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Saeki N, Inui-Yamamoto C, Ikeda Y, Kanai R, Hata K, Itoh S, Inubushi T, Akiyama S, Ohba S, Abe M. Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice. Hum Mol Genet 2024; 33:1618-1629. [PMID: 38899779 DOI: 10.1093/hmg/ddae102] [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: 02/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.
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Affiliation(s)
- Naoya Saeki
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Chizuko Inui-Yamamoto
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Rinna Kanai
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Fixed Prosthodontics and Orofacial Function, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shousaku Itoh
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shigehisa Akiyama
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Makoto Abe
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
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Thiam F, Diop G, Coulonges C, Derbois C, Thiam A, Diouara AAM, Mbaye MN, Diop M, Nguer CM, Dieye Y, Mbengue B, Zagury JF, Deleuze JF, Dieye A. An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant. BMC Infect Dis 2024; 24:275. [PMID: 38438955 PMCID: PMC10910704 DOI: 10.1186/s12879-024-09149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
Malaria infection is a multifactorial disease partly modulated by host immuno-genetic factors. Recent evidence has demonstrated the importance of Interleukin-17 family proinflammatory cytokines and their genetic variants in host immunity. However, limited knowledge exists about their role in parasitic infections such as malaria. We aimed to investigate IL-17A serum levels in patients with severe and uncomplicated malaria and gene polymorphism's influence on the IL-17A serum levels. In this research, 125 severe (SM) and uncomplicated (UM) malaria patients and 48 free malaria controls were enrolled. IL-17A serum levels were measured with ELISA. PCR and DNA sequencing were used to assess host genetic polymorphisms in IL-17A. We performed a multivariate regression to estimate the impact of human IL-17A variants on IL-17A serum levels and malaria outcomes. Elevated serum IL-17A levels accompanied by increased parasitemia were found in SM patients compared to UM and controls (P < 0.0001). Also, the IL-17A levels were lower in SM patients who were deceased than in those who survived. In addition, the minor allele frequencies (MAF) of two IL-17A polymorphisms (rs3819024 and rs3748067) were more prevalent in SM patients than UM patients, indicating an essential role in SM. Interestingly, the heterozygous rs8193038 AG genotype was significantly associated with higher levels of IL-17A than the homozygous wild type (AA). According to our results, it can be concluded that the IL-17A gene rs8193038 polymorphism significantly affects IL-17A gene expression. Our results fill a gap in the implication of IL-17A gene polymorphisms on the cytokine level in a malaria cohort. IL-17A gene polymorphisms also may influence cytokine production in response to Plasmodium infections and may contribute to the hyperinflammatory responses during severe malaria outcomes.
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Affiliation(s)
- Fatou Thiam
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal.
| | - Gora Diop
- Departement de Biologie Animale, Faculte Des Sciences Et Techniques, Unite Postulante de Biologie GenetiqueGenomique Et Bio-Informatique (G2B), Universite Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
- Pole d'Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, 36, Avenue Pasteur, Dakar, BP: 220, Senegal
| | - Cedric Coulonges
- Equipe GBA «GenomiqueBioinformatique & Applications», Conservatoire National Des Arts Et Metiers, 292, Rue Saint Martin, Paris Cedex 03, Paris, 75141, France
| | - Celine Derbois
- Centre National de Recherche en Génétique Humaine (CNRGH), Institut de Biologie François Jacob, 2 Rue Gaston Crémieux, CP 5721, Evry Cedex, 91057, France
| | - Alassane Thiam
- Pole d'Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, 36, Avenue Pasteur, Dakar, BP: 220, Senegal
| | - Abou Abdallah Malick Diouara
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Mame Ndew Mbaye
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Mamadou Diop
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Cheikh Momar Nguer
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Yakhya Dieye
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
- Pôle de Microbiologie, Institut Pasteur de Dakar, 36 Avenue Pasteur, Dakar, BP 220, Senegal
| | - Babacar Mbengue
