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Ranjan G, Scaria V, Sivasubbu S. Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution. Gene 2025; 933:148988. [PMID: 39378975 DOI: 10.1016/j.gene.2024.148988] [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: 04/17/2024] [Revised: 07/12/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with cis-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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2
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Caño-Carrillo S, Garcia-Padilla C, Aranega AE, Lozano-Velasco E, Franco D. Mef2c- and Nkx2-5-Divergent Transcriptional Regulation of Chick WT1_76127 and Mouse Gm14014 lncRNAs and Their Implication in Epicardial Cell Migration. Int J Mol Sci 2024; 25:12904. [PMID: 39684625 DOI: 10.3390/ijms252312904] [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: 10/17/2024] [Revised: 11/25/2024] [Accepted: 11/28/2024] [Indexed: 12/18/2024] Open
Abstract
Cardiac development is a complex developmental process. The early cardiac straight tube is composed of an external myocardial layer and an internal endocardial lining. Soon after rightward looping, the embryonic heart becomes externally covered by a new epithelial lining, the embryonic epicardium. A subset of these embryonic epicardial cells migrate and colonize the embryonic myocardium, contributing to the formation of distinct cell types. In recent years, our understanding of the molecular mechanisms that govern proepicardium and embryonic epicardium formation has greatly increased. We have recently witnessed the discovery of a novel layer of complexity governing gene regulation with the discovery of non-coding RNAs. Our laboratory recently identified three distinct lncRNAs, adjacent to the Wt1, Bmp4 and Fgf8 chicken gene loci, with enhanced expression in the proepicardium that are distinctly regulated by Bmp, Fgf and thymosin β4, providing support for their plausible implication in epicardial formation. The expression of lncRNAs was analyzed in different chicken and mouse tissues as well as their subcellular distribution in chicken proepicardial, epicardial, ventricle explants and in different murine cardiac cell types. lncRNA transcriptional regulation was analyzed by using siRNAs and expression vectors of different transcription factors in chicken and mouse models, whereas antisense oligonucleotides were used to inhibit Gm14014 expression. Furthermore, RT-qPCR, immunocytochemistry, RNA pulldown, Western blot, viability and cell migration assays were conducted to investigate the biological functions of Wt1_76127 and Gm14014. We demonstrated that Wt1_76127 in chicken and its putative conserved homologue Gm14014 in mice are widely distributed in different embryonic and adult tissues and distinctly regulated by cardiac-enriched transcription factors, particularly Mef2c and Nkx2.5. Furthermore, silencing assays demonstrated that mouse Gm14014, but not chicken Wt1_76127, is essential for epicardial, but not endocardial or myocardial, cell migration. Such processes are governed by partnering with Myl9, promoting cytoskeletal remodeling. Our data show that Gm14014 plays a pivotal role in epicardial cell migration essential for heart regeneration under these experimental conditions.
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Affiliation(s)
- Sheila Caño-Carrillo
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain
| | - Carlos Garcia-Padilla
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain
| | - Amelia E Aranega
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain
- Fundación Medina, 18016 Granada, Spain
| | - Estefania Lozano-Velasco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain
- Fundación Medina, 18016 Granada, Spain
| | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaen, 23071 Jaen, Spain
- Fundación Medina, 18016 Granada, Spain
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Altoum AA, Oghenemaro EF, Pallathadka H, Sanghvi G, Hjazi A, Abbot V, Kumar MR, Sharma R, Zwamel AH, Taha ZA. lncRNA-mediated immune system dysregulation in RIF; a comprehensive insight into immunological modifications and signaling pathways' dysregulation. Hum Immunol 2024; 85:111170. [PMID: 39549305 DOI: 10.1016/j.humimm.2024.111170] [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: 08/24/2024] [Revised: 10/13/2024] [Accepted: 10/26/2024] [Indexed: 11/18/2024]
Abstract
The initial stage of biological pregnancy is referred to as implantation, during which the interaction between the endometrium and the fetus is crucial for successful implantation. Around 10% of couples undergoing in vitro fertilization and embryo transfer encounter recurrent implantation failure (RIF), a clinical condition characterized by the absence of implantation after multiple embryo transfers. It is believed that implantation failure may be caused by inadequate or excessive endometrial inflammatory responses during the implantation window, as the female immune system plays a complex role in regulating endometrial receptivity and embryo implantation. Recent approaches to enhance the likelihood of pregnancy in RIF patients have focused on modifying the mother's immune response during implantation by regulating inflammation. Long non-coding RNAs (lncRNAs) play a significant role in gene transcription during the inflammatory response. Current research suggests that dysfunctional lncRNAs are linked to various human disorders, such as cancer, diabetes, allergies, asthma, and inflammatory bowel disease. These non-coding RNAs are crucial for immune functions as they control protein interactions or the ability of RNA and DNA to form complexes, which are involved in differentiation, cell migration, and the production of inflammatory mediators. Given the apparent involvement of the immune system in RIF and the modulatory effect of lncRNAs on the immune system, this review aims to delve into the role of lncRNAs in immune system modulation and their potential contribution to RIF.
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Affiliation(s)
- Abdelgadir Alamin Altoum
- Department of Medical Laboratory Sciences, College of Health Sciences, Gulf Medical University, Ajman, United Arab Emirates
| | - Enwa Felix Oghenemaro
- Delta State University, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, PMB 1, Abraka, Delta State, Nigeria
| | | | - Gaurav Sanghvi
- Marwadi University Research Center, Department of Microbiology, Faculty of Science, Marwadi University, Rajkot 360003, Gujarat, India
| | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Vikrant Abbot
- Chandigarh Pharmacy College, Chandigarh Group of Colleges-Jhanjeri, Mohali 140307, Punjab, India
| | - M Ravi Kumar
- Department of Basic Science & Humanities, Raghu Engineering College, Visakhapatnam, India
| | - Rajesh Sharma
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University, Jaipur, Rajasthan 302131, India
| | - Ahmed Hussein Zwamel
- Department of Medical Analysis, Medical Laboratory Technique College, The Islamic University, Najaf, Iraq; Department of Medical Analysis, Medical Laboratory Technique College, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; Department of Medical Analysis, Medical Laboratory Technique College, The Islamic University of Babylon, Babylon, Iraq
| | - Zahraa Ahmed Taha
- Medical Laboratory Techniques Department, College of Health and Medical Techniques, Al-Mustaqbal University, 51001 Babylon, Iraq
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Espadas I, Wingfield JL, Nakahata Y, Chanda K, Grinman E, Ghosh I, Bauer KE, Raveendra B, Kiebler MA, Yasuda R, Rangaraju V, Puthanveettil S. Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity. Nat Commun 2024; 15:2694. [PMID: 38538603 PMCID: PMC10973417 DOI: 10.1038/s41467-024-46972-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in maintaining cell homeostasis and function. However, it remains largely unknown whether and how neuronal activity impacts the transcriptional regulation of lncRNAs, or if this leads to synapse-related changes and contributes to the formation of long-term memories. Here, we report the identification of a lncRNA, SLAMR, which becomes enriched in CA1-hippocampal neurons upon contextual fear conditioning but not in CA3 neurons. SLAMR is transported along dendrites via the molecular motor KIF5C and is recruited to the synapse upon stimulation. Loss of function of SLAMR reduces dendritic complexity and impairs activity-dependent changes in spine structural plasticity and translation. Gain of function of SLAMR, in contrast, enhances dendritic complexity, spine density, and translation. Analyses of the SLAMR interactome reveal its association with CaMKIIα protein through a 220-nucleotide element also involved in SLAMR transport. A CaMKII reporter reveals a basal reduction in CaMKII activity with SLAMR loss-of-function. Furthermore, the selective loss of SLAMR function in CA1 disrupts the consolidation of fear memory in male mice, without affecting their acquisition, recall, or extinction, or spatial memory. Together, these results provide new molecular and functional insight into activity-dependent changes at the synapse and consolidation of contextual fear.
