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Fan K, Qian Z, He Y, Chen J, Ye F, Zhu X, Lin W, Cui L, Lan T, Li Z. Comprehensive molecular evolutionary analysis of small heat shock proteins in five diploid Gossypium species. THE PLANT GENOME 2024:e20478. [PMID: 38863371 DOI: 10.1002/tpg2.20478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 06/13/2024]
Abstract
The small heat shock proteins (sHSPs) are important components in plant growth and development, and stress response. However, a systematical understanding of the sHSP family is yet to be reported in five diploid Gossypium species. In this study, 34 GlsHSPs, 36 GrsHSPs, 37 GtsHSPs, 37 GasHSPs, and 38 GhesHSPs were identified in Gossypium longicalyx, Gossypium raimondii, Gossypium turneri, Gossypium arboreum, and Gossypium herbaceum, respectively. These sHSP members can be clustered into 10 subfamilies. Different subfamilies had different member numbers, motif distributions, gene structures, gene duplication events, gene loss numbers, and cis-regulatory elements. Besides, the paleohexaploidization event in cotton ancestor led to expanding the sHSP members and it was also inherited by five diploid Gossypium species. After the cotton ancestor divergence, the sHSP members had the relatively conserved evolution in five diploid Gossypium species. The comprehensive evolutionary history of the sHSP family was revealed in five diploid Gossypium species. Furthermore, several GasHSPs and GhesHSPs were important candidates in plant growth and development, and stress response. These current findings can provide valuable information for the molecular evolution and further functional research of the sHSP family in cotton.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhengyi Qian
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuxi He
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayuan Chen
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fangting Ye
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaogang Zhu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lili Cui
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Tao Lan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhaowei Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [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: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
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Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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3
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Coxe T, Burks DJ, Singh U, Mittler R, Azad RK. Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using the Arabidopsis thaliana Genome. PLANTS (BASEL, SWITZERLAND) 2024; 13:582. [PMID: 38475429 DOI: 10.3390/plants13050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
The utmost goal of selecting an RNA-Seq alignment software is to perform accurate alignments with a robust algorithm, which is capable of detecting the various intricacies underlying read-mapping procedures and beyond. Most alignment software tools are typically pre-tuned with human or prokaryotic data, and therefore may not be suitable for applications to other organisms, such as plants. The rapidly growing plant RNA-Seq databases call for the assessment of the alignment tools on curated plant data, which will aid the calibration of these tools for applications to plant transcriptomic data. We therefore focused here on benchmarking RNA-Seq read alignment tools, using simulated data derived from the model organism Arabidopsis thaliana. We assessed the performance of five popular RNA-Seq alignment tools that are currently available, based on their usage (citation count). By introducing annotated single nucleotide polymorphisms (SNPs) from The Arabidopsis Information Resource (TAIR), we recorded alignment accuracy at both base-level and junction base-level resolutions for each alignment tool. In addition to assessing the performance of the alignment tools at their default settings, accuracies were also recorded by varying the values of numerous parameters, including the confidence threshold and the level of SNP introduction. The performances of the aligners were found consistent under various testing conditions at the base-level accuracy; however, the junction base-level assessment produced varying results depending upon the applied algorithm. At the read base-level assessment, the overall performance of the aligner STAR was superior to other aligners, with the overall accuracy reaching over 90% under different test conditions. On the other hand, at the junction base-level assessment, SubRead emerged as the most promising aligner, with an overall accuracy over 80% under most test conditions.