- Service d'Immunologie, Faculté de Médecine, de Pharmacie Et d'Odontostomatologie, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
| | - Jean-Francois Zagury
- Equipe GBA «GenomiqueBioinformatique & Applications», Conservatoire National Des Arts Et Metiers, 292, Rue Saint Martin, Paris Cedex 03, Paris, 75141, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génétique Humaine (CNRGH), Institut de Biologie François Jacob, 2 Rue Gaston Crémieux, CP 5721, Evry Cedex, 91057, France
| | - Alioune Dieye
- Service d'Immunologie, Faculté de Médecine, de Pharmacie Et d'Odontostomatologie, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
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Yuan J, Fei S, Gui Z, Wang Z, Chen H, Sun L, Tao J, Han Z, Ju X, Tan R, Gu M, Huang Z. Association of UGT1A Gene Polymorphisms with BKV Infection in Renal Transplantation Recipients. Curr Drug Metab 2024; 25:188-196. [PMID: 38509677 DOI: 10.2174/0113892002282727240307072255] [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: 11/28/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND BK virus (BKV) infection is an opportunistic infectious complication and constitutes a risk factor for premature graft failure in kidney transplantation. Our research aimed to identify associations and assess the impact of single-nucleotide polymorphisms (SNPs) on metabolism-related genes in patients who have undergone kidney transplantation with BKV infection. MATERIAL/METHODS The DNA samples of 200 eligible kidney transplant recipients from our center, meeting the inclusion criteria, have been collected and extracted. Next-generation sequencing was used to genotype SNPs on metabolism-associated genes (CYP3A4/5/7, UGT1A4/7/8/9, UGT2B7). A general linear model (GLM) was used to identify and eliminate confounding factors that may influence the outcome events. Multiple inheritance models and haplotype analyses were utilized to identify variation loci associated with infection caused by BKV and ascertain haplotypes, respectively. RESULTS A total of 141 SNPs located on metabolism-related genes were identified. After Hardy-Weinberg equilibrium (HWE) and minor allele frequency (MAF) analysis, 21 tagger SNPs were selected for further association analysis. Based on GLM results, no confounding factor was significant in predicting the incidence of BK polyomavirus-associated infection. Then, multiple inheritance model analyses revealed that the risk of BKV infection was significantly associated with rs3732218 and rs4556969. Finally, we detect significant associations between haplotype T-A-C of block 2 (rs4556969, rs3732218, rs12468274) and infection caused by BKV (P = 0.0004). CONCLUSION We found that genetic variants in the UGT1A gene confer BKV infection susceptibility after kidney transplantation.
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Affiliation(s)
- Jingwen Yuan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Shuang Fei
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zeping Gui
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
- Department of Urology, The Second Affiliated Hospital with Nanjing Medical University, Nanjing, 210011, China
| | - Zhengkai Huang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, China
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Liu D, Guo R, Chen M, Shi B, Weng J, Fu Z. Study on the Mutation of FⅨ Gene in 31 Patients with Type B Hemophilia. Clin Appl Thromb Hemost 2024; 30:10760296241275454. [PMID: 39135443 PMCID: PMC11322947 DOI: 10.1177/10760296241275454] [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: 06/05/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
Hemophilia B (HB) is an inherited bleeding disorder caused by defects in the FⅨ gene, leading to severe coagulation dysfunction. This study designed eight pairs of primers covering eight exons of the FⅨ gene and used PCR and DNA sequencing to detect FⅨ gene mutations in 31 HB patients. Sequencing results were compared with normal sequences using Chromas software on Blast to identify mutation sites. Findings revealed the CpG dinucleotide region as a mutation hotspot and the 192nd nucleotide (FⅨ192) as a dinucleotide polymorphism site in the Chinese population. Pathogenic mutations included point mutations, deletions, insertions, and mutations affecting amino acids or splicing sites. For cases with only polymorphic sites, further exon sequencing is needed. This study adds new mutation data to the global HB database, supports research on racial differences in FⅨ gene mutations, and contributes to domestic HB statistics. The results aid in understanding the FⅨ gene's role in coagulation, elucidating HB pathogenesis, and providing a basis for future gene therapy.
