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Dayal Aggarwal D, Mishra P, Yadav G, Mitra S, Patel Y, Singh M, Sahu RK, Sharma V. Decoding the connection between lncRNA and obesity: Perspective from humans and Drosophila. Heliyon 2024; 10:e35327. [PMID: 39166041 PMCID: PMC11334870 DOI: 10.1016/j.heliyon.2024.e35327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
Background Obesity is a burgeoning global health problem with an escalating prevalence and severe implications for public health. New evidence indicates that long non-coding RNAs (lncRNAs) may play a pivotal role in regulating adipose tissue function and energy homeostasis across various species. However, the molecular mechanisms underlying obesity remain elusive. Scope of review This review discusses obesity and fat metabolism in general, highlighting the emerging importance of lncRNAs in modulating adipogenesis. It describes the regulatory networks, latest tools, techniques, and approaches to enhance our understanding of obesity and its lncRNA-mediated epigenetic regulation in humans and Drosophila. Major conclusions This review analyses large datasets of human and Drosophila lncRNAs from published databases and literature with experimental evidence supporting lncRNAs role in fat metabolism. It concludes that lncRNAs play a crucial role in obesity-related metabolism. Cross-species comparisons highlight the relevance of Drosophila findings to human obesity, emphasizing their potential role in adipose tissue biology. Furthermore, it discusses how recent technological advancements and multi-omics data integration enhance our capacity to characterize lncRNAs and their function. Additionally, this review briefly touches upon innovative methodologies like experimental evolution and advanced sequencing technologies for identifying novel genes and lncRNA regulators in Drosophila, which can potentially contribute to obesity research.
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Affiliation(s)
- Dau Dayal Aggarwal
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Prachi Mishra
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Gaurav Yadav
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Shrishti Mitra
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Yashvant Patel
- Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Manvender Singh
- Department of Biotechnology, UIET, MD University, Rohtak, India
| | - Ranjan Kumar Sahu
- Department of Neurology, Houston Methodist Research Insititute, Houston, Tx, USA
| | - Vijendra Sharma
- Department of Biomedical Sciences, University of Windsor, Ontario, Canada
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2
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Zhou H, Huang Y, Jia C, Pang Y, Liu L, Xu Y, Jin P, Qian J, Ma F. NF-κB factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210. Nucleic Acids Res 2024; 52:6906-6927. [PMID: 38742642 PMCID: PMC11229355 DOI: 10.1093/nar/gkae394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial regulatory roles in controlling immune responses, but their dynamic expression mechanisms are poorly understood. Here, we firstly confirm that the conserved miRNA miR-210 negatively regulates innate immune responses of Drosophila and human via targeting Toll and TLR6, respectively. Secondly, our findings demonstrate that the expression of miR-210 is dynamically regulated by NF-κB factor Dorsal in immune response of Drosophila Toll pathway. Thirdly, we find that Dorsal-mediated transcriptional inhibition of miR-210 is dependent on the transcriptional repressor Su(Hw). Mechanistically, Dorsal interacts with Su(Hw) to modulate cooperatively the dynamic expression of miR-210 in a time- and dose-dependent manner, thereby controlling the strength of Drosophila Toll immune response and maintaining immune homeostasis. Fourthly, we reveal a similar mechanism in human cells, where NF-κB/RelA cooperates with E4F1 to regulate the dynamic expression of hsa-miR-210 in the TLR immune response. Overall, our study reveals a conservative regulatory mechanism that maintains animal innate immune homeostasis and provides new insights into the dynamic regulation of miRNA expression in immune response.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
- Institute of Laboratory Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, 210002 Nanjing, Jiangsu, China
| | - Yu Huang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Chaolong Jia
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Yujia Pang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
- Institute of Laboratory Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, 210002 Nanjing, Jiangsu, China
| | - Li Liu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Yina Xu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023 Nanjing, Jiangsu, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
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3
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Musselman LP, Truong HG, DiAngelo JR. Transcriptional Control of Lipid Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38782870 DOI: 10.1007/5584_2024_808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Transcriptional control of lipid metabolism uses a framework that parallels the control of lipid metabolism at the protein or enzyme level, via feedback and feed-forward mechanisms. Increasing the substrates for an enzyme often increases enzyme gene expression, for example. A paucity of product can likewise potentiate transcription or stability of the mRNA encoding the enzyme or enzymes needed to produce it. In addition, changes in second messengers or cellular energy charge can act as on/off switches for transcriptional regulators to control transcript (and protein) abundance. Insects use a wide range of DNA-binding transcription factors (TFs) that sense changes in the cell and its environment to produce the appropriate change in transcription at gene promoters. These TFs work together with histones, spliceosomes, and additional RNA processing factors to ultimately regulate lipid metabolism. In this chapter, we will first focus on the important TFs that control lipid metabolism in insects. Next, we will describe non-TF regulators of insect lipid metabolism such as enzymes that modify acetylation and methylation status, transcriptional coactivators, splicing factors, and microRNAs. To conclude, we consider future goals for studying the mechanisms underlying the control of lipid metabolism in insects.
