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Wang T, Tian S, Tikhonova EB, Karamyshev AL, Wang JJ, Zhang F, Wang D. The Enrichment of miRNA-Targeted mRNAs in Translationally Less Active over More Active Polysomes. BIOLOGY 2023; 12:1536. [PMID: 38132362 PMCID: PMC10741098 DOI: 10.3390/biology12121536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
miRNAs moderately inhibit the translation and enhance the degradation of their target mRNAs via cognate binding sites located predominantly in the 3'-untranslated regions (UTR). Paradoxically, miRNA targets are also polysome-associated. We studied the polysome association by the comparative translationally less-active light- and more-active heavy-polysome profiling of a wild type (WT) human cell line and its isogenic mutant (MT) with a disrupted DICER1 gene and, thus, mature miRNA production. As expected, the open reading frame (ORF) length is a major determinant of light- to heavy-polysome mRNA abundance ratios, but is rendered less powerful in WT than in MT cells by miRNA-regulatory activities. We also observed that miRNAs tend to target mRNAs with longer ORFs, and that adjusting the mRNA abundance ratio with the ORF length improves its correlation with the 3'-UTR miRNA-binding-site count. In WT cells, miRNA-targeted mRNAs exhibit higher abundance in light relative to heavy polysomes, i.e., light-polysome enrichment. In MT cells, the DICER1 disruption not only significantly abrogated the light-polysome enrichment, but also narrowed the mRNA abundance ratio value range. Additionally, the abrogation of the enrichment due to the DICER1 gene disruption, i.e., the decreases of the ORF-length-adjusted mRNA abundance ratio from WT to MT cells, exhibits a nearly perfect linear correlation with the 3'-UTR binding-site count. Transcription factors and protein kinases are the top two most enriched mRNA groups. Taken together, the results provide evidence for the light-polysome enrichment of miRNA-targeted mRNAs to reconcile polysome association and moderate translation inhibition, and that ORF length is an important, though currently under-appreciated, transcriptome regulation parameter.
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Affiliation(s)
- Tingzeng Wang
- Department of Environmental Toxicology, and The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX 79416, USA; (T.W.); (S.T.)
| | - Shuangmei Tian
- Department of Environmental Toxicology, and The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX 79416, USA; (T.W.); (S.T.)
| | - Elena B. Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (E.B.T.); (A.L.K.)
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; (E.B.T.); (A.L.K.)
| | - Jing J. Wang
- Department of Cancer Biology and Genetics, James Comprehensive Cancer Center, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA;
| | - Fangyuan Zhang
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79416, USA;
| | - Degeng Wang
- Department of Environmental Toxicology, and The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX 79416, USA; (T.W.); (S.T.)
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Lambert N, Kengne-Ouafo JA, Rissy WM, Diane U, Murithi K, Kimani P, Awe OI, Dillman A. Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.30.498338. [PMID: 35794887 PMCID: PMC9258287 DOI: 10.1101/2022.06.30.498338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The clinical presentation overlap between malaria and COVID-19 poses special challenges for rapid diagnosis in febrile children. In this study, we collected RNA-seq data of children with malaria and COVID-19 infection from the public databases as raw data in fastq format paired end files. A group of six, five and two biological replicates of malaria, COVID-19 and healthy donors respectively were used for the study. We conducted differential gene expression analysis to visualize differences in the expression profiles. Using edgeR, we explored particularly gene expression levels in different phenotype groups and found that 1084 genes and 2495 genes were differentially expressed in the malaria samples and COVID-19 samples respectively when compared to healthy controls. The highly expressed gene in the COVID-19 group we found CD151 gene which is facilitates in T cell proliferation, while in the malaria group, among the highly expressed gene we identified GBP5 gene which involved in inflammatory response and response to bacterium. By comparing both malaria and COVID-19 infections, the overlap of 62 differentially expressed genes patterns were identified. Among them, three genes (ENSG00000234998, H2AC19 and TXNDC5) were highly upregulated in both infections. Strikingly, we observed 13 genes such as HBQ1, HBM, SLC7A5, SERINC2, ATP6V0C, ST6GALNAC4, RAD23A, PNPLA2, GAS2L1, TMEM86B, SLC6A8, UBALD1, RNF187 were downregulated in children with malaria and uniquely upregulated in children with COVID-19, thus may be further validated as potential biomarkers to delineate COVID-19 from malaria-related febrile infection. The hemoglobin complexes and lipid metabolism biological pathways are highly expressed in both infections. Our study provided new insights for further investigation of the biological pattern in hosts with malaria and COVID-19 coinfection.