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Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Karl E Bauer
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
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Angom RS, Joshi A, Patowary A, Sivadas A, Ramasamy S, K. V. S, Kaushik K, Sabharwal A, Lalwani MK, K. S, Singh N, Scaria V, Sivasubbu S. Forward genetic screen using a gene-breaking trap approach identifies a novel role of grin2bb-associated RNA transcript ( grin2bbART) in zebrafish heart function. Front Cell Dev Biol 2024; 12:1339292. [PMID: 38533084 PMCID: PMC10964321 DOI: 10.3389/fcell.2024.1339292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 03/28/2024] Open
Abstract
LncRNA-based control affects cardiac pathophysiologies like myocardial infarction, coronary artery disease, hypertrophy, and myotonic muscular dystrophy. This study used a gene-break transposon (GBT) to screen zebrafish (Danio rerio) for insertional mutagenesis. We identified three insertional mutants where the GBT captured a cardiac gene. One of the adult viable GBT mutants had bradycardia (heart arrhythmia) and enlarged cardiac chambers or hypertrophy; we named it "bigheart." Bigheart mutant insertion maps to grin2bb or N-methyl D-aspartate receptor (NMDAR2B) gene intron 2 in reverse orientation. Rapid amplification of adjacent cDNA ends analysis suggested a new insertion site transcript in the intron 2 of grin2bb. Analysis of the RNA sequencing of wild-type zebrafish heart chambers revealed a possible new transcript at the insertion site. As this putative lncRNA transcript satisfies the canonical signatures, we called this transcript grin2bb associated RNA transcript (grin2bbART). Using in situ hybridization, we confirmed localized grin2bbART expression in the heart, central nervous system, and muscles in the developing embryos and wild-type adult zebrafish atrium and bulbus arteriosus. The bigheart mutant had reduced Grin2bbART expression. We showed that bigheart gene trap insertion excision reversed cardiac-specific arrhythmia and atrial hypertrophy and restored grin2bbART expression. Morpholino-mediated antisense downregulation of grin2bbART in wild-type zebrafish embryos mimicked bigheart mutants; this suggests grin2bbART is linked to bigheart. Cardiovascular tissues use Grin2bb as a calcium-permeable ion channel. Calcium imaging experiments performed on bigheart mutants indicated calcium mishandling in the heart. The bigheart cardiac transcriptome showed differential expression of calcium homeostasis, cardiac remodeling, and contraction genes. Western blot analysis highlighted Camk2d1 and Hdac1 overexpression. We propose that altered calcium activity due to disruption of grin2bbART, a putative lncRNA in bigheart, altered the Camk2d-Hdac pathway, causing heart arrhythmia and hypertrophy in zebrafish.
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Affiliation(s)
- Ramcharan Singh Angom
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL, United States
| | - Adita Joshi
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Ashok Patowary
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Soundhar Ramasamy
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Shamsudheen K. V.
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Kriti Kaushik
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ankit Sabharwal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Mukesh Kumar Lalwani
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Subburaj K.
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Naresh Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- GN Ramachandran Knowledge Center for Genome Informatics, Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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6
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Aranega AE, Franco D. Posttranscriptional Regulation by Proteins and Noncoding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:313-339. [PMID: 38884719 DOI: 10.1007/978-3-031-44087-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Posttranscriptional regulation comprises those mechanisms occurring after the initial copy of the DNA sequence is transcribed into an intermediate RNA molecule (i.e., messenger RNA) until such a molecule is used as a template to generate a protein. A subset of these posttranscriptional regulatory mechanisms essentially are destined to process the immature mRNA toward its mature form, conferring the adequate mRNA stability, providing the means for pertinent introns excision, and controlling mRNA turnover rate and quality control check. An additional layer of complexity is added in certain cases, since discrete nucleotide modifications in the mature RNA molecule are added by RNA editing, a process that provides large mature mRNA diversity. Moreover, a number of posttranscriptional regulatory mechanisms occur in a cell- and tissue-specific manner, such as alternative splicing and noncoding RNA-mediated regulation. In this chapter, we will briefly summarize current state-of-the-art knowledge of general posttranscriptional mechanisms, while major emphases will be devoted to those tissue-specific posttranscriptional modifications that impact on cardiac development and congenital heart disease.
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Affiliation(s)
- Amelia E Aranega
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Diego Franco
- Cardiovascular Research Group, Department of Experimental Biology, University of Jaén, Jaén, Spain.
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Espadas I, Wingfield J, Grinman E, Ghosh I, Chanda K, Nakahata Y, Bauer K, Raveendra B, Kiebler M, Yasuda R, Rangaraju V, Puthanveettil S. SLAMR, a synaptically targeted lncRNA, facilitates the consolidation of contextual fear memory. RESEARCH SQUARE 2023:rs.3.rs-2489387. [PMID: 36993323 PMCID: PMC10055528 DOI: 10.21203/rs.3.rs-2489387/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
LncRNAs are involved in critical processes for cell homeostasis and function. However, it remains largely unknown whether and how the transcriptional regulation of long noncoding RNAs results in activity-dependent changes at the synapse and facilitate formation of long-term memories. Here, we report the identification of a novel lncRNA, SLAMR, that becomes enriched in CA1- but not in CA3-hippocampal neurons upon contextual fear conditioning. SLAMR is transported to dendrites via the molecular motor KIF5C and recruited to the synapse in response to stimulation. Loss of function of SLAMR reduced dendritic complexity and impaired activity dependent changes in spine structural plasticity. Interestingly, gain of function of SLAMR enhanced dendritic complexity, and spine density through enhanced translation. Analyses of the SLAMR interactome revealed its association with CaMKIIα protein through a 220-nucleotide element and its modulation of CaMKIIα activity. Furthermore, loss-of-function of SLAMR in CA1 selectively impairs consolidation but neither acquisition, recall, nor extinction of fear memory and spatial memory. Together, these results establish a new mechanism for activity dependent changes at the synapse and consolidation of contextual fear.
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Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute, Jupiter, FL, USA
| | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Karl Bauer
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael Kiebler
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | | | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
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Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
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Kumari J, Haque MI, Jha RK, Rathore MS. The red seaweed Kappaphycus alvarezii antiporter gene (KaNa +/H +) confers abiotic stress tolerance in transgenic tobacco. Mol Biol Rep 2022; 49:3729-3743. [PMID: 35141817 DOI: 10.1007/s11033-022-07213-7] [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: 10/08/2021] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Plant establishment, growth, development and productivity are adversely affected by abiotic stresses that are dominant characteristics of environmentally challenged/degraded habitats created in the Anthropocene. Crop breeding for climate resilience properties is need of the hour to sustain the crop productivity. We report on the characterization of Kappaphycus alvarezii (a red seaweed) Na+/H+ antiporter gene (KaNa+/H+) for enhanced salt and osmotic stress tolerance. METHODS The KaNa+/H+ antiporter gene was cloned and over-expressed in tobacco under the control of CaMV35S promoter. Transgenic analysis was carried out to assess the stress tolerance ability of tobacco over-expressing KaNa+/H+ antiporter gene. RESULTS Over-expression of KaNa+/H+ gene improved the seed germination and seed vigor index under stress. Transgenic plants grew better and exhibited delayed leaf senescence. Improved K+/Na+, carotenoid/total chlorophyll and relative water content; lower accumulation of reactive oxygen species (ROS), MDA and Na+; lower electrolyte leakage; better membrane stability index and accumulation of K+, photosynthetic pigment, starch, sugar, free amino acid, proline and polyphenol contents indicated better physiological health of the transgenic tobacco under stress. Transgenic tobacco exhibited higher photosynthesis, photosystem II efficiency, electron transfer rate, photochemical quenching and activity of water splitting complex. Compared with control tobacco, transgenic tobacco exhibited higher expression of stress-defence genes under stress and better recovery after long-term osmotic stress. CONCLUSIONS Lower Na+ cytotoxicity, lower accumulation of ROS and maintenance of the membrane integrity helped transgenic tobacco to maintain the physiological functioning under stress. Present results established K. alvarezii as a potential gene resource and the KaNa+/H+ antiporter gene as a potential candidate gene in molecular breeding of crops for development of the degraded land.
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Affiliation(s)
- Jyoti Kumari
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Md Intesaful Haque
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Rajesh K Jha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Mangal S Rathore
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), G.B. Marg, Bhavnagar, Gujarat, 364002, India.
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11
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Rauner M, Foessl I, Formosa MM, Kague E, Prijatelj V, Lopez NA, Banerjee B, Bergen D, Busse B, Calado Â, Douni E, Gabet Y, Giralt NG, Grinberg D, Lovsin NM, Solan XN, Ostanek B, Pavlos NJ, Rivadeneira F, Soldatovic I, van de Peppel J, van der Eerden B, van Hul W, Balcells S, Marc J, Reppe S, Søe K, Karasik D. Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. Front Endocrinol (Lausanne) 2021; 12:731217. [PMID: 34938269 PMCID: PMC8686830 DOI: 10.3389/fendo.2021.731217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.