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Affiliation(s)
- Tallon Coxe
- Department of Biological Sciences and BioDiscovery Institute, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017, USA
| | - David J Burks
- Department of Biological Sciences and BioDiscovery Institute, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017, USA
| | - Utkarsh Singh
- Texas Academy of Mathematics and Science, University of North Texas, Denton, TX 76203, USA
| | - Ron Mittler
- The Division of Plant Science and Technology, and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center University of Missouri, 1201 Rollins St., Columbia, MO 65201, USA
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017, USA
- Department of Mathematics, University of North Texas, Denton, TX 76203-5017, USA
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4
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Huang P, Yu X, Liu H, Ding M, Wang Z, Xu JR, Jiang C. Regulation of TRI5 expression and deoxynivalenol biosynthesis by a long non-coding RNA in Fusarium graminearum. Nat Commun 2024; 15:1216. [PMID: 38332031 PMCID: PMC10853542 DOI: 10.1038/s41467-024-45502-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
Deoxynivalenol (DON) is the most frequently detected mycotoxin in cereal grains and processed food or feed. Two transcription factors, Tri6 and Tri10, are essential for DON biosynthesis in Fusarium graminearum. In this study we conduct stranded RNA-seq analysis with tri6 and tri10 mutants and show that Tri10 acts as a master regulator controlling the expression of sense and antisense transcripts of TRI6 and over 450 genes with diverse functions. TRI6 is more specific for regulating TRI genes although it negatively regulates TRI10. Two other TRI genes, including TRI5 that encodes a key enzyme for DON biosynthesis, also have antisense transcripts. Both Tri6 and Tri10 are essential for TRI5 expression and for suppression of antisense-TRI5. Furthermore, we identify a long non-coding RNA (named RNA5P) that is transcribed from the TRI5 promoter region and is also regulated by Tri6 and Tri10. Deletion of RNA5P by replacing the promoter region of TRI5 with that of TRI12 increases TRI5 expression and DON biosynthesis, indicating that RNA5P suppresses TRI5 expression. However, ectopic constitutive overexpression of RNA5P has no effect on DON biosynthesis and TRI5 expression. Nevertheless, elevated expression of RNA5P in situ reduces TRI5 expression and DON production. Our results indicate that TRI10 and TRI6 regulate each other's expression, and both are important for suppressing the expression of RNA5P, a long non-coding RNA with cis-acting inhibitory effects on TRI5 expression and DON biosynthesis in F. graminearum.
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Affiliation(s)
- Panpan Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiao Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huiquan Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingyu Ding
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zeyi Wang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Cong Jiang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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5
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Liao Z, Zhang Q, Yang L, Li H, Mo W, Song Z, Huang X, Wen S, Cheng X, He M. Increased hsa-miR-100-5p Expression Improves Hepatocellular Carcinoma Prognosis in the Asian Population with PLK1 Variant rs27770A>G. Cancers (Basel) 2023; 16:129. [PMID: 38201556 PMCID: PMC10778516 DOI: 10.3390/cancers16010129] [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: 09/26/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) has the highest incidence and mortality in the Asian population, and race is an independent risk factor affecting survival time in liver cancer. Micro RNAs (miRNAs) are remarkably dysregulated in HCC and closely associated with HCC prognosis. Recent studies show that genetic variability between ethnic groups may result in differences in the specificity of HCC miRNA biomarkers. Here, we reveal a high expression level of hsa-miR-100-5p, an HCC prognosis-related miRNA, which improves HCC prognosis in the Asian Population with Polo-like kinase 1 (PLK1) variant rs27770A>G. In this study, we discovered that hsa-miR-100-5p was downregulated in various HCC cell lines. While mimics transient transfection and mouse liver cancer model confirmed the interaction between hsa-miR-100-5p and PLK1, a stratified analysis based on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data suggest both low hsa-miR-100-5p expression level and high PLK1 expression level associated with poor HCC prognosis, especially in the Asian population. According to the 1000 Genomes Project database, the SNP rs27770 located in 3'UTR of PLK1 had a significantly higher G allele frequency in the East Asian population. Bioinformatics analysis suggested that rs27770 A>G affects PLK1 mRNA secondary structure and alters the hsa-miR-100-5p/PLK1 interaction by forming an additional seedless binding site. This racial variation caused PLK1 to be more vulnerable to hsa-miR-100-5p inhibition, resulting in hsa-miR-100-5p being more favorable for HCC prognosis in the Asian population.