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Affiliation(s)
- Nzungize Lambert
- Liverpool School of Tropical Medicine Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591, Cameroon
- Synthetic Biology and Omics Data Center, SynbioRwanda, Rwanda
| | - Jonas A. Kengne-Ouafo
- Liverpool School of Tropical Medicine Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591, Cameroon
| | - Wesonga Makokha Rissy
- African Institute of biomedical science and technology (AiBST), Wilkins Hospital, Block C, Corner J. Tongogara and R. Zimbabwe
- Chinhoyi University of Technology (CUT), P.BAG 7724, Zimbabwe
| | | | - Ken Murithi
- International Centre of Insect Physiology and Ecology (ICIPE) P.O. Box 30772-00100, Kenya
| | - Peter Kimani
- International Centre of Insect Physiology and Ecology (ICIPE) P.O. Box 30772-00100, Kenya
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Mining Candidate Genes Related to Heavy Metals in Mature Melon ( Cucumis melo L.) Peel and Pulp Using WGCNA. Genes (Basel) 2022; 13:genes13101767. [PMID: 36292652 PMCID: PMC9602089 DOI: 10.3390/genes13101767] [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: 08/09/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/04/2022] Open
Abstract
The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H+-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT–PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.
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Cheng Z, Liu Z, Xu Y, Ma L, Chen J, Gou J, Su L, Wu W, Chen Y, Yu W, Wang P. Fine mapping and identification of the candidate gene BFS for fruit shape in wax gourd (Benincasa hispida). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3983-3995. [PMID: 34480584 DOI: 10.1007/s00122-021-03942-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/18/2021] [Indexed: 05/18/2023]
Abstract
Non-synonymous mutations in the BFS gene, which encodes the IQD protein, are responsible for the shape of wax gourd fruits. Fruit shape is an important agronomic trait in wax gourds. Therefore, in this study, we employed bulked segregant analysis (BSA) to identify a candidate gene for fruit shape in wax gourds within F2 populations derived by crossing GX-71 (long cylindrical fruit, fruit shape index = 4.56) and MY-1 (round fruit, fruit shape index = 1.06) genotypes. According to BSA, the candidate gene is located in the 17.18 Mb region on chromosome 2. Meanwhile, kompetitive allele-specific PCR (KASP) markers were used to reduce it to a 19.6 Kb region. Only one gene was present within the corresponding region of the reference genome, namely Bch02G016830 (designated BFS). Subsequently, BFS was sequenced in six wax gourd varieties with different fruit shapes. Sequence analysis revealed two non-synonymous mutations in the round wax gourd and one non-synonymous mutation in the cylindrical wax gourd. Quantitative real‑time PCR (qRT-PCR) analysis further showed that the expression of BFS in round fruits was significantly higher than in long cylindrical fruits at the ovary formation stage. Therefore, BFS is a candidate gene for determination wax gourd shape. The predicted protein encoded by the BFS gene belongs to the IQ67-domain protein family, which have the structural characteristics of scaffold proteins and coordinate Ca2+ CaM signaling from the membrane to the nucleus. Ultimately, two derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to facilitate marker-assisted selection for wax gourds breeding.
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Affiliation(s)
- Zhikui Cheng
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Zhengguo Liu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Yuanchao Xu
- SinoDutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lianlian Ma
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Jieying Chen
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Jiquan Gou
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Liwen Su
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Wenting Wu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Yong Chen
- Institute for New Rural Development, Guangxi University, Guangxi, 530004, China
| | - Wenjin Yu
- College of Agriculture, Guangxi University, Guangxi, 530004, China
| | - Peng Wang
- College of Agriculture, Guangxi University, Guangxi, 530004, China.
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Guangxi, 530004, China.
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Lucero L, Ferrero L, Fonouni-Farde C, Ariel F. Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps. THE NEW PHYTOLOGIST 2021; 229:1251-1260. [PMID: 32880949 DOI: 10.1111/nph.16903] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/05/2020] [Indexed: 05/27/2023]
Abstract
The extraordinary maturation in high-throughput sequencing technologies has revealed the existence of a complex network of transcripts in eukaryotic organisms, including thousands of long noncoding (lnc) RNAs with little or no protein-coding capacity. Subsequent discoveries have shown that lncRNAs participate in a wide range of molecular processes, controlling gene expression and protein activity though direct interactions with proteins, DNA or other RNA molecules. Although significant advances have been achieved in the understanding of lncRNA biology in the animal kingdom, the functional characterization of plant lncRNAs is still in its infancy and remains a major challenge. In this review, we report emerging functional and mechanistic paradigms of plant lncRNAs and partner molecules, and discuss how cutting-edge technologies may help to identify and classify yet uncharacterized transcripts into functional groups.
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Affiliation(s)
- Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Lucía Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, 3000, Argentina
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