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Affiliation(s)
- Martina Rauner
- Department of Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ines Foessl
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Endocrine Lab Platform, Medical University of Graz, Graz, Austria
| | - Melissa M. Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Erika Kague
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- The Generation R Study, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nerea Alonso Lopez
- Rheumatology and Bone Disease Unit, CGEM, Institute of Genetics and Cancer (IGC), Edinburgh, United Kingdom
| | - Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Dylan Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ângelo Calado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Eleni Douni
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
- Institute for Bioinnovation, B.S.R.C. “Alexander Fleming”, Vari, Greece
| | - Yankel Gabet
- Department of Anatomy & Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Natalia García Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Nika M. Lovsin
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Xavier Nogues Solan
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Nathan J. Pavlos
- Bone Biology & Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | | | - Ivan Soldatovic
- Institute of Medical Statistics and Informatic, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Wim van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Sjur Reppe
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kent Søe
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel
- Marcus Research Institute, Hebrew SeniorLife, Boston, MA, United States
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12
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He Y, Yu H, Zhao H, Zhu H, Zhang Q, Wang A, Shen Y, Xu X, Li J. Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella). BMC Genomics 2021; 22:620. [PMID: 34399686 PMCID: PMC8369720 DOI: 10.1186/s12864-021-07924-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/06/2021] [Indexed: 01/23/2023] Open
Abstract
Background Grass carp (Ctenopharyngodon idella) is one of the most widely cultivated fishes in China. High stocking density can reportedly affect fish growth and immunity. Herein we performed PacBio long-read single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to evaluate the effects of high stocking density on grass carp transcriptome. Results SMRT sequencing led to the identification of 33,773 genes (14,946 known and 18,827 new genes). From the structure analysis, 8,009 genes were detected with alternative splicing events, 10,219 genes showed alternative polyadenylation sites and 15,521 long noncoding RNAs. Further, 1,235, 962, and 213 differentially expressed genes (DEGs) were identified in the intestine, muscle, and brain tissues, respectively. We performed functional enrichment analyses of DEGs, and they were identified to be significantly enriched in nutrient metabolism and immune function. The expression levels of several genes encoding apolipoproteins and activities of enzymes involved in carbohydrate enzymolysis were found to be upregulated in the high stocking density group, indicating that lipid metabolism and carbohydrate decomposition were accelerated. Besides, four isoforms of grass carp major histocompatibility complex class II antigen alpha and beta chains in the aforementioned three tissue was showed at least a 4-fold decrease. Conclusions The results suggesting that fish farmed at high stocking densities face issues associated with the metabolism and immune system. To conclude, our results emphasize the importance of maintaining reasonable density in grass carp aquaculture. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07924-4.
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Affiliation(s)
- Yan He
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Hongyan Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Honggang Zhao
- Department of Natural Resources, Cornell University, 14853, Ithaca, New York, USA
| | - Hua Zhu
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, 100068, Beijing, China
| | - Qingjing Zhang
- Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, 100068, Beijing, China
| | - Anqi Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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13
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Wei S, Chen Y, Huang L, Ma H, Qi L, Wang Q, Sun M, Zhang X, Sha Z. Analysis of lncRNA and mRNA expression profiles in peripheral blood leukocytes of the half-smooth tongue sole (Cynoglossus semilaevis) treated with chitosan oligosaccharide. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 120:104043. [PMID: 33621610 DOI: 10.1016/j.dci.2021.104043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Long noncoding RNAs (lncRNAs) play a multifaceted role in transcriptional regulation and are important regulators of immune function. Scarce information is available regarding lncRNAs in fish. Peripheral blood mononuclear cells participate in the immune response of fish and aid resistance to infection with pathogenic microorganisms. Chitosan oligosaccharide can improve cellular and humoral immunity to enhance disease resistance in fish. In this study, we obtained peripheral blood leukocytes from half-smooth tongue sole and studied the effect of chitosan oligosaccharide on the lncRNA-mRNA expression profile of these cells using high-throughput sequencing and bioinformatics techniques. A total of 609 differentially expressed mRNAs and 50 differentially expressed lncRNAs were identified. The GO term enrichment analysis of the differentially expressed genes was annotated by 220 GO terms, 137 biological processes, 18 cellular components, and 65 molecular functions. Sixteen KEGG pathways, including immune signaling pathways, metabolism, and genetic information processing, were significantly enriched in differentially expressed genes. Thirty-six differentially expressed lncRNAs and 32 differentially expressed mRNAs produced a coexpression network containing 90 relationship pairs. The prediction of lncRNA target genes revealed 244 lncRNAs that potentially cis-regulated 294 differentially expressed mRNAs. qPCR verified that the expression levels of 17 differentially expressed lncRNAs and 15 differentially expressed mRNAs were consistent with the RNA-Seq results. Among them, 6 lncRNAs and 7 mRNAs were differentially expressed genes obtained from the prediction and analysis of lncRNA target genes, and 8 lncRNAs and 4 mRNAs were differentially expressed genes that participated in the construction of the coexpression network. In peripheral blood leukocytes after chitosan oligosaccharide treatment, as well as in peripheral blood and spleen after Vibrio anguillarum stimulation, lncRNAs and mRNAs showed significant differential expression. The results indicated that they may be related to the immune response, providing novel reference information for further research on the role of lncRNAs in immune regulation in half-smooth tongue sole.
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Affiliation(s)
- Shu Wei
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yadong Chen
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lin Huang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Hui Ma
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Longjiang Qi
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Qian Wang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Mengjie Sun
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xue Zhang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhenxia Sha
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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14
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Sehgal P, Mathew S, Sivadas A, Ray A, Tanwar J, Vishwakarma S, Ranjan G, Shamsudheen KV, Bhoyar RC, Pateria A, Leonard E, Lalwani M, Vats A, Pappuru RR, Tyagi M, Jakati S, Sengupta S, B K B, Chakrabarti S, Kaur I, Motiani RK, Scaria V, Sivasubbu S. LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy. EMBO J 2021; 40:e107134. [PMID: 34180064 PMCID: PMC8327952 DOI: 10.15252/embj.2020107134] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial‐associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2gib005Δ8/+) induced cranial hemorrhage. In vitro and in vivo studies revealed that veal2 competes with diacylglycerol for interaction with protein kinase C beta‐b (Prkcbb) and regulates its kinase activity. Using PRKCB2 as bait, we identified functional ortholog of veal2 in humans from HUVECs and named it as VEAL2. Overexpression and knockdown of VEAL2 affected tubulogenesis and permeability in HUVECs. VEAL2 was differentially expressed in choroid tissue in eye and blood from patients with diabetic retinopathy, a disease where PRKCB2 is known to be hyperactivated. Further, VEAL2 could rescue the effects of PRKCB2‐mediated turnover of endothelial junctional proteins thus reducing hyperpermeability in hyperglycemic HUVEC model of diabetic retinopathy. Based on evidence from zebrafish and hyperglycemic HUVEC models and diabetic retinopathy patients, we report a hitherto unknown VEAL2 lncRNA‐mediated regulation of PRKCB2, for modulating junctional dynamics and maintenance of endothelial permeability.
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Affiliation(s)
- Paras Sehgal
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ambily Sivadas
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arjun Ray
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Jyoti Tanwar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India.,Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Gyan Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhishek Pateria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Elvin Leonard
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mukesh Lalwani
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajeev R Pappuru
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Mudit Tyagi
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Saumya Jakati
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Inderjeet Kaur
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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15
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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16
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Wang L, Song F, Zhu W, Fu J, Dong Z, Xu P. The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio. Genomics 2020; 113:20-28. [PMID: 33271329 DOI: 10.1016/j.ygeno.2020.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/23/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles during six main early development stages (2 h post-fertilization hpf, 6 hpf, 12 hpf, 20 hpf, 64 hpf and 1 day post-hatching). A total of 51,979 lncRNAs were identified. We screened the top 10 abundance lncRNAs and mRNAs and stage-specific lncRNAs and mRNAs (specificity measure SPM > 0.9). We identified significant differentially expressed lncRNAs and mRNAs (|log2 (fold change)| ≥ 1 and false discovery rate FDR of <0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified numerous signaling pathways. Additionally, the lncRNA-mRNA co-regulated network analysis of two lncRNAs (lncrps25 and malat1) and two mRNAs (mitf and troponin T) were investigated. Our results provide new insight into the role of lncRNAs and mRNAs, and would advance the understanding of lncRNA-mediated mechanisms in early development of fish.
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Affiliation(s)
- Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wenbin Zhu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Jianjun Fu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China.