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Affiliation(s)
- Laura Palanker Musselman
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY, USA
| | - Huy G Truong
- Division of Science, Pennsylvania State University, Berks Campus, Reading, PA, USA
| | - Justin R DiAngelo
- Division of Science, Pennsylvania State University, Berks Campus, Reading, PA, USA.
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4
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Ozcelik G, Koca MS, Sunbul B, Yilmaz-Atay F, Demirhan F, Tiryaki B, Cilenk K, Selvi S, Ozturk N. Interactions of drosophila cryptochrome. Photochem Photobiol 2024. [PMID: 38314442 DOI: 10.1111/php.13916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/06/2024]
Abstract
In this study, we investigate the intricate regulatory mechanisms underlying the circadian clock in Drosophila, focusing on the light-induced conformational changes in the cryptochrome (DmCry). Upon light exposure, DmCry undergoes conformational changes that prompt its binding to Timeless and Jetlag proteins, initiating a cascade crucial for the starting of a new circadian cycle. DmCry is subsequently degraded, contributing to the desensitization of the resetting mechanism. The transient and short-lived nature of DmCry protein-protein interactions (PPIs), leading to DmCry degradation within an hour of light exposure, presents a challenge for comprehensive exploration. To address this, we employed proximity-dependent biotinylation techniques, combining engineered BioID (TurboID) and APEX (APEX2) enzymes with mass spectrometry. This approach enabled the identification of the in vitro DmCry interactome in Drosophila S2 cells, uncovering several novel PPIs associated with DmCry. Validation of these interactions through a novel co-immunoprecipitation technique enhances the reliability of our findings. Importantly, our study suggests the potential of this method to reveal additional circadian clock- or magnetic field-dependent PPIs involving DmCry. This exploration of the DmCry interactome not only advances our understanding of circadian clock regulation but also establishes a versatile framework for future investigations into light- and time-dependent protein interactions in Drosophila.
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Affiliation(s)
- Gozde Ozcelik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Mehmet Serdar Koca
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Buket Sunbul
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Fatma Yilmaz-Atay
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Feride Demirhan
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Busra Tiryaki
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Kevser Cilenk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Saba Selvi
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
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Bernardo-Colón A, Dong L, Abu-Asab M, Brush RS, Agbaga MP, Becerra SP. Ablation of pigment epithelium-derived factor receptor (PEDF-R/Pnpla2) causes photoreceptor degeneration. J Lipid Res 2023; 64:100358. [PMID: 36934843 PMCID: PMC10233210 DOI: 10.1016/j.jlr.2023.100358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/19/2023] Open
Abstract
Photoreceptor cells express the patatin-like phospholipase domain-containing 2 (PNPLA2) gene that codes for pigment epithelium-derived factor receptor (PEDF-R) (also known as ATGL). PEDF-R exhibits phospholipase activity that mediates the neurotrophic action of its ligand PEDF. Because phospholipids are the most abundant lipid class in the retina, we investigated the role of PEDF-R in photoreceptors by generating CRISPR Pnpla2 knock-out mouse lines in a retinal degeneration-free background. Pnpla2-/- mice had undetectable retinal Pnpla2 gene expression and PEDF-R protein levels as assayed by RT-PCR and immunofluorescence, respectively. The photoreceptors of mice deficient in PEDF-R had deformities as examined by histology and transmission electron microscopy. Pnpla2 knockdown diminished the PLA2 enzymatic activity of PEDF-R in the retina. Lipidomic analyses revealed the accumulation of lysophosphatidyl choline-DHA and lysophosphatidyl ethanolamine-DHA in PEDF-R-deficient retinas, suggesting a possible causal link to photoreceptor dysfunction. Loss of PEDF-R decreased levels of rhodopsin, opsin, PKCα, and synaptophysin relative to controls. Pnpla2-/- photoreceptors had surface-exposed phosphatidylserine, and their nuclei were TUNEL positive and condensed, revealing an apoptotic onset. Paralleling its structural defects, PEDF-R deficiency compromised photoreceptor function in vivo as indicated by the attenuation of photoreceptor a- and b-waves in Pnpla2-/- and Pnpla2+/- mice relative to controls as determined by electroretinography. In conclusion, ablation of PEDF-R in mice caused alteration in phospholipid composition associated with malformation and malperformance of photoreceptors. These findings identify PEDF-R as an important component for photoreceptor structure and function, highlighting its role in phospholipid metabolism for retinal survival and its consequences.
