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Beopoulos A, Géa M, Fasano A, Iris F. RNA epitranscriptomics dysregulation: A major determinant for significantly increased risk of ASD pathogenesis. Front Neurosci 2023; 17:1101422. [PMID: 36875672 PMCID: PMC9978375 DOI: 10.3389/fnins.2023.1101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Autism spectrum disorders (ASDs) are perhaps the most severe, intractable and challenging child psychiatric disorders. They are complex, pervasive and highly heterogeneous and depend on multifactorial neurodevelopmental conditions. Although the pathogenesis of autism remains unclear, it revolves around altered neurodevelopmental patterns and their implications for brain function, although these cannot be specifically linked to symptoms. While these affect neuronal migration and connectivity, little is known about the processes that lead to the disruption of specific laminar excitatory and inhibitory cortical circuits, a key feature of ASD. It is evident that ASD has multiple underlying causes and this multigenic condition has been considered to also dependent on epigenetic effects, although the exact nature of the factors that could be involved remains unclear. However, besides the possibility for differential epigenetic markings directly affecting the relative expression levels of individual genes or groups of genes, there are at least three mRNA epitranscriptomic mechanisms, which function cooperatively and could, in association with both genotypes and environmental conditions, alter spatiotemporal proteins expression patterns during brain development, at both quantitative and qualitative levels, in a tissue-specific, and context-dependent manner. As we have already postulated, sudden changes in environmental conditions, such as those conferred by maternal inflammation/immune activation, influence RNA epitranscriptomic mechanisms, with the combination of these processes altering fetal brain development. Herein, we explore the postulate whereby, in ASD pathogenesis, RNA epitranscriptomics might take precedence over epigenetic modifications. RNA epitranscriptomics affects real-time differential expression of receptor and channel proteins isoforms, playing a prominent role in central nervous system (CNS) development and functions, but also RNAi which, in turn, impact the spatiotemporal expression of receptors, channels and regulatory proteins irrespective of isoforms. Slight dysregulations in few early components of brain development, could, depending upon their extent, snowball into a huge variety of pathological cerebral alterations a few years after birth. This may very well explain the enormous genetic, neuropathological and symptomatic heterogeneities that are systematically associated with ASD and psychiatric disorders at large.
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Affiliation(s)
| | - Manuel Géa
- Bio-Modeling Systems, Tour CIT, Paris, France
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Center for Celiac Research and Treatment, Massachusetts General Hospital for Children, Boston, MA, United States
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Jian G, Mo Y, Hu Y, Huang Y, Ren L, Zhang Y, Hu H, Zhou S, Liu G, Guo J, Ling Y. Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress. Rice (N Y) 2022; 15:56. [PMID: 36326968 PMCID: PMC9633917 DOI: 10.1186/s12284-022-00599-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.
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Affiliation(s)
- Guihua Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Shuangxi Zhou
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2019, Australia
| | - Gang Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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Wang L, Yang T, Lin Q, Wang B, Li X, Luan S, Yu F. Receptor kinase FERONIA regulates flowering time in Arabidopsis. BMC Plant Biol 2020; 20:26. [PMID: 31948398 PMCID: PMC6966814 DOI: 10.1186/s12870-019-2223-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/30/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND The receptor-like kinase FEROINA (FER) plays a crucial role in controlling plant vegetative growth partially by sensing the rapid alkalinization factor (RALF) peptide. However, the role of RALF1-FER in the vegetative-reproductive growth transition remains unknown. Here, we analyze the mechanism through which FER affects the flowering time in Arabidopsis. RESULTS We found that the FER mRNA levels exhibit an oscillating pattern with a diurnal rhythm and that the clock oscillator CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) up-regulates the expression of FER by associating with its chromatin. In addition, FER expression is regulated by clock genes, and FER also modulates the expression patterns of clock genes. Consistent with its gene expression pattern, FER positively regulates flowering by modulating the transcript accumulation and mRNA alternative splicing of certain flowering-related genes, including FLOWERING LOCUS C (FLC) and its homolog MADS AFFECTING FLOWERING (MAF). However, the RALF1 ligand negatively regulates flowering compared with FER. CONCLUSIONS We found that FER, which is up-regulated by CCA1, controls the flowering time by regulating the transcript accumulation and mRNA alternative splicing (AS) of some important flowering genes, and these findings link FER to the floral transition.