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17
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Chen H, Shan G. The physiological function of long-noncoding RNAs. Noncoding RNA Res 2020; 5:178-184. [PMID: 32959025 PMCID: PMC7494506 DOI: 10.1016/j.ncrna.2020.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
The physiological processes of cells and organisms are regulated by various biological macromolecules, including long-noncoding RNAs (lncRNAs), which cannot be translated into protein and are different from small-noncoding RNAs on their length. In animals, lncRNAs are involved in development, metabolism, reproduction, aging and other life events by cis or trans effects. For many functional lncRNAs, there is growing evidence that they play different roles on cellular level and organismal level. On the other hand, many annotated lncRNAs are not essential and could be transcription noises. In this minireview, we investigate the physiological function of lncRNAs in cells and focus on their functions and functional mechanisms on the organismal level. The studies on lncRNAs using different classic animal models such as worms and flies are summarized and discussed in this article.
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Affiliation(s)
- He Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
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18
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Banerjee B, Koner D, Karasik D, Saha N. Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain. Genomics 2020; 113:29-43. [PMID: 33264657 DOI: 10.1016/j.ygeno.2020.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/22/2023]
Abstract
Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer's disease (AD). From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified novel lncRNAs, whose potential cis targets showed involvement in neuronal development and differentiation pathways. Under hypoxia, several lncRNAs and mRNAs were differentially expressed. Co-expression studies indicated that the Fb and Hb regions' potential lncRNA target genes were involved in the AD pathogenesis. In contrast, those in Mb (cry1b, per1a, cipca) was responsible for regulating circadian rhythm. We identified specific lncRNAs present in the syntenic regions between zebrafish and humans, possibly functionally conserved. We thus identified several conserved lncRNAs as the probable regulators of AD genes (adrb3b, cav1, stat3, bace2, apoeb, psen1, s100b).
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Affiliation(s)
- Bodhisattwa Banerjee
- Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel.
| | - Debaprasad Koner
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India
| | - David Karasik
- Musculoskeletal Genetics Laboratory, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Nirmalendu Saha
- Biochemical Adaptation Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India.
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19
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Hong F, Mo SH, Lin XY, Niu J, Yin J, Wei D. The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource. Front Genet 2020; 11:558394. [PMID: 33304379 PMCID: PMC7693467 DOI: 10.3389/fgene.2020.558394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
The tea aphid, Aphis aurantii, has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of A. aurantii was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of A. aurantii. It will assist the future functional study of genes involved in its development and reproduction.
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Affiliation(s)
- Feng Hong
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Si-Hua Mo
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Xing-Yu Lin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jinzhi Niu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jian Yin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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20
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Das T, Deb A, Parida S, Mondal S, Khatua S, Ghosh Z. LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. RNA Biol 2020; 18:1136-1151. [PMID: 33112702 DOI: 10.1080/15476286.2020.1833529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
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Affiliation(s)
- Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Aritra Deb
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sibun Parida
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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21
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Papadaki M, Kaitetzidou E, Mylonas CC, Sarropoulou E. Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:683-695. [PMID: 32876760 DOI: 10.1007/s10126-020-09991-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Non-coding RNAs (ncRNAs) are involved in several different regulatory pathways including reproduction. In teleost fish, efficacious reproduction is heavily dependent on the completion of the reproductive cycle. The presence of ncRNA, however, and their expression dynamics and putative regulatory role in mature and immature gonads have not yet been extensively explored. Therefore, the abundance of ncRNAs in mature and immature female sharpsnout seabream (Diplodus puntazzo) was investigated. The sharpsnout seabream is a rudimentary hermaphrodite which, in captivity, displays dysfunctions in the gonad maturation process. Our analyses revealed a gonad specific read length distribution with two main peaks representing miRNAs (21-26 nt) and PIWI RNA (27-34 nt). Besides, distinct expression patterns for several ncRNA biotypes including microRNAs (miRNAs), PIWI RNAs (piRNAs), and ribosomal RNAs (rRNAs) were detected. Identified miRNA accounted to 938, corresponding to ~ 13% of obtained transcripts. Among the differential expressed ncRNAs, 10 (~ 7%) were annotated as miRNA, out of which 2 were found in higher abundance in immature gonads (miR-125c and miR-24) and 8 (miR-451, miR-7a, miR-122-1, miR190a, miR129, ENSGACT00000029608, ENSGACT00000029489, and ENSGACT00000029667) were found to be higher expressed in mature gonads. Putative miRNA targets, including long non-coding RNAs (lncRNAs) and genes, are proposed. Target genes are involved in several processes of fish oocyte development, such as steroidogenesis, proteolysis, and apoptosis, and may explain hormone regulation. This study demonstrates a gonad maturation biased ncRNA profile which in turn may support the role of ncRNAs in ovarian physiology and reproductive performance of fish, stressing the specific function of each RNA biotype in oocyte development.
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Affiliation(s)
- Maria Papadaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Iraklion, Crete, Greece
- Department of Biology, University of Crete, P.O. Box 2208, 71409, Iraklion, Crete, Greece
| | - Elisavet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Iraklion, Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Iraklion, Crete, Greece
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Iraklion, Crete, Greece.
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22
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Li WJ, Song YJ, Han HL, Xu HQ, Wei D, Smagghe G, Wang JJ. Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC Genomics 2020; 21:600. [PMID: 32867696 PMCID: PMC7457495 DOI: 10.1186/s12864-020-07014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited. Results We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process. Conclusions This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.
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Affiliation(s)
- Wei-Jun Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yu-Jia Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hong-Liang Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hui-Qian Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guy Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China. .,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China. .,Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium.
| | - Jin-Jun Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China. .,International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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23
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Lumley AI, Zhang L, Ernens I, Leszek P, Devaux Y. The Long Noncoding RNA Landscape of Cardiac Regeneration in Zebrafish. Can J Cardiol 2020; 37:484-492. [PMID: 32835855 DOI: 10.1016/j.cjca.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/24/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Novel therapeutic targets of heart failure (HF) are needed. Long noncoding RNAs (lncRNAs) are engaged during cardiac regeneration. Unlike in humans, zebrafish naturally undergo cardiac regeneration after HF. We aimed to describe the landscape of lncRNAs during regeneration in a zebrafish model of HF and to investigate their human homologs. METHODS HF was established in adult zebrafish through thrice-weekly incubations with an anemia-inducing drug, phenylhydrazine hydrochloride (PHZ). After 5 weeks, PHZ treatment ceased and the fish were followed through a regeneration period of 14 days. Total RNA was extracted from the hearts of adult zebrafish after establishment of HF and at 2, 5, and 9 days after treatment cessation (9 hearts per condition at each time point). Gene regulation patterns were characterized with the use of bioinformatics and validated with the use of quantitative polymerase chain reaction. RESULTS We obtained 14,340 lncRNAs from the reannotated Affymetrix zebrafish microarray. Of these, 187 lncRNAs were found to be differentially expressed (false discovery rate < 0.05 and fold change ≥ 2) at at least 1 time point. 85% of differentially expressed lncRNAs overlapped or were close to (distance < 10 kb) protein-coding genes which were mostly related to muscle development in Gene Ontology analyses. Fifty-seven lncRNAs had human homologs, according to orientation relative to their conserved protein-coding neighbours. CONCLUSIONS LncRNAs are differentially expressed during regeneration after HF in adult zebrafish and could be potential future therapeutic targets. The extent to which lncRNAs contribute to cardiac regeneration is a worthy avenue for future research.
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Affiliation(s)
- Andrew I Lumley
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Lu Zhang
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Isabelle Ernens
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Przemyslaw Leszek
- Heart Failure and Transplantology Department, Institute of Cardiology, Warsaw, Poland
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg.
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24
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Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass ( Dicentrarchus labrax L.). BIOLOGY 2020; 9:biology9070165. [PMID: 32679770 PMCID: PMC7407339 DOI: 10.3390/biology9070165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are being increasingly recognised as key modulators of various biological mechanisms, including the immune response. Although investigations in teleosts are still lagging behind those conducted in mammals, current research indicates that lncRNAs play a pivotal role in the response of fish to a variety of pathogens. During the last several years, interest in lncRNAs has increased considerably, and a small but notable number of publications have reported the modulation of the lncRNA profile in some fish species after pathogen challenge. This study was the first to identify lncRNAs in the commercial species European sea bass. A total of 12,158 potential lncRNAs were detected in the head kidney and brain. We found that some lncRNAs were not common for both tissues, and these lncRNAs were located near coding genes that are primarily involved in tissue-specific processes, reflecting a degree of cellular specialisation in the synthesis of lncRNAs. Moreover, lncRNA modulation was analysed in both tissues at 24 and 72 h after infection with nodavirus. Enrichment analysis of the neighbouring coding genes of the modulated lncRNAs revealed many terms related to the immune response and viral infectivity but also related to the stress response. An integrated analysis of the lncRNAs and coding genes showed a strong correlation between the expression of the lncRNAs and their flanking coding genes. Our study represents the first systematic identification of lncRNAs in European sea bass and provides evidence regarding the involvement of these lncRNAs in the response to nodavirus.