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Affiliation(s)
- Alexandra Bernardo-Colón
- Section of Protein Structure and Function, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lijin Dong
- Genetic Engineering Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mones Abu-Asab
- Histopathology Core Facility, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard S Brush
- Department of Ophthalmology(,) and Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Martin-Paul Agbaga
- Department of Ophthalmology(,) and Dean A. McGee Eye Institute, Oklahoma City, OK, USA; Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - S Patricia Becerra
- Section of Protein Structure and Function, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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Akaba Y, Takahashi S, Suzuki K, Kosaki K, Tsujimura K. miR-514a promotes neuronal development in human iPSC-derived neurons. Front Cell Dev Biol 2023; 11:1096463. [PMID: 36824367 PMCID: PMC9941156 DOI: 10.3389/fcell.2023.1096463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Proper development and function of the central nervous system require precise regulation of gene expression. MicroRNAs (miRNAs), a group of small non-coding RNAs that can negatively regulate gene expression at the post-transcriptional level, are critical regulators of neuronal development, and dysregulation of microRNAs has been implicated in various neurological disorders. Changes in microRNA expression and repertoire are related to the emergence of social and behavioral variations in closely related primates, including humans, during evolution. MicroRNA-514a (miR-514a) is an X-linked miRNA that is conserved in species with higher social and cognitive functions, and frequent tandem duplications of miR-514a have been found in primate genomes. Here, we demonstrate that miR-514a plays a crucial role in neuronal development in neurons derived from human induced pluripotent stem cells (iPSCs). Overexpression of miR-514a increased dendritic length, soma size, and activity levels of mammalian target of rapamycin (mTOR) signaling in induced pluripotent stem cell-derived neurons, whereas blocking of endogenous miR-514a inhibited neuronal development. Furthermore, we performed a functional analysis of the miR-514a variation found during primate evolution, to investigate the impact of miR-514a sequence variation and associated changes in expression on brain development during evolution. We found that mutation in miR-514a significantly reduced the expression of the mature form and abolished the effects observed when native miR-514a was expressed. Our findings provide new insights into the functional role of miR-514a in the regulation of neuronal development and evolution of primate brain development.
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Affiliation(s)
- Yuichi Akaba
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Satoru Takahashi
- Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan,Graduate School of Engineering Science, Osaka University, Osaka, Japan,Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Keita Tsujimura
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,*Correspondence: Keita Tsujimura,
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7
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Carpineto P, Di Filippo ES, Aharrh Gnama A, Bondi D, Iafigliola C, Licata AM, Fulle S. MicroRNA Expression in Subretinal Fluid in Eyes Affected by Rhegmatogenous Retinal Detachment. Int J Mol Sci 2023; 24:ijms24033032. [PMID: 36769354 PMCID: PMC9917592 DOI: 10.3390/ijms24033032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Proliferative vitreoretinopathy (PVR) is an abnormal intraocular scarring process that can complicate cases of rhegmatogenous retinal detachment (RRD). Although previous studies have examined the relevance of microRNAs (miRNAs) in ophthalmic diseases, only a few studies have evaluated the expression profiles of microRNAs in subretinal fluid. We hypothesized that the expression profiles of specific miRNAs may change in response to RRD, in the subretinal fluid that is directly in contact with photoreceptors and the retinal pigment epithelium (RPE). We looked for a potential correlation between the expression of specific miRNAs in eyes with RRD and known clinical risk factors of PVR. A total of 24 patients (59 ± 11 years) who underwent scleral buckling procedure were enrolled in this prospective study. Twenty-four undiluted subretinal fluid samples were collected, RNA was isolated and qRT-PCR was performed to analyze the expression of 12 miRNAs. We found the existence of a positive association between the expression of miR-21 (p = 0.017, r = 0.515) and miR-34 (p = 0.030, r = 0.624) and the duration of symptoms related to retinal detachment. Moreover, the expression of miR-146a tended to decrease in patients who developed PVR. Subretinal fluid constitutes an intriguing biological matrix to evaluate the role of miRNAs leading to the development of PVR.