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Affiliation(s)
- Zhouxiang Liao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Qi Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Lichao Yang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Hui Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Wanling Mo
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Zhenyu Song
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Xuejing Huang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Sha Wen
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Xiaojing Cheng
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Life Sciences Institute, Guangxi Medical University, Nanning 530021, China
| | - Min He
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning 530021, China
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Ataei A, Tahsili M, Hayadokht G, Daneshvar M, Mohammadi Nour S, Soofi A, Masoudi A, Kabiri M, Natami M. Targeting long noncoding RNAs in neuroblastoma: Progress and prospects. Chem Biol Drug Des 2023; 102:640-652. [PMID: 37291742 DOI: 10.1111/cbdd.14263] [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: 02/04/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 06/10/2023]
Abstract
Neuroblastoma (NB) is the third most prevalent tumor that mostly influences infants and young children. Although different treatments have been developed for the treatment of NB, high-risk patients have been reported to have low survival rates. Currently, long noncoding RNAs (lncRNAs) have shown an attractive potential in cancer research and a party of investigations have been performed to understand mechanisms underlying tumor development through lncRNA dysregulation. Researchers have just newly initiated to exhibit the involvement of lncRNAs in NB pathogenesis. In this review article, we tried to clarify the point we stand with respect to the involvement of lncRNAs in NB. Moreover, implications for the pathologic roles of lncRNAs in the development of NB have been discussed. It seems that some of these lncRNAs have promising potential to be applied as biomarkers for NB prognosis and treatment.
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Affiliation(s)
- Ali Ataei
- School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Golsa Hayadokht
- School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Alireza Masoudi
- Department of Laboratory Sciences, Faculty of Alied Medical Sciences, Qom University of Medical Sciences, Qom, Iran
| | - Maryam Kabiri
- Faculty of Medicine, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Xia L, Li C, Zhao Y, Zhang W, Hu C, Qu Y, Li H, Yan J, Zhou K, Li P. Expression analysis of alpha keratins and corneous beta-protein genes during embryonic development of Gekko japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101116. [PMID: 37567027 DOI: 10.1016/j.cbd.2023.101116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
Epidermal appendages of birds and reptiles, including claws, feathers, scales, and setae, are primarily composed of alpha keratins (KRTs) and corneous beta-proteins (CBPs). A comprehensive and systematic knowledge of KRTs and CBPs in Schlegel's Japanese gecko (Gekko japonicus) is still lacking. In this study, 22 candidate Gecko japonicus keratin (GjKRT) family genes (12 type I genes, 10 type II genes) were identified in the G. japonicus genome. The majority of GjKRT genes across various subgroups had undergone a prolonged and highly conservative evolutionary process. Through a combination of morphological observation, RNA-seq analysis, and qRT-PCR assay, it was possible to discern the dynamic alterations in the expression of GjKRTs and Gecko japonicus corneous beta-proteins genes (GjCBPs). These findings strongly indicate that GjKRTs gradually accumulate to constitute an α-layer, which is subsequently succeeded by the formation of the corneous beta layer containing GjCBPs at late stages (40-42) of embryonic development. The epidermal appendages in G. japonicus may result from the joint accumulation of KRTs and CBPs, with stages 40-42 being critical for their development. These findings provide novel insights into KRTs and CBPs of G. japonicus and offer a foundation for investigating the functions of GjKRT and GjCBP gene families. Furthermore, this knowledge contributes to unraveling the molecular mechanisms underlying the formation of epidermal appendages in G. japonicus.
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Affiliation(s)
- Longjie Xia
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Chao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Yue Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Wenyi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Yanfu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, PR China.