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25
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Wang F, Ren D, Liang X, Ke S, Zhang B, Hu B, Song X, Wang X. A long noncoding RNA cluster-based genomic locus maintains proper development and visual function. Nucleic Acids Res 2020; 47:6315-6329. [PMID: 31127312 PMCID: PMC6614851 DOI: 10.1093/nar/gkz444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/29/2019] [Accepted: 05/10/2019] [Indexed: 01/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent a group of regulatory RNAs that play critical roles in numerous cellular events, but their functional importance in development remains largely unexplored. Here, we discovered a series of previously unidentified gene clusters harboring conserved lncRNAs at the nonimprinting regions in brain (CNIBs). Among the seven identified CNIBs, human CNIB1 locus is located at Chr 9q33.3 and conserved from Danio rerio to Homo sapiens. Chr 9q33.3-9q34.11 microdeletion has previously been linked to human nail-patella syndrome (NPS) which is frequently accompanied by developmental and visual deficiencies. By generating CNIB1 deletion alleles in zebrafish, we demonstrated the requirement of CNIB1 for proper growth and development, and visual activities. Furthermore, we found that the role of CNIB1 on visual activity is mediated through a regulator of ocular development-lmx1bb. Collectively, our study shows that CNIB1 lncRNAs are important for zebrafish development and provides an lncRNA cluster-mediated pathophysiological mechanism for human Chr 9q33.3-9q34.11 microdeletion syndrome.
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Affiliation(s)
- Fei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dalong Ren
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaolin Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shengwei Ke
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bowen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bing Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiangting Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
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26
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Yuan W, Jiang S, Sun D, Wu Z, Wei C, Dai C, Jiang L, Peng S. Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio). BMC Genomics 2019; 20:830. [PMID: 31703616 PMCID: PMC6842217 DOI: 10.1186/s12864-019-6197-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking. Results In this study, the mRNA and lncRNA expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs. Conclusions We found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain.
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Affiliation(s)
- Wenliang Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China.,School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, 314001, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China
| | | | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, 201306, China. .,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai, 201306, China. .,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, China.
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27
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Comparative modulation of lncRNAs in wild-type and rag1-heterozygous mutant zebrafish exposed to immune challenge with spring viraemia of carp virus (SVCV). Sci Rep 2019; 9:14174. [PMID: 31578442 PMCID: PMC6775065 DOI: 10.1038/s41598-019-50766-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
Although the modulation of immune-related genes after viral infection has been widely described in vertebrates, the potential implications of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs), in immunity are still a nascent research field. The model species zebrafish could serve as a useful organism for studying the functionality of lncRNAs due to the numerous advantages of this teleost, including the existence of numerous mutant lines. In this work, we conducted a whole-transcriptome analysis of wild-type (WT) and heterozygous rag1 mutant (rag1+/-) zebrafish after infection with the pathogen spring viraemia of carp virus (SVCV). WT and rag1+/- zebrafish were infected with SVCV for 24 h. Kidney samples were sampled from infected and uninfected fish for transcriptome sequencing. From a total of 198,540 contigs, 12,165 putative lncRNAs were identified in zebrafish. Most of the putative lncRNAs were shared by the two zebrafish lines. However, by comparing the lncRNA profiles induced after SVCV infection in WT and rag1+/- fish, most of the lncRNAs that were significantly induced after viral challenge were exclusive to each line, reflecting a highly differential response to the virus. Analysis of the neighboring genes of lncRNAs that were exclusively modulated in WT revealed high representation of metabolism-related terms, whereas those from rag1+/- fish showed enrichment in terms related to the adaptive immune response, among others. On the other hand, genes involved in numerous antiviral processes surrounded commonly modulated lncRNAs, as expected. These results clearly indicate that after SVCV infection in zebrafish, the expression of an array of lncRNAs with functions in different aspects of immunity is induced.
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Conserved Pseudoknots in lncRNA MEG3 Are Essential for Stimulation of the p53 Pathway. Mol Cell 2019; 75:982-995.e9. [PMID: 31444106 PMCID: PMC6739425 DOI: 10.1016/j.molcel.2019.07.025] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 01/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures ("kissing loops"). Mutations that disrupt these interactions impair MEG3-dependent p53 stimulation in vivo and disrupt MEG3 folding in vitro. These findings provide mechanistic insights into regulation of the p53 pathway by MEG3 and reveal how conserved motifs of tertiary structure can regulate lncRNA biological function.
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29
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Gallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña G, Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts S. Catching the complexity of salmon-louse interactions. FISH & SHELLFISH IMMUNOLOGY 2019; 90:199-209. [PMID: 31048036 DOI: 10.1016/j.fsi.2019.04.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.
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Affiliation(s)
- Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile.
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Gustavo Núñez-Acuña
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Crisleri Carrera
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Ana Teresa Gonçalves
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Bárbara P Benavente
- Interdisciplinary Center for Aquaculture Research, Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, USA
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30
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Luo M, Wang L, Yin H, Zhu W, Fu J, Dong Z. Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp. BMC Genomics 2019; 20:515. [PMID: 31226932 PMCID: PMC6588874 DOI: 10.1186/s12864-019-5894-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/10/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics were conducted on black, white, and red skin of Koi carp (Cyprinus carpio L.). RESULTS A total of 590,415,050 clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs. Ccr_lnc5622441 and Ccr_lnc765201 were up-regulated in black and red skin, Ccr_lnc14074601 and Ccr_lnc2382951 were up-regulated in white skin, and premelanosome protein a (Pmela), Pmelb and tyrosinase (Tyr) were up-regulated in black skin. The expression patterns of 18 randomly selected differentially expressed genes were validated using the quantitative real-time PCR method. Moreover, 70 lncRNAs acting on 107 target mRNAs in cis and 79 lncRNAs acting on 41,625 target mRNAs in trans were investigated. The resulting co-expression networks revealed that a single lncRNA can connect with numerous mRNAs, and vice versa. To further reveal their potential functions, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, and membrane, pigment cell development, cAMP signaling, melanogenesis and tyrosine metabolism appear to affect skin pigmentation. Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues. CONCLUSIONS The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp.
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Affiliation(s)
- Mingkun Luo
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 Jiangsu China
| | - Lanmei Wang
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081 Jiangsu China
| | - Haoran Yin
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 Jiangsu China
| | - Wenbin Zhu
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081 Jiangsu China
| | - Jianjun Fu
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081 Jiangsu China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081 Jiangsu China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081 Jiangsu China
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31
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Xu H, Cao L, Sun B, Wei Y, Liang M. Transcriptomic Analysis of Potential "lncRNA-mRNA" Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios. Front Physiol 2019; 10:331. [PMID: 31001132 PMCID: PMC6454198 DOI: 10.3389/fphys.2019.00331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/11/2019] [Indexed: 01/22/2023] Open
Abstract
Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost.
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Affiliation(s)
- Houguo Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lin Cao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Beijing Institute of Feed Control, Beijing, China
| | - Bo Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yuliang Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mengqing Liang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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32
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Sharma D, Sehgal P, Mathew S, Vellarikkal SK, Singh AR, Kapoor S, Jayarajan R, Scaria V, Sivasubbu S. A genome-wide map of circular RNAs in adult zebrafish. Sci Rep 2019; 9:3432. [PMID: 30837568 PMCID: PMC6401160 DOI: 10.1038/s41598-019-39977-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are transcript isoforms generated by back-splicing of exons and circularisation of the transcript. Recent genome-wide maps created for circular RNAs in humans and other model organisms have motivated us to explore the repertoire of circular RNAs in zebrafish, a popular model organism. We generated RNA-seq data for five major zebrafish tissues - Blood, Brain, Heart, Gills and Muscle. The repertoire RNA sequence reads left over after reference mapping to linear transcripts were used to identify unique back-spliced exons utilizing a split-mapping algorithm. Our analysis revealed 3,428 novel circRNAs in zebrafish. Further in-depth analysis suggested that majority of the circRNAs were derived from previously well-annotated protein-coding and long noncoding RNA gene loci. In addition, many of the circular RNAs showed extensive tissue specificity. We independently validated a subset of circRNAs using polymerase chain reaction (PCR) and divergent set of primers. Expression analysis using quantitative real time PCR recapitulate selected tissue specificity in the candidates studied. This study provides a comprehensive genome-wide map of circular RNAs in zebrafish tissues.