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Affiliation(s)
- Danjuan Liu
- Department of Critical Care Medicine, the Affiliated Hospital of Putian University, Putian 351100, China
| | - Rongjie Guo
- Department of Critical Care Medicine, the Affiliated Hospital of Putian University, Putian 351100, China
| | - Min Chen
- Department of Critical Care Medicine, the Affiliated Hospital of Putian University, Putian 351100, China
| | - Bingbing Shi
- Department of Critical Care Medicine, the Affiliated Hospital of Putian University, Putian 351100, China
| | - Junting Weng
- Department of Critical Care Medicine, the Affiliated Hospital of Putian University, Putian 351100, China
| | - Zhifang Fu
- Department of Clinical lab, Zhenhai Street Community Health Service Center, Licheng District, Putian, 351100, Fujian, China
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Cao VD, Luo G, Korynta S, Liu H, Liang Y, Shanklin J, Altpeter F. Intron-mediated enhancement of DIACYLGLYCEROL ACYLTRANSFERASE1 expression in energycane promotes a step change for lipid accumulation in vegetative tissues. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:153. [PMID: 37838699 PMCID: PMC10576891 DOI: 10.1186/s13068-023-02393-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/09/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Metabolic engineering for hyperaccumulation of lipids in vegetative tissues is a novel strategy for enhancing energy density and biofuel production from biomass crops. Energycane is a prime feedstock for this approach due to its high biomass production and resilience under marginal conditions. DIACYLGLYCEROL ACYLTRANSFERASE (DGAT) catalyzes the last and only committed step in the biosynthesis of triacylglycerol (TAG) and can be a rate-limiting enzyme for the production of TAG. RESULTS In this study, we explored the effect of intron-mediated enhancement (IME) on the expression of DGAT1 and resulting accumulation of TAG and total fatty acid (TFA) in leaf and stem tissues of energycane. To maximize lipid accumulation these evaluations were carried out by co-expressing the lipogenic transcription factor WRINKLED1 (WRI1) and the TAG protect factor oleosin (OLE1). Including an intron in the codon-optimized TmDGAT1 elevated the accumulation of its transcript in leaves by seven times on average based on 5 transgenic lines for each construct. Plants with WRI1 (W), DGAT1 with intron (Di), and OLE1 (O) expression (WDiO) accumulated TAG up to a 3.85% of leaf dry weight (DW), a 192-fold increase compared to non-modified energycane (WT) and a 3.8-fold increase compared to the highest accumulation under the intron-less gene combination (WDO). This corresponded to TFA accumulation of up to 8.4% of leaf dry weight, a 2.8-fold or 6.1-fold increase compared to WDO or WT, respectively. Co-expression of WDiO resulted in stem accumulations of TAG up to 1.14% of DW or TFA up to 2.08% of DW that exceeded WT by 57-fold or 12-fold and WDO more than twofold, respectively. Constitutive expression of these lipogenic "push pull and protect" factors correlated with biomass reduction. CONCLUSIONS Intron-mediated enhancement (IME) of the expression of DGAT resulted in a step change in lipid accumulation of energycane and confirmed that under our experimental conditions it is rate limiting for lipid accumulation. IME should be applied to other lipogenic factors and metabolic engineering strategies. The findings from this study may be valuable in developing a high biomass feedstock for commercial production of lipids and advanced biofuels.
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Affiliation(s)
- Viet Dang Cao
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Guangbin Luo
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Shelby Korynta
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Hui Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA
| | - Yuanxue Liang
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Upton, NY, USA.
- Biosciences Department, Brookhaven National Laboratory, Upton, NY, USA.
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, IFAS, Gainesville, FL, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA.
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Bai M, Wang W, Chen Y, Fan C, Sun J, Lu J, Liu J, Wang C. The intragenic cis-elements mediate temperature response of RrKSN. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107983. [PMID: 37611488 DOI: 10.1016/j.plaphy.2023.107983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Gene regulation via intragenic sequences is becoming more recognized in many eukaryotes. However, the intragenic sequences mediated gene expressions in response to environmental stimuli have been largely uncharacterized. Here, we showed that the first intron of RrKSN from the Rosa rugosa cultivar 'Purple branch' had a positive effect on RrKSN expression, and the effect depends on its position and orientation. Further analyses revealed that the four adjacent cis-elements (T)CGATT/AATCG(A) within the first intron were critical for the positive regulation, and the RrKSN promotion was significantly suppressed with mutations of these elements. These cis-elements were further evidenced as binding sites for RrARR1, the homologous of Arabidopsis type-B ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) transcription factor. The first intron-mediated RrKSN expression was enhanced with over-expressing of RrARR1, but abolished with RrARR1 silencing in rose seedlings. Moreover, the expression difference of RrKSN between 16°C and 28°C was eliminated along with RrARR1-silencing. Taken together, these results suggested both RrARR1 and its binding elements are required for the first intron-mediated RrKSN expression in response to varying temperatures. Therefore, our results reveal a unique intragenic regulation mechanism of gene expression by which plants perceive the signal of ambient temperature in rose.