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8
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Rogalska ME, Vivori C, Valcárcel J. Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects. Nat Rev Genet 2023; 24:251-269. [PMID: 36526860 DOI: 10.1038/s41576-022-00556-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/23/2022]
Abstract
The removal of introns from mRNA precursors and its regulation by alternative splicing are key for eukaryotic gene expression and cellular function, as evidenced by the numerous pathologies induced or modified by splicing alterations. Major recent advances have been made in understanding the structures and functions of the splicing machinery, in the description and classification of physiological and pathological isoforms and in the development of the first therapies for genetic diseases based on modulation of splicing. Here, we review this progress and discuss important remaining challenges, including predicting splice sites from genomic sequences, understanding the variety of molecular mechanisms and logic of splicing regulation, and harnessing this knowledge for probing gene function and disease aetiology and for the design of novel therapeutic approaches.
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Affiliation(s)
- Malgorzata Ewa Rogalska
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Claudia Vivori
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- The Francis Crick Institute, London, UK
| | - Juan Valcárcel
- Genome Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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9
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Wei H, Liu G, Qin J, Zhang Y, Chen J, Zhang X, Yu C, Chen Y, Lian B, Zhong F, Movahedi A, Zhang J. Genome-wide characterization, chromosome localization, and expression profile analysis of poplar non-specific lipid transfer proteins. Int J Biol Macromol 2023; 231:123226. [PMID: 36641014 DOI: 10.1016/j.ijbiomac.2023.123226] [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: 11/12/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023]
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are small and have a broad biological function involved in reproductive development and abiotic stress resistance. Although a small part of plant nsLTPs have been identified, these proteins have not been characterized in poplar at the genomic level. A genome-wide characterization and expression identification of poplar nsLTP members were performed in this study. A total of 42 poplar nsLTP genes were identified from the poplar genome. A comprehensive analysis of poplar nsLTPs was conducted by a phylogenetic tree, duplication events, gene structures, and conserved motifs. The cis-elements of poplar nsLTPs were predicted to respond to light, hormone, and abiotic stress. Many transcription factors (TFs) were identified to interact with poplar nsLTP cis-elements. The tested poplar nsLTPs were expressed in leaves, stems, and roots, but their expression levels differed among tested tissues. Most poplar nsLTP expression levels were changed by abiotic stress, implying that poplar nsLTP may be involved in abiotic stress resistance. Network analysis showed that poplar nsLTPs are putative genes involved in fatty acid (FA) metabolism. This research provides sight into the further study to explain the regulatory mechanism of the poplar nsLTPs.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Jin Qin
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Yanyan Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
| | - Jinxin Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Xingyue Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Bolin Lian
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
| | - Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China.
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10
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Gao S, Wang Y, Zeng Z, Zhang M, Yi N, Liu B, Wang R, Long S, Gong J, Liu T, Xu Y. Integrated bioinformatic and physiological analyses reveal the pivotal role of hydrogen sulfide in enhancing low-temperature tolerance in alfalfa. PHYSIOLOGIA PLANTARUM 2023; 175:e13885. [PMID: 36852715 DOI: 10.1111/ppl.13885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/12/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen sulfide (H2 S) is an important gaseous signal molecule that regulates plant growth and stress resistance. However, research on the H2 S synthase (HSase) genes is still limited in the model legume plant Medicago truncatula Gaertn. In the present study, a total of 40 HSase family members were first identified and analyzed in the M. truncatula genome, and these genes distributed across eight chromosomes and were clustered into five groups (I-V) based on their conserved gene structures and protein motifs. Expression analysis revealed that the MtHSase genes were expressed in all the tested abiotic stresses, albeit with expression level differences. This study also showed that H2 S improves low temperature tolerance of alfalfa seedlings by regulating the antioxidant defense system and enhancing photosynthetic capacity. Thus, the study provides new insights into how the H2 S signal regulates tolerance to low-temperature stress and provides the basis for further gene function and detection.