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Affiliation(s)
- Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Paras Sehgal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Samatha Mathew
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Angom Ramcharan Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Shruti Kapoor
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India. .,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India. .,Academy of Scientific and Innovative Research, CSIR Institute of Genomics and Integrative Biology South Campus, Mathura Road, Delhi, 110025, India.
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33
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Chen W, Zhang G, Li J, Zhang X, Huang S, Xiang S, Hu X, Liu C. CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. Nucleic Acids Res 2019; 47:D63-D68. [PMID: 30285246 PMCID: PMC6324000 DOI: 10.1093/nar/gky904] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022] Open
Abstract
The CRISPR/Cas9 system, as a revolutionary genome editing tool for all areas of molecular biology, provides new opportunities for research on lncRNA's function. However, designing a CRISPR/Cas9 single guide RNA (sgRNA) for lncRNA is not easy with an unwarrantable effectiveness. Thus, it is worthy of collecting validated sgRNAs, to assist in efficiently choosing sgRNA with an expected activity. CRISPRlnc (http://www.crisprlnc.org or http://crisprlnc.xtbg.ac.cn) is a manually curated database of validated CRISPR/Cas9 sgRNAs for lncRNAs from all species. After manually reviewing more than 200 published literature, the current version of CRISPRlnc contains 305 lncRNAs and 2102 validated sgRNAs across eight species, including mammalian, insect and plant. We handled the ID, position in the genome, sequence and functional description of these lncRNAs, as well as the sequence, protoacceptor-motif (PAM), CRISPR type and validity of their paired sgRNAs. In CRISPRlnc, we provided the tools for browsing, searching and downloading data, as well as online BLAST service and genome browse server. As the first database against the validated sgRNAs of lncRNAs, CRISPRlnc will provide a new and powerful platform to promote CRISPR/Cas9 applications for future functional studies of lncRNAs.
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Affiliation(s)
- Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Guoqiang Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Shulan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
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34
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Goudarzi M, Berg K, Pieper LM, Schier AF. Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility. eLife 2019; 8:40815. [PMID: 30620332 PMCID: PMC6347452 DOI: 10.7554/elife.40815] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 01/08/2019] [Indexed: 12/28/2022] Open
Abstract
Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs have no overt roles in embryogenesis, viability and fertility.
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Affiliation(s)
- Mehdi Goudarzi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Kathryn Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Lindsey M Pieper
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Center for Brain Science, Harvard University, Cambridge, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, United States.,Biozentrum, University of Basel, Basel, Switzerland
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35
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Mathew S, Sivadas A, Sehgal P, Kaushik K, Vellarikkal SK, Scaria V, Sivasubbu S. Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing. Methods Mol Biol 2019; 1912:77-110. [PMID: 30635891 DOI: 10.1007/978-1-4939-8982-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Long noncoding RNAs (lncRNAs) belong to a class of RNA transcripts that do not have the potential to code for proteins. LncRNAs were largely discovered in the transcriptomes of human and several model organisms, using next-generation sequencing (NGS) approaches, which have enabled a comprehensive genome scale annotation of transcripts. LncRNAs are known to have dynamic expression status and have the potential to orchestrate gene regulation at the epigenetic, transcriptional, and posttranscriptional levels. Here we describe the experimental methods involved in the discovery of lncRNAs from the transcriptome of a popular model organism zebrafish (Danio rerio). A structured and well-designed computational analysis pipeline subsequent to the RNA sequencing can be instrumental in revealing the diversity of the lncRNA transcripts. We describe one such computational pipeline used for the discovery of novel lncRNA transcripts in zebrafish. We also detail the validation of the putative novel lncRNA transcripts using qualitative and quantitative assays in zebrafish.
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Affiliation(s)
- Samatha Mathew
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Ambily Sivadas
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
- G.N. Ramachandran Knowledge Centre for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Paras Sehgal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Kriti Kaushik
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Shamsudheen K Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
- G.N. Ramachandran Knowledge Centre for Bioinformatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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36
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Li X, Xing X, Xu S, Zhang M, Wang Y, Wu H, Sun Z, Huo Z, Chen F, Yang T. Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress. PLoS One 2018; 13:e0204506. [PMID: 30427847 PMCID: PMC6235259 DOI: 10.1371/journal.pone.0204506] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Root-knot nematodes (RKNs, Meloidogyne spp.) are destructive plant parasites with a wide host range. They severely reduce crop quality and yield worldwide. Tobacco is a versatile model plant organism for studying RKNs-host interactions and a key plant material for molecular research. Long noncoding RNAs (lncRNAs) play critical roles in post transcriptional and transcriptional regulation in a wide range of biological pathways, especially plant development and stress response. In the present study, we obtained 5,206 high-confidence lncRNAs based on RNA sequencing data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the target genes of these lncRNAs are mainly involved in plant biotic and abiotic stresses, plant hormone signal transduction, induced systemic resistance, plant-type hypersensitive response, plant-type cell wall organization or biogenesis. The 565 differentially expressed lncRNAs found to be involved in nematode stress response were validated by quantitative PCR using 15 randomly-selected lncRNA genes. Our study provides insights into the molecular mechanisms of RKNs-plant interactions that might help preventing nematode damages to crops.
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Affiliation(s)
- Xiaohui Li
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Xuexia Xing
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Shixiao Xu
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Mingzhen Zhang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Yuan Wang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Hengyan Wu
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Zhihao Sun
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Zhaoguang Huo
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Fang Chen
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Tiezhao Yang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
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37
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Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genomics 2018; 19:729. [PMID: 30286721 PMCID: PMC6172845 DOI: 10.1186/s12864-018-5115-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited. Results Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs. Conclusions This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia. Electronic supplementary material The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C. Comparative analysis of long non-coding RNAs in Atlantic and Coho salmon reveals divergent transcriptome responses associated with immunity and tissue repair during sea lice infestation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:36-50. [PMID: 29803715 DOI: 10.1016/j.dci.2018.05.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/19/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
The increasing capacity of transcriptomic analysis by high throughput sequencing has highlighted the presence of a large proportion of transcripts that do not encode proteins. In particular, long non-coding RNAs (lncRNAs) are sequences with low coding potential and conservation among species. Moreover, cumulative evidence has revealed important roles in post-transcriptional gene modulation in several taxa. In fish, the role of lncRNAs has been scarcely studied and even less so during the immune response against sea lice. In the present study we mined for lncRNAs in Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynkus kisutch), which are affected by the sea louse Caligus rogercresseyi, evaluating the degree of sequence conservation between these two fish species and their putative roles during the infection process. Herein, Atlantic and Coho salmon were infected with 35 lice/fish and evaluated after 7 and 14 days post-infestation (dpi). For RNA sequencing, samples from skin and head kidney were collected. A total of 5658/4140 and 3678/2123 lncRNAs were identified in uninfected/infected Atlantic and Coho salmon transcriptomes, respectively. Species-specific transcription patterns were observed in exclusive lncRNAs according to the tissue analyzed. Furthermore, neighbor gene GO enrichment analysis of the top 100 highly regulated lncRNAs in Atlantic salmon showed that lncRNAs were localized near genes related to the immune response. On the other hand, in Coho salmon the highly regulated lncRNAs were localized near genes involved in tissue repair processes. This study revealed high regulation of lncRNAs closely localized to immune and tissue repair-related genes in Atlantic and Coho salmon, respectively, suggesting putative roles for lncRNAs in salmon against sea lice infestation.
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Affiliation(s)
- Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, University of Concepcion, Barrio Universitario s/n, Concepción, Chile.
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Chen W, Zhang X, Li J, Huang S, Xiang S, Hu X, Liu C. Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish. BMC Genomics 2018; 19:112. [PMID: 29764394 PMCID: PMC5954278 DOI: 10.1186/s12864-018-4458-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Zebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing. Results We systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts. Conclusions By integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human. Electronic supplementary material The online version of this article (10.1186/s12864-018-4458-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Xuan Zhang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jing Li
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Shulan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China.
| | - Changning Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.