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Affiliation(s)
- Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, People's Republic of China
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Tao Yang
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, People's Republic of China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha, 410004, People's Republic of China.
| | - Bingqian Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, People's Republic of China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Feng Yu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, People's Republic of China.
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Abstract
Currently there is no sensitive, precise, and reproducible method to quantitate alternative splicing of mRNA transcripts. Droplet digital™ PCR (ddPCR™) analysis allows for accurate digital counting for quantification of gene expression. Human telomerase reverse transcriptase (hTERT) is one of the essential components required for telomerase activity and for the maintenance of telomeres. Several alternatively spliced forms of hTERT mRNA in human primary and tumor cells have been reported in the literature. Using one pair of primers and two probes for hTERT, four alternatively spliced forms of hTERT (α-/β+, α+/β- single deletions, α-/β- double deletion, and nondeletion α+/β+) were accurately quantified through a novel analysis method via data collected from a single ddPCR reaction. In this chapter, we describe this ddPCR method that enables direct quantitative comparison of four alternatively spliced forms of the hTERT messenger RNA without the need for internal standards or multiple pairs of primers specific for each variant, eliminating the technical variation due to differential PCR amplification efficiency for different amplicons and the challenges of quantification using standard curves. This simple and straightforward method should have general utility for quantifying alternatively spliced gene transcripts.
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Affiliation(s)
- Bing Sun
- Georgetown University, Washington, DC, USA
| | - Yun-Ling Zheng
- Georgetown University, Washington, DC, USA. .,Cancer Prevention and Control Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.
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Mager LF, Koelzer VH, Stuber R, Thoo L, Keller I, Koeck I, Langenegger M, Simillion C, Pfister SP, Faderl M, Genitsch V, Tcymbarevich I, Juillerat P, Li X, Xia Y, Karamitopoulou E, Lyck R, Zlobec I, Hapfelmeier S, Bruggmann R, McCoy KD, Macpherson AJ, Müller C, Beutler B, Krebs P. The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife 2017; 6:28366. [PMID: 28975893 PMCID: PMC5665647 DOI: 10.7554/elife.28366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant alternative pre-mRNA splicing (AS) events have been associated with several disorders. However, it is unclear whether deregulated AS directly contributes to disease. Here, we reveal a critical role of the AS regulator epithelial splicing regulator protein 1 (ESRP1) for intestinal homeostasis and pathogenesis. In mice, reduced ESRP1 function leads to impaired intestinal barrier integrity, increased susceptibility to colitis and altered colorectal cancer (CRC) development. Mechanistically, these defects are produced in part by modified expression of ESRP1-specific Gpr137 isoforms differently activating the Wnt pathway. In humans, ESRP1 is downregulated in inflamed biopsies from inflammatory bowel disease patients. ESRP1 loss is an adverse prognostic factor in CRC. Furthermore, generation of ESRP1-dependent GPR137 isoforms is altered in CRC and expression of a specific GPR137 isoform predicts CRC patient survival. These findings indicate a central role of ESRP1-regulated AS for intestinal barrier integrity. Alterations in ESRP1 function or expression contribute to intestinal pathology.
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Affiliation(s)
- Lukas Franz Mager
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Regula Stuber
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Lester Thoo
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Ivonne Koeck
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Cedric Simillion
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simona P Pfister
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Martin Faderl
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Irina Tcymbarevich
- Division of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Pascal Juillerat
- Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Xiaohong Li
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yu Xia
- Department of Genetics, The Scripps Research Institute, La Jolla, United States
| | | | - Ruth Lyck
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Kathy D McCoy
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Andrew J Macpherson
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Bruce Beutler
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
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