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Affiliation(s)
- Mengjuan Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Weinan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yeqing Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunguo Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Lu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Petrillo E. Do not panic: An intron-centric guide to alternative splicing. THE PLANT CELL 2023; 35:1752-1761. [PMID: 36648241 PMCID: PMC10226583 DOI: 10.1093/plcell/koad009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/05/2022] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
This review is an attempt to establish concepts of splicing and alternative splicing giving proper relevance to introns, the key actors in this mechanism. It might also work as a guide for those who found their favorite gene undergoes alternative splicing and could benefit from gaining a theoretical framework to understand the possible impacts of this process. This is not a thorough review of all the work in the field, but rather a critical review of some of the most relevant work done to understand the underlying mechanisms of splicing and the key questions that remain unanswered such as: What is the physiological relevance of alternative splicing? What are the functions of the different outcomes? To what extent do different alternative splicing types contribute to the proteome? Intron retention is the most frequent alternative splicing event in plants and, although scientifically neglected, it is also common in animals. This is a heterogeneous type of alternative splicing that includes different sub-types with features that have distinctive consequences in the resulting transcripts. Remarkably, intron retention can be a dead end for a transcript, but it could also be a stable intermediate whose processing is resumed upon a particular signal or change in the cell status. New sequencing technologies combined with the study of intron lariats in different conditions might help to answer key questions and could help us to understand the actual relevance of introns in gene expression regulation.
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Affiliation(s)
- Ezequiel Petrillo
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA Buenos Aires, Argentina
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Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol Cell 2023; 83:237-251.e7. [PMID: 36599352 DOI: 10.1016/j.molcel.2022.12.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023]
Abstract
N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.
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Affiliation(s)
- Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - David Dierks
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Oh Sung Kwon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Cindy Burel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7630031, Israel
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel; Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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KUMARI RAGINI, KUMAR RAKESH, SINHA BEENA, SINHA REBEKA, GUPTA ISHWARDAYAL, VERMA ARCHANA. Novel polymorphisms of the KCNB1 gene and their association with production traits in Indian Sahiwal cattle. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i12.117454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mastitis in cattle is a prevalent mammary gland disease that contributes significantly to the increase in veterinary expenditures in the dairy sector. KCNB1 (Potassium voltage-gated channel, subfamily B member 1) gene is involved in regulating apoptosis, cell proliferation and differentiation, udder epithelial tissue maintenance and repair, mammary gland development and recommended as a candidate gene for production related traits in cattle. The purpose of this research was to detect the genetic variants of KCNB1 gene in Sahiwal cattle and to analyze the association between polymorphisms with milk production traits, udder traits, and teat traits in Sahiwal cattle. A total of 87 cattle were genotyped by polymerase chain reaction-restriction fragment length polymorphism technique. Two single nucleotide polymorphisms within the non-coding sequence of KCNB1 gene were identified (g.78216220G>A and g.78216335A>G). Analysis of productivity traits within the genotyped animals revealed that the SNP1-Msp1 locus (g.78216220G>A) located at intron 1 was associated with milk production traits, but the SNP2-BspHI locus (g.78216335A>G) had no association with milk production. Significant associations were also observed between SNP1-Msp1 and SNP2-BspHI loci with both udder and teat traits. Our results demonstrate that polymorphisms in the cattle KCNB1 gene were associated with milk production, udder and teat traits and might be utilized as a genetic marker for marker-assisted selection in cattle breeding programs.