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40
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Goyal N, Kesharwani D, Datta M. Lnc-ing non-coding RNAs with metabolism and diabetes: roles of lncRNAs. Cell Mol Life Sci 2018; 75:1827-1837. [PMID: 29387902 PMCID: PMC11105777 DOI: 10.1007/s00018-018-2760-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/29/2017] [Accepted: 01/24/2018] [Indexed: 12/15/2022]
Abstract
Type 2 diabetes is a complex metabolic disorder characterized by insulin resistance and pancreatic β-cell dysfunction. Deregulated glucose and lipid metabolism are the primary underlying manifestations associated with this disease and its complications. Long non-coding RNAs (lncRNAs) are a novel class of functional RNAs that regulate a variety of biological processes by a diverse interplay of mechanisms including recruitment of epigenetic modifiers, transcriptional and post-transcriptional regulation, control of mRNA decay, and sequestration of transcription factors. Although the underlying causes that define the diabetic phenotype are extremely intricate, most of the studies in the last decades were mostly centered on protein-coding genes. However, current opinion in the recent past has authenticated the contributions of diverse lncRNAs as critical regulatory players during the manifestation of diabetes. The current review will highlight the importance of lncRNAs in regulating cellular processes that govern metabolic homeostasis in key metabolic tissues. A more in-depth understanding of lncRNAs may enable their exploitation as biomarkers or for therapeutic applications during diabetes and its associated complications.
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Affiliation(s)
- Neha Goyal
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Devesh Kesharwani
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Malabika Datta
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.
- Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India.
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41
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Zhong L, Mu H, Wen B, Zhang W, Wei Q, Gao G, Han J, Cao S. Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction. Sci Rep 2018; 8:6649. [PMID: 29703926 PMCID: PMC5923264 DOI: 10.1038/s41598-018-24863-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNA) play a key role in the orchestration of transcriptional regulation during development and many other cellular processes. The importance of the regulatory co-expression network was highlighted in the identification of the mechanism of these processes in humans and mice. However, elucidation of the properties of porcine lncRNAs involved in the regulatory network during pre-implantation embryonic development and fibroblast reprogramming to induced pluripotent stem cell (iPSC) has been limited to date. Using a weighted gene co-expression network analysis, we constructed the regulatory network and determined that the novel lncRNAs were functionally involved in key events of embryonic development during the pre-implantation period; moreover, reprogramming could be delineated by a small number of potentially functional modules of co-expressed genes. These findings indicate that lncRNAs may be involved in the transcriptional regulation of zygotic genome activation, first lineage segregation and somatic reprogramming to pluripotency. Furthermore, we performed a conservation and synteny analysis with the significant lncRNAs involved in these vital events and validated the results via experimental assays. In summary, the current findings provide a valuable resource to dissect the protein coding gene and lncRNA regulatory networks that underlie the progressive development of embryos and somatic reprogramming.
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Affiliation(s)
- Liang Zhong
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China.,State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haiyuan Mu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bingqiang Wen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qingqing Wei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
| | - Suying Cao
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China. .,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China.
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42
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Kaushik K, Sivadas A, Vellarikkal SK, Verma A, Jayarajan R, Pandey S, Sethi T, Maiti S, Scaria V, Sivasubbu S. RNA secondary structure profiling in zebrafish reveals unique regulatory features. BMC Genomics 2018; 19:147. [PMID: 29448945 PMCID: PMC5815192 DOI: 10.1186/s12864-018-4497-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 01/28/2018] [Indexed: 01/08/2023] Open
Abstract
Background RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure. Results We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented. We identified RNA secondary structural features embedded in functional units of zebrafish mRNAs. Translation start and stop sites were demarcated by weak structural signals. The coding regions were characterized by the three-nucleotide periodicity of secondary structure and display a codon base specific structural constrain. The splice sites of transcripts were also delineated by distinct signature signals. Relatively higher structural signals were observed at 3’ Untranslated Regions (UTRs) compared to Coding DNA Sequence (CDS) and 5’ UTRs. The 3′ ends of transcripts were also marked by unique structure signals. Secondary structural signals in long non-coding RNAs were also explored to better understand their molecular function. Conclusions Our study presents the first PARS-enabled transcriptome-wide secondary structure map of zebrafish, which documents pairing probability of RNA at single nucleotide precision. Our findings open avenues for exploring structural features in zebrafish RNAs and their influence on gene expression. Electronic supplementary material The online version of this article (10.1186/s12864-018-4497-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kriti Kaushik
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ambily Sivadas
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Satyaprakash Pandey
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Tavprithesh Sethi
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Souvik Maiti
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Vinod Scaria
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
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43
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Hu J, Xu J, Pang L, Zhao H, Li F, Deng Y, Liu L, Lan Y, Zhang X, Zhao T, Xu C, Xu C, Xiao Y, Li X. Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis. Oncotarget 2018; 7:71087-71098. [PMID: 27661005 PMCID: PMC5342065 DOI: 10.18632/oncotarget.12122] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are severe neuropsychiatric disorders with serious impact on patients, together termed “major psychosis”. Recently, long intergenic non-coding RNAs (lincRNAs) were reported to play important roles in mental diseases. However, little was known about their molecular mechanism in pathogenesis of SZ and BD. Here, we performed RNA sequencing on 82 post-mortem brain tissues from three brain regions (orbitofrontal cortex (BA11), anterior cingulate cortex (BA24) and dorsolateral prefrontal cortex (BA9)) of patients with SZ and BD and control subjects, generating over one billion reads. We characterized lincRNA transcriptome in the three brain regions and identified 20 differentially expressed lincRNAs (DELincRNAs) in BA11 for BD, 34 and 1 in BA24 and BA9 for SZ, respectively. Our results showed that these DELincRNAs exhibited brain region-specific patterns. Applying weighted gene co-expression network analysis, we revealed that DELincRNAs together with other genes can function as modules to perform different functions in different brain regions, such as immune system development in BA24 and oligodendrocyte differentiation in BA9. Additionally, we found that DNA methylation alteration could partly explain the dysregulation of lincRNAs, some of which could function as enhancers in the pathogenesis of major psychosis. Together, we performed systematical characterization of dysfunctional lincRNAs in multiple brain regions of major psychosis, which provided a valuable resource to understand their roles in SZ and BD pathology and helped to discover novel biomarkers.
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Affiliation(s)
- Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ling Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tingting Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chun Xu
- Department of Psychiatry, Texas Tech University Health Science Center, El Paso, Texas, United States of America
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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Babu A, Kamaraj M, Basu M, Mukherjee D, Kapoor S, Ranjan S, Swamy MM, Kaypee S, Scaria V, Kundu TK, Sachidanandan C. Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi Syndrome in zebrafish. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1203-1215. [PMID: 29409755 DOI: 10.1016/j.bbadis.2018.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/08/2018] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
Abstract
EP300 is a member of the EP300/CBP family of lysine acetyltransferases (KATs) with multiple roles in development and physiology. Loss of EP300/CBP activity in humans causes a very rare congenital disorder called Rubinstein Taybi Syndrome (RSTS). The zebrafish genome has two co-orthologs of lysine acetyltransferase EP300 (KAT3B) in zebrafish viz. ep300a and ep300b. Chemical inhibition of Ep300 with C646, a competitive inhibitor and morpholino-based genetic knockdown of ep300a and ep300b cause defects in embryonic development reminiscent of the human RSTS syndrome. Remarkably, overexpression of Ep300a KAT domain results in near complete rescue of the jaw development defects, a characteristic feature of RSTS in human suggesting the dispensability of the protein-interaction and DNA-binding domains for at least some developmental roles of Ep300. We also perform a chemical screen and identify two inhibitors of deacetylases, CHIC35 and HDACi III, that can partially rescue the RSTS-like phenotypes. Thus, modeling rare human genetic disorders in zebrafish allows for functional understanding of the genes involved and can also yield small molecule candidates towards therapeutic goals.
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Affiliation(s)
- Aswini Babu
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Mageshi Kamaraj
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India
| | - Moumita Basu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Debanjan Mukherjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Shruti Kapoor
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Shashi Ranjan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India
| | - Mahadeva M Swamy
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Vinod Scaria
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India.
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India.
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45
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Clark BS, Blackshaw S. Understanding the Role of lncRNAs in Nervous System Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:253-282. [PMID: 28815543 DOI: 10.1007/978-981-10-5203-3_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development. Additionally, we focus on recent endeavors that attempt to assign function to lncRNAs during nervous system development. We highlight discrepancies that have been observed between in vitro and in vivo studies of lncRNA function and the challenges facing researchers in conducting mechanistic analyses of lncRNAs in the developing nervous system. Altogether, this chapter highlights the emerging role of lncRNAs in the developing brain and sheds light on novel, RNA-mediated mechanisms by which nervous system development is controlled.