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Affiliation(s)
- Shuanghong Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Yifan Wang
- College of Agronomy, Northwest A&F University, Yangling, People's Republic of China
| | - Zhen Zeng
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Menglei Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Na Yi
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Bowen Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Ruijia Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Si Long
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Jiongjiong Gong
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Tieyuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
| | - Yuefei Xu
- College of Grassland Agriculture, Northwest A&F University, Yangling, People's Republic of China
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11
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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12
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Guo J, Wu Y, Wang T, Xin Y, Wang G, Zhou Q, Xu LA. GbFLSa overexpression negatively regulates proanthocyanin biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1093656. [PMID: 36875575 PMCID: PMC9975577 DOI: 10.3389/fpls.2023.1093656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Flavonoids are important secondary metabolites with extensive pharmacological functions. Ginkgo biloba L. (ginkgo) has attracted extensive attention because of its high flavonoid medicinal value. However, little is understood about ginkgo flavonol biosynthesis. Herein, we cloned the full-length gingko GbFLSa gene (1314 bp), which encodes a 363 amino acid protein that has a typical 2-oxoglutarate (2OG)-Fe(II) oxygenase region. Recombinant GbFLSa protein with a molecular mass of 41 kDa was expressed in Escherichia coli BL21(DE3). The protein was localized to the cytoplasm. Moreover, proanthocyanins, including catechin, epicatechin, epigallocatechin and gallocatechin, were significantly less abundant in transgenic poplar than in nontransgenic (CK) plants. In addition, dihydroflavonol 4-reductase, anthocyanidin synthase and leucoanthocyanidin reductase expression levels were significantly lower than those of their CK counterparts. GbFLSa thus encodes a functional protein that might negatively regulate proanthocyanin biosynthesis. This study helps elucidate the role of GbFLSa in plant metabolism and the potential molecular mechanism of flavonoid biosynthesis.
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Affiliation(s)
- Jing Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Yue Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Qi Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Forest Breeding Institute, Zhejiang Academy of Forestry, Hangzhou, China
| | - Li-An Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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13
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Anbari DM, Al-Harithy RN. Ghrelin intronic lncRNAs, lnc-GHRL-3:2 and lnc-GHRL-3:3, as novel biomarkers in type 2 diabetes mellitus. Arch Physiol Biochem 2023; 129:241-245. [PMID: 32921167 DOI: 10.1080/13813455.2020.1817095] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND We aim to identify circulating lncRNAs located in the region of the ghrelin (GHRL) gene that play a role in the development of T2DM. METHODS Bioinformatic tool was used to identify candidates GHRL-lncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to compare the expression levels of selected lncRNAs on diabetic patients and non-diabetic controls.Receiver operating characteristic (ROC) curve analysis was performed to evaluate the discriminatory power of selected GHRL-lncRNAs. RESULTS The bioinformatic analysis predicted three antisense and eight sense-intronic GHRL- lncRNAs. Two differentially expressed GHRL-lncRNAs were detected in diabetic patients. The expression levels of lnc-GHRL-3:2, lnc-GHRL-3:3, and the GHRL mRNA were significantly (p ≤ .0001) lower in the diabetic patients. ROC analysis showed that the area under the curve (AUC) value was 0.93 for lnc-GHRL-3:2 and 0.90 for lnc-GHRL-3:3. CONCLUSION lnc-GHRL-3:2 and lnc-GHRL-3:3 are novel biomarkers and might play a regulatory role in T2DM pathogenesis.