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Affiliation(s)
- Paolo Carpineto
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Ophthalmology Clinic, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Correspondence:
| | - Ester Sara Di Filippo
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Agbeanda Aharrh Gnama
- Ophthalmology Clinic, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Danilo Bondi
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Carla Iafigliola
- Ophthalmology Clinic, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Arturo Maria Licata
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
- Ophthalmology Clinic, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Stefania Fulle
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
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Feng X, Cai Z, Mu T, Yu B, Wang Y, Ma R, Liu J, Wang C, Zhang J, Gu Y. CircRNA screening and ceRNA network construction for milk fat metabolism in dairy cows. Front Vet Sci 2022; 9:995629. [PMID: 36439356 PMCID: PMC9684208 DOI: 10.3389/fvets.2022.995629] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/27/2022] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Milk fat is one of the main reference elements for evaluating milk quality and is a primary objective trait in dairy cattle breeding. In recent years, circular RNAs (circRNAs) have been found to play crucial roles in many biological processes. However, the function and expression profiles of circRNAs in milk fat synthesis in cows are not completely understood. We performed RNA sequencing to analyze the genome-wide expression of circRNA transcripts in bovine mammary epithelial cells (BMECs) from cows with extreme differences in milk fat percentage. We identified candidate differential circRNAs associated with milk fat metabolism using functional enrichment analysis and constructed a lipid metabolism-related competing endogenous RNA (ceRNA) interactive regulatory network. RESULTS A total of 290 circRNAs were significantly differentially expressed (DE-circRNAs) in high milk fat percentage (HMF) cows compared to that in low milk fat percentage (LMF) cows. Of the 290 circRNAs, 142 were significantly upregulated and 148 were significantly downregulated. Enrichment analysis (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) identified four DE-circRNAs (circ_0001122, circ_0007367, circ_0018269, and circ_0015179) that potentially regulate milk fat metabolism. Among them, circ_0001122, circ_0007367, and circ_0015179 had relatively high expression levels in cow mammary gland tissue compared to other tissues (heart, liver, kidney, uterus, ovaries, and small intestine) of cows. The regulatory networks circ_0001122:miR-12043:LIPG, circ_0007367:miR-331-3p:CIDEA/PML, and circ_0018269:miR-11989:RORC/HPX are potential networks to explore the mechanism of milk fat regulation. CONCLUSIONS These results reveal the possible role of circRNAs in milk fat metabolism in dairy cows. Several important circRNAs and ceRNAs affecting milk fat synthesis were identified, providing insights into the complex biology of milk fat synthesis as well as a novel theoretical perspective for future research on lactation, milk quality, and breed improvement in dairy cows.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yaling Gu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
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Liu J, Jin T, Ran L, Zhao Z, Zhu R, Xie G, Bi X. Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation. Hereditas 2022; 159:41. [PMID: 36271387 PMCID: PMC9587650 DOI: 10.1186/s41065-022-00254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Background ATM (ataxia-telangiectasia mutated) protein kinase is highly conserved in metazoan, and plays a critical role at DNA damage response, oxidative stress, metabolic stress, immunity, RNA biogenesis etc. Systemic profiling of ATM regulated genes, including protein-coding genes, miRNAs, and long non-coding RNAs, will greatly improve our understanding of ATM functions and its regulation. Results 1) differentially expressed protein-coding genes, miRNAs, and long non-coding RNAs in atm mutated flies were identified at physiological condition and after X-ray irradiation. 2) functions of differentially expressed genes in atm mutated flies, regardless of protein-coding genes or non-coding RNAs, are closely related with metabolic process, immune response, DNA damage response or oxidative stress. 3) these phenomena are persistent after irradiation. 4) there is a cross-talk regulation towards miRNAs by ATM, E2f1, and p53 during development and after irradiation. 5) knock-out flies or knock-down flies of most irradiation-induced miRNAs were sensitive to ionizing radiation. Conclusions We provide a valuable resource of protein-coding genes, miRNAs, and long non-coding RNAs, for understanding ATM functions and regulations. Our work provides the new evidence of inter-dependence among ATM-E2F1-p53 for the regulation of miRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00254-9.