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Affiliation(s)
- Brian S Clark
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth Blackshaw
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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46
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Hu X, Chen W, Li J, Huang S, Xu X, Zhang X, Xiang S, Liu C. ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5134219. [PMID: 30335154 PMCID: PMC6193196 DOI: 10.1093/database/bay114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/26/2018] [Indexed: 02/04/2023]
Abstract
There is emerging evidence showing that lncRNAs can be involved in various critical biological processes. Zebrafish is a fully developed model system being used in a variety of basic research and biomedical studies. Hence, it is an ideal model organism to study the functions and mechanisms of lncRNAs. Here, we constructed ZFLNC—a comprehensive database of zebrafish lncRNA that is dedicated to providing a zebrafish-based platform for deep exploration of zebrafish lncRNAs and their mammalian counterparts to the relevant academic communities. The main data resources of lncRNAs in this database come from the NCBI, Ensembl, NONCODE, zflncRNApedia and literature. We also obtained lncRNAs as a supplement by analysing RNA-Seq datasets from SRA database. With these IncRNAs, we further carried out expression profiling, co-expression network prediction, Gene Ontology (GO)/Kyoto Encyclopedia
of Genes and Genomes (KEGG)/Online Mendelian Inheritance in Man (OMIM) annotation and conservation analysis. As far as we know, ZFLNC is the most comprehensive and well-annotated database for zebrafish lncRNA.
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Affiliation(s)
- Xiang Hu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Shulan Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Xuling Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, School of Life Sciences, Hunan Normal University, Changsha, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
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Sarasamma S, Varikkodan MM, Liang ST, Lin YC, Wang WP, Hsiao CD. Zebrafish: A Premier Vertebrate Model for Biomedical Research in Indian Scenario. Zebrafish 2017; 14:589-605. [PMID: 29023224 DOI: 10.1089/zeb.2017.1447] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The zebrafish (Danio rerio) is a versatile model organism that has been used in biomedical research for several decades to study a wide range of biological phenomena. There are many technical advantages of using zebrafish over other vertebrate models. They are readily available, hardy, easy, and inexpensive to maintain in the laboratory, have a short life cycle, and have excellent fecundity. Due to its optical clarity and reproducible capabilities, it has become one of the predominant models of human genetic diseases. Zebrafish research has made rapid strides in the United States and Europe, but in India the field is at an early stage and many researchers still remain unaware of the full research potential of this tiny fish. The zebrafish model system was introduced into India in the early 2000s. Up to now, more than 200 scientific referred articles have been published by Indian researchers. This review gives an overview of the current state of knowledge for zebrafish research in India, with the aim of promoting wider utilization of zebrafish for high level biological studies.
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Affiliation(s)
- Sreeja Sarasamma
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,3 Department of Chemical Biology, Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram, Kerala, India
| | - Muhammed Muhsin Varikkodan
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,4 Department of Biotechnology and Genetic Engineering, Bharathidasan University , Tiruchirapalli, India
| | - Sung-Tzu Liang
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan
| | - Yen-Chang Lin
- 5 Graduate Institute of Biotechnology, Chinese Culture University , Taipei, Taiwan
| | - Wen-Pin Wang
- 6 Institute of Medical Sciences, Tzu-Chi University , Hualien, Taiwan .,7 Department of Molecular Biology and Human Genetics, Tzu-Chi University , Hualien, Taiwan
| | - Chung-Der Hsiao
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,8 Center for Biomedical Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,9 Center for Nanotechnology, Chung Yuan Christian University , Chung-Li, Taiwan
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48
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Perry RBT, Ulitsky I. The functions of long noncoding RNAs in development and stem cells. Development 2017; 143:3882-3894. [PMID: 27803057 DOI: 10.1242/dev.140962] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, with tens of thousands of RNAs emanating from uni- and bi-directional promoters and from active enhancers. In vertebrates, thousands of loci in each species produce a class of transcripts called long noncoding RNAs (lncRNAs) that are typically expressed at low levels and do not appear to give rise to functional proteins. Substantial numbers of lncRNAs are expressed at specific stages of embryonic development, in many cases from regions flanking key developmental regulators. Here, we review the known biological functions of such lncRNAs and the emerging paradigms of their modes of action. We also provide an overview of the growing arsenal of methods for lncRNA identification, perturbation and functional characterization.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
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Goyal N, Sivadas A, Shamsudheen KV, Jayarajan R, Verma A, Sivasubbu S, Scaria V, Datta M. RNA sequencing of db/db mice liver identifies lncRNA H19 as a key regulator of gluconeogenesis and hepatic glucose output. Sci Rep 2017; 7:8312. [PMID: 28814771 PMCID: PMC5559625 DOI: 10.1038/s41598-017-08281-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/10/2017] [Indexed: 12/30/2022] Open
Abstract
Liver plays a key role in maintaining glucose homeostasis and impaired hepatic glucose metabolism is associated with type 2 diabetes. In the present study, we used RNA sequencing to profile the transcriptome of the livers of diabetic db/db mice as compared to the normal db/+ mice and identified 218 differentially expressed genes. Amongst these, there were 3 lncRNAs that were significantly downregulated and H19 was the most altered lncRNA in the livers of db/db mice. H19 expression significantly correlated with the expression of genes of the glycolysis and gluconeogenesis pathways, which suggest that altered hepatic H19 levels can directly or indirectly modulate their expression. Inhibition of H19 using specific siRNA in HepG2 cells and primary mouse hepatocytes significantly increased the levels of gluconeogenic genes. This was subsequently accompanied by increased hepatic glucose output. Further,H19 depletion in HepG2 cells impaired insulin signaling and increased nuclear localization of FoxO1, an important transcriptional regulator of gluconeogenic gene expression. Our results reveal a novel link between decreased H19 levels and impaired gluconeogenesis via regulation of FoxO1 nuclear levels. These put forth interesting observations on the regulatory role of H19 in altering hepatic physiology during diabetes.
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Affiliation(s)
- Neha Goyal
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Ambily Sivadas
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Rijith Jayarajan
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Ankit Verma
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India.,GN Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India
| | - Malabika Datta
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi, 110007, India. .,Academy of Scientific and Innovative Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, India.
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Garcia GR, Goodale BC, Wiley MW, La Du JK, Hendrix DA, Tanguay RL. In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression. Mol Pharmacol 2017; 91:609-619. [PMID: 28385905 PMCID: PMC5438132 DOI: 10.1124/mol.117.108233] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/31/2017] [Indexed: 01/08/2023] Open
Abstract
Xenobiotic activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) prevents the proper formation of craniofacial cartilage and the heart in developing zebrafish. Downstream molecular targets responsible for AHR-dependent adverse effects remain largely unknown; however, in zebrafish sox9b has been identified as one of the most-reduced transcripts in several target organs and is hypothesized to have a causal role in TCDD-induced toxicity. The reduction of sox9b expression in TCDD-exposed zebrafish embryos has been shown to contribute to heart and jaw malformation phenotypes. The mechanisms by which AHR2 (functional ortholog of mammalian AHR) activation leads to reduced sox9b expression levels and subsequent target organ toxicity are unknown. We have identified a novel long noncoding RNA (slincR) that is upregulated by strong AHR ligands and is located adjacent to the sox9b gene. We hypothesize that slincR is regulated by AHR2 and transcriptionally represses sox9b. The slincR transcript functions as an RNA macromolecule, and slincR expression is AHR2 dependent. Antisense knockdown of slincR results in an increase in sox9b expression during both normal development and AHR2 activation, which suggests relief in repression. During development, slincR was expressed in tissues with sox9 essential functions, including the jaw/snout region, otic vesicle, eye, and brain. Reducing the levels of slincR resulted in altered neurologic and/or locomotor behavioral responses. Our results place slincR as an intermediate between AHR2 activation and the reduction of sox9b mRNA in the AHR2 signaling pathway.
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Affiliation(s)
- Gloria R Garcia
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
| | - Britton C Goodale
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
| | - Michelle W Wiley
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
| | - Jane K La Du
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
| | - David A Hendrix
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center (G.R.G., J.K.L.D., R.L.T.), and Department of Biochemistry and Biophysics (M.W.W., D.A.H), Oregon State University, Corvallis, Oregon; and Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire (B.C.G.)
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