peptides.
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Guennewig B, Cooper AA. The Central Role of Noncoding RNA in the Brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:153-94. [DOI: 10.1016/b978-0-12-801105-8.00007-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Abstract
Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.
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Affiliation(s)
- Sean R Eddy
- Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147;
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36
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De Coninck B, Carron D, Tavormina P, Willem L, Craik DJ, Vos C, Thevissen K, Mathys J, Cammue BPA. Mining the genome of Arabidopsis thaliana as a basis for the identification of novel bioactive peptides involved in oxidative stress tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5297-307. [PMID: 24043855 DOI: 10.1093/jxb/ert295] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Although evidence has accumulated on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. Using tiling arrays, we identified 176 unannotated transcriptionally active regions (TARs) in Arabidopsis thaliana that were induced upon oxidative stress generated by the herbicide paraquat (PQ). These 176 TARs could be translated into 575 putative oxidative stress-induced peptides (OSIPs). A high-throughput functional assay was used in the eukaryotic model organism Saccharomyces cerevisiae allowing us to test for bioactive peptides that increase oxidative stress tolerance. In this way, we identified three OSIPs that, upon overexpression in yeast, resulted in a significant rise in tolerance to hydrogen peroxide (H2O2). For one of these peptides, the decapeptide OSIP108, exogenous application to H2O2-treated yeast also resulted in significantly increased survival. OSIP108 is contained within a pseudogene and is induced in A. thaliana leaves by both the reactive oxygen species-inducer PQ and the necrotrophic fungal pathogen Botrytis cinerea. Moreover, infiltration and overexpression of OSIP108 in A. thaliana leaves resulted in increased tolerance to treatment with PQ. In conclusion, the identification and characterization of OSIP108 confirms the validity of our high-throughput approach, based on tiling array analysis in A. thaliana and functional screening in yeast, to identify bioactive peptides.
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Affiliation(s)
- Barbara De Coninck
- Centre for Microbial and Plant Genetics, KU Leuven, 3001 Heverlee, Belgium
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37
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Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genomics 2013; 14:648. [PMID: 24059539 PMCID: PMC3852105 DOI: 10.1186/1471-2164-14-648] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/13/2013] [Indexed: 11/23/2022] Open
Abstract
Background It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e.g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs. Results Using bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides. Conclusion Our combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides.
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Mamon LA, Kliver SF, Golubkova EV. Evolutionarily conserved features of the retained intron in alternative transcripts of the <i>nxf1</i> (nuclear export factor) genes in different organisms. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojgen.2013.33018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Plagge A. Non-Coding RNAs at the Gnas and Snrpn-Ube3a Imprinted Gene Loci and Their Involvement in Hereditary Disorders. Front Genet 2012; 3:264. [PMID: 23226156 PMCID: PMC3509947 DOI: 10.3389/fgene.2012.00264] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 11/05/2012] [Indexed: 12/02/2022] Open
Abstract
Non-coding RNAs (ncRNAs) have long been recognized at imprinted gene loci and provided early paradigms to investigate their functions and molecular mechanisms of action. The characteristic feature of imprinted genes, their monoallelic, parental-origin-dependent expression, is achieved through complex epigenetic regulation, which is modulated by ncRNAs. This minireview focuses on two imprinted gene clusters, in which changes in ncRNA expression contribute to human disorders. At the GNAS locus loss of NESP RNA can cause autosomal dominant Pseudohypoparathyroidism type 1b (AD-PHP-Ib), while at the SNRPN-UBE3A locus a long ncRNA and processed snoRNAs play a role in Angelman-Syndrome (AS) and Prader–Willi-Syndrome (PWS). The ncRNAs silence overlapping protein-coding transcripts in sense or anti-sense orientation through changes in histone modifications as well as DNA methylation at CpG-rich sequence motifs. Their epigenetic modulatory functions are required in early development in the pre-implantation embryo or already in the parental germ cells. However, it remains unclear whether the sequence homology-carrying ncRNA itself is required, or whether the process of its transcription through other promoters causes the silencing effect.