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Affiliation(s)
- Jun Liu
- School of Medicine, Nantong University, Nantong, 226001, China
| | - Tianyu Jin
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Lanxi Ran
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Ze Zhao
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Rui Zhu
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Gangcai Xie
- School of Medicine, Nantong University, Nantong, 226001, China.
| | - Xiaolin Bi
- School of Medicine, Nantong University, Nantong, 226001, China. .,College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China.
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10
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miR-275/305 cluster is essential for maintaining energy metabolic homeostasis by the insulin signaling pathway in Bactrocera dorsalis. PLoS Genet 2022; 18:e1010418. [PMID: 36197879 PMCID: PMC9534453 DOI: 10.1371/journal.pgen.1010418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022] Open
Abstract
Increasing evidence indicates that miRNAs play crucial regulatory roles in various physiological processes of insects, including systemic metabolism. However, the molecular mechanisms of how specific miRNAs regulate energy metabolic homeostasis remain largely unknown. In the present study, we found that an evolutionarily conserved miR-275/305 cluster was essential for maintaining energy metabolic homeostasis in response to dietary yeast stimulation in Bactrocera dorsalis. Depletion of miR-275 and miR-305 by the CRISPR/Cas9 system significantly reduced triglyceride and glycogen contents, elevated total sugar levels, and impaired flight capacity. Combined in vivo and in vitro experiments, we demonstrated that miR-275 and miR-305 can bind to the 3'UTR regions of SLC2A1 and GLIS2 to repress their expression, respectively. RNAi-mediated knockdown of these two genes partially rescued metabolic phenotypes caused by inhibiting miR-275 and miR-305. Furthermore, we further illustrated that the miR-275/305 cluster acting as a regulator of the metabolic axis was controlled by the insulin signaling pathway. In conclusion, our work combined genetic and physiological approaches to clarify the molecular mechanism of metabolic homeostasis in response to different dietary stimulations and provided a reference for deciphering the potential targets of physiologically important miRNAs in a non-model organism.
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11
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Colaianni D, De Pittà C. The Role of microRNAs in the Drosophila Melanogaster Visual System. Front Cell Dev Biol 2022; 10:889677. [PMID: 35493095 PMCID: PMC9053400 DOI: 10.3389/fcell.2022.889677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs (∼22 nucleotides in length) that negatively regulate protein-coding gene expression post-transcriptionally by targeting mRNAs and triggering either translational repression or RNA degradation. MiRNA genes represent approximately 1% of the genome of different species and it has been estimated that every miRNA can interact with an average of 200 mRNA transcripts, with peaks of 1,500 mRNA targets per miRNA molecule. As a result, miRNAs potentially play a fundamental role in several biological processes including development, metabolism, proliferation, and apoptotic cell death, both in physiological and pathological conditions. Since miRNAs were discovered, Drosophila melanogaster has been used as a model organism to shed light on their functions and their molecular mechanisms in the regulation of many biological and behavioral processes. In this review we focus on the roles of miRNAs in the fruit fly brain, at the level of the visual system that is composed by the compound eyes, each containing ∼800 independent unit eyes called ommatidia, and each ommatidium is composed of eight photoreceptor neurons that project into the optic lobes. We describe the roles of a set of miRNAs in the development and in the proper function of the optic lobes (bantam, miR-7, miR-8, miR-210) and of the compound eyes (bantam, miR-7, miR-9a, miR-210, miR-263a/b, miR-279/996), summarizing also the pleiotropic effects that some miRNAs exert on circadian behavior.