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Cui C, Ma Z, Wan H, Gao J, Zhou B. GhALKBH10 negatively regulates salt tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:87-100. [PMID: 36215791 DOI: 10.1016/j.plaphy.2022.09.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The alpha-ketoglutarate-dependent dioxygenase (AlkB) gene family plays an essential role in regulating plant development and stress response. However, the AlkB gene family is still not well understood in cotton. In this study, 40 AlkB genes in cotton and Arabidopsis are identified and classified into three classes based on phylogenetic analysis. Their protein motifs and exon/intron structures are highly conserved. Chromosomal localization and synteny analysis suggested that segmental or whole-genome duplication and polyploidization events contributed to the expansion of the cotton AlkB gene family. Furthermore, the AlkB genes showed dynamic spatiotemporal expression patterns and diverse responses to abiotic stresses. Among them, GhALKBH10 was down-regulated under various abiotic stresses and its subcellular expression was localized in cytoplasm and nucleus. Silencing GhALKBH10 in cotton increased antioxidant capacity and reduced cytoplasmic Na+ concentration, thereby improved the plant tolerance to salinity. Conversely, overexpression (OE) of GhALKBH10 in Arabidopsis markedly weakened the plant tolerance to salinity. The global m6A levels measured in VIGS and OE transgenic lines showed that they were significantly higher in TRV: GhALKBH10 plants (VIGS) than in TRV: 00 plants but significantly lower in OE plants than wild-type plants under salt stress, which could be considered as a potential m6A demethylase in cotton. Our results suggest that the GhALKBH10 gene negatively regulates salt tolerance in plants, which provides information of the cotton AlkB family and an understanding of GhALKBH10 function under salt condition as well as a new gene for salt-tolerant cotton breeding.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Zhifeng Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China.
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Ametrano A, Picchietti S, Guerra L, Giacomelli S, Oreste U, Coscia MR. Comparative Analysis of the pIgR Gene from the Antarctic Teleost Trematomus bernacchii Reveals Distinctive Features of Cold-Adapted Notothenioidei. Int J Mol Sci 2022; 23:7783. [PMID: 35887127 PMCID: PMC9321927 DOI: 10.3390/ijms23147783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein, we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to the pIgR of multiple teleost species belonging to five perciform suborders, including 11 Antarctic and 1 non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in the less-cold peri-Antarctic sea. Antarctic pIgR genes displayed particularly long introns marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to the Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold-adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold-adapted species, pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.
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Affiliation(s)
- Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Laura Guerra
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Stefano Giacomelli
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
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Dwyer K, Agarwal N, Gega A, Ansari A. Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron. Front Mol Biosci 2021; 8:712639. [PMID: 34291091 PMCID: PMC8287100 DOI: 10.3389/fmolb.2021.712639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/25/2021] [Indexed: 11/15/2022] Open
Abstract
An evolutionarily conserved feature of introns is their ability to enhance expression of genes that harbor them. Introns have been shown to regulate gene expression at the transcription and post-transcription level. The general perception is that a promoter-proximal intron is most efficient in enhancing gene expression and the effect diminishes with the increase in distance from the promoter. Here we show that the intron regains its positive influence on gene expression when in proximity to the terminator. We inserted ACT1 intron into different positions within IMD4 and INO1 genes. Transcription Run-On (TRO) analysis revealed that the transcription of both IMD4 and INO1 was maximal in constructs with a promoter-proximal intron and decreased with the increase in distance of the intron from the promoter. However, activation was partially restored when the intron was placed close to the terminator. We previously demonstrated that the promoter-proximal intron stimulates transcription by affecting promoter directionality through gene looping-mediated recruitment of termination factors in the vicinity of the promoter region. Here we show that the terminator-proximal intron also enhances promoter directionality and results in compact gene architecture with the promoter and terminator regions in close physical proximity. Furthermore, we show that both the promoter and terminator-proximal introns facilitate assembly or stabilization of the preinitiation complex (PIC) on the promoter. On the basis of these findings, we propose that proximity to both the promoter and the terminator regions affects the transcription regulatory potential of an intron, and the terminator-proximal intron enhances transcription by affecting both the assembly of preinitiation complex and promoter directionality.
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Affiliation(s)
| | | | | | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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