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Affiliation(s)
- Antonius Plagge
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool Liverpool, UK
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40
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Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 2012; 13:528-41. [PMID: 22814587 DOI: 10.1038/nrn3234] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are being characterized at a rapid pace, driven by recent paradigm shifts in our understanding of genomic architecture, regulation and transcriptional output, as well as by innovations in sequencing technologies and computational and systems biology. These ncRNAs can interact with DNA, RNA and protein molecules; engage in diverse structural, functional and regulatory activities; and have roles in nuclear organization and transcriptional, post-transcriptional and epigenetic processes. This expanding inventory of ncRNAs is implicated in mediating a broad spectrum of processes including brain evolution, development, synaptic plasticity and disease pathogenesis.
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Niazi F, Valadkhan S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs. RNA (NEW YORK, N.Y.) 2012; 18:825-43. [PMID: 22361292 PMCID: PMC3312569 DOI: 10.1261/rna.029520.111] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent transcriptome analyses have indicated that a large part of mammalian genomes are transcribed into long non-protein-coding RNAs (lncRNAs). However, only a very small fraction of them have been individually studied, and whether the majority of lncRNAs found in large-scale studies have a cellular role is debated. To gain insight into the sequence features and genomic architecture of the subset of lncRNAs that have been proven to be functional, we created a database containing studied lncRNAs manually culled from the literature along with a parallel database containing all annotated protein-coding human RNAs. The Functional lncRNA Database, which contains 204 lncRNAs and their splicing variants, is available at valadkhanlab.org/database. Analysis of the lncRNAs and their comparison to protein-coding transcripts revealed sequence features including paucity of introns and low GC content in lncRNAs, which could explain several biological characteristics of these transcripts, such as their nuclear localization and low expression level. The predicted ORFs in lncRNAs have poor start codon and ORF contexts, which would lead to activation of the nonsense-mediated decay pathways and thus make it unlikely for most lncRNAs to code for even short peptides. Interestingly, our analyses revealed significant similarities between the lncRNAs and the 3' untranslated regions (3' UTRs) in protein-coding RNAs in structural features and sequence composition. The presence of these intriguing parallels between the lncRNAs and 3' UTRs, which constitute the two main components of the RNA-mediated cellular regulatory system, indicates that highly similar evolutionary constraints govern the function of regulatory RNA sequences in the cell.
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Affiliation(s)
- Farshad Niazi
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Corresponding authors.E-mail .E-mail .
| | - Saba Valadkhan
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Corresponding authors.E-mail .E-mail .
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Molecular Functions of Long Non-Coding RNAs in Plants. Genes (Basel) 2012; 3:176-90. [PMID: 24704849 PMCID: PMC3899965 DOI: 10.3390/genes3010176] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
The past decade has seen dramatic changes in our understanding of the scale and complexity of eukaryotic transcriptome owing to the discovery of diverse types of short and long non-protein-coding RNAs (ncRNAs). While short ncRNA-mediated gene regulation has been extensively studied and the mechanisms well understood, the function of long ncRNAs remains largely unexplored, especially in plants. Nevertheless, functional insights generated in recent studies with mammalian systems have indicated that long ncRNAs are key regulators of a variety of biological processes. They have been shown to act as transcriptional regulators and competing endogenous RNAs (ceRNAs), to serve as molecular cargos for protein re-localization and as modular scaffolds to recruit the assembly of multiple protein complexes for chromatin modifications. Some of these functions have been found to be conserved in plants. Here, we review our current understanding of long ncRNA functions in plants and discuss the challenges in functional characterization of plant long ncRNAs.
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Caudron-Herger M, Rippe K. Nuclear architecture by RNA. Curr Opin Genet Dev 2012; 22:179-87. [PMID: 22281031 DOI: 10.1016/j.gde.2011.12.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/20/2011] [Accepted: 12/24/2011] [Indexed: 12/15/2022]
Abstract
The dynamic organization of the cell nucleus into subcompartments with distinct biological activities represents an important determinant of cell function. Recent studies point to a crucial role of RNA as an architectural factor for shaping the genome and its nuclear environment. Here, we outline general principles by which RNA organizes functionally different nuclear subcompartments in mammalian cells. RNA is a structural component of mobile DNA-free nuclear bodies like paraspeckles or Cajal bodies, and is involved in establishing specific chromatin domains. The latter group comprises largely different structures that require RNA for the formation of active or repressive chromatin compartments with respect to gene expression as well as separating boundaries between these.
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Affiliation(s)
- Maïwen Caudron-Herger
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum and BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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