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Chandler JA, Innocent LV, Martinez DJ, Huang IL, Yang JL, Eisen MB, Ludington WB. Microbiome-by-ethanol interactions impact Drosophila melanogaster fitness, physiology, and behavior. iScience 2022; 25:104000. [PMID: 35313693 PMCID: PMC8933687 DOI: 10.1016/j.isci.2022.104000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/24/2021] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota can affect how animals respond to ingested toxins, such as ethanol, which is prevalent in the diets of diverse animals and often leads to negative health outcomes in humans. Ethanol is a complex dietary factor because it acts as a toxin, behavioral manipulator, and nutritional source, with both direct effects on the host as well as indirect ones through the microbiome. Here, we developed a model for chronic, non-intoxicating ethanol ingestion in the adult fruit fly, Drosophila melanogaster, and paired this with the tractability of the fly gut microbiota, which can be experimentally removed. We linked numerous physiological, behavioral, and transcriptional variables to fly fitness, including a combination of intestinal barrier integrity, stored triglyceride levels, feeding behavior, and the immunodeficiency pathway. Our results reveal a complex tradeoff between lifespan and fecundity that is microbiome-dependent and modulated by dietary ethanol and feeding behavior.
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Affiliation(s)
- James Angus Chandler
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Lina Victoria Innocent
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | - Isaac Li Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jane Lani Yang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael Bruce Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - William Basil Ludington
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera. BMC Genomics 2022; 23:257. [PMID: 35379185 PMCID: PMC8978429 DOI: 10.1186/s12864-022-08478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08478-9.
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Affiliation(s)
- Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gabriele Buchmann
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul Young
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute NSW 2010, Darlinghurst, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Emily J Remnant
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mitch Shambrook
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia.,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Benjamin P Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia. .,Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany.
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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Butera A, Roy M, Zampieri C, Mammarella E, Panatta E, Melino G, D’Alessandro A, Amelio I. p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer. Biol Direct 2022; 17:6. [PMID: 35255936 PMCID: PMC8902766 DOI: 10.1186/s13062-022-00319-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/10/2022] [Indexed: 12/28/2022] Open
Abstract
Adaptation of the lipid metabolism participates in cancer pathogenesis, facilitating energy storage and influencing cell fate and control of molecular signalling. The tumour suppressor protein p53 is a molecular hub of cell metabolism, supporting antioxidant capabilities and counteracting oncogene-induced metabolic switch. Despite extensive work has described the p53-dependent metabolic pathways, a global profiling of p53 lipidome is still missing. By high-throughput untargeted lipidomic analysis of pancreatic ductal adenocarcinoma (PDAC) cells, we profile the p53-dependent lipidome, revealing intracellular and secreted lysophospholipids as one of the most affected class. Lysophospholipids are hydrolysed forms of phospholipids that results from phospholipase activity, which can function as signalling molecules, exerting non-cell-autonomous effects and instructing cancer microenvironment and immunity. Here, we reveal that p53 depletion reduces abundance of intracellular lysophosphatidyl-choline, -ethanolamine and -serine and their secretion in the extracellular environment. By integrating this with genomic and transcriptomic studies from in vitro models and human PDAC patients, we identified potential clinically relevant candidate p53-dependent phospholipases. In particular PLD3, PLCB4 and PLCD4 expression is regulated by p53 and chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) indicates a direct transcriptional control on their chromatin accessible genomic loci. Consistently, PLD3, PLCB4 and PLCD4 expression correlates with p53 mutational status in PDAC patients, and these genes display prognostic significance. Overall, our data provide insights into lipidome rewiring driven by p53 loss and identify alterations of lysophospholipids as a potential molecular mechanism for p53-mediated non-cell-autonomous molecular signalling that instructs cancer microenvironment and immunity during PDAC pathogenesis.
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Affiliation(s)
- Alessio Butera
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Micaela Roy
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Carlotta Zampieri
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eleonora Mammarella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Emanuele Panatta
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | | | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
- School of Life Sciences, University of Nottingham, Nottingham, UK
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