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Affiliation(s)
- Dalia M Anbari
- Department of Biochemistry, King AbdulAziz University, Jeddah, Saudi Arabia
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14
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Liu Y, Huang Y, Li Z, Feng M, Ge W, Zhong C, Xue R. Genome-wide identification of the TGA genes in common bean ( Phaseolus vulgaris) and revealing their functions in response to Fusarium oxysporum f. sp. phaseoli infection. Front Genet 2023; 14:1137634. [PMID: 36755571 PMCID: PMC9901207 DOI: 10.3389/fgene.2023.1137634] [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: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
Fusarium wilt, which affects common bean all across the world, is caused by Fusarium oxysporum f. sp. Phaseoli (Fop). It is necessary to have functional genes in response to Fop infection because they might be used to manage disease. As a crucial regulator, TGA-binding transcription factor (TGA) is engaged in the defense mechanism of plants against pathogens. The role of TGA regulators in common bean in response to Fop infection, however, has not been documented. Hence, we performed genome-wide identified and characterized eight TGA genes in common bean. In this study, eight PvTGA genes were distributed on six chromosomes and classified into four subgroups. The PvTGA genes have the same conserved bZIP and DOG1 domains, but there are specific sequence structures in different PvTGAs. Phylogenetic and synteny analysis explained that PvTGA gene has a close genetic relationship with legume TGAs and that PvTGA03 and PvTGA05 may play an important role in evolution. Transcriptome data explained that expression levels of PvTGA genes showed diversity in different tissues. After Fop inoculation, the expression levels of PvTGA03 and PvTGA07 were significantly different between resistant and susceptible genotypes. Under SA treatment, the expression levels of PvTGA03, PvTGA04, PvTGA06, PvTGA07 and PvTGA08 were significantly different. These results imply that PvTGA03 and PvTGA07 play key roles in SA-mediated resistance to Fusarium wilt. Together, these findings advance knowledge of the PvTGA gene family in common bean and will help future studies aimed at reducing Fusarium wilt.
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Affiliation(s)
- Yu Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, China,Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Yuning Huang
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Zhao Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Ming Feng
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Weide Ge
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China
| | - Chao Zhong
- College of Agronomy, Shenyang Agricultural University, Shenyang, China,*Correspondence: Chao Zhong, ; Renfeng Xue,
| | - Renfeng Xue
- Crop Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China,Liaoning Provincial Key Laboratory of Miscellaneous Grain Germplasm Innovation and Genetic Breeding, Shenyang, China,*Correspondence: Chao Zhong, ; Renfeng Xue,
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15
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Bo S, Sun Q, Ning P, Yuan N, Weng Y, Liang Y, Wang H, Lu Z, Li Z, Zhao X. A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA. Front Genet 2023; 14:1151172. [PMID: 36923795 PMCID: PMC10008863 DOI: 10.3389/fgene.2023.1151172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5'and 3'untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5'and 3'UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%-80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5'and 3'UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process.
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Affiliation(s)
- Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Qiuying Sun
- Department of Oncology, Inner Mongolia Cancer Hospital and The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Pengfei Ning
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ningping Yuan
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Yujie Weng
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ying Liang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Huitao Wang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhongxian Li
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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16
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Bo S, Sun Q, Li Z, Aodun G, Ji Y, Wei L, Wang C, Lu Z, Zhang Q, Zhao X. Ubiquitous conservative interaction patterns between post-spliced introns and their mRNAs revealed by genome-wide interspecies comparison. Front Genet 2023; 14:1151703. [PMID: 37124607 PMCID: PMC10132729 DOI: 10.3389/fgene.2023.1151703] [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: 01/26/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Introns, as important vectors of biological functions, can influence many stages of mRNA metabolism. However, in recent research, post-spliced introns are rarely considered. In this study, the optimal matched regions between introns and their mRNAs in nine model organism genomes were investigated with improved Smith-Waterman local alignment software. Our results showed that the distributions of mRNA optimal matched frequencies were highly consistent or universal. There are optimal matched frequency peaks in the UTR regions, which are obvious, especially in the 3'-UTR. The matched frequencies are relatively low in the CDS regions of the mRNA. The distributions of the optimal matched frequencies around the functional sites are also remarkably changed. The centers of the GC content distributions for different sequences are different. The matched rate distributions are highly consistent and are located mainly between 60% and 80%. The most probable value of the optimal matched segments is about 20 bp for lower eukaryotes and 30 bp for higher eukaryotes. These results show that there are abundant functional units in the introns, and these functional units are correlated structurally with all kinds of sequences of mRNA. The interaction between the post-spliced introns and their corresponding mRNAs may play a key role in gene expression.
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Affiliation(s)
- Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Qiuying Sun
- Department of Oncology, Inner Mongolia Cancer Hospital and the Affiliated People’s Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhongxian Li
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Gerile Aodun
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Yucheng Ji
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Lihua Wei
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Chao Wang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- School of Life Science, Inner Mongolia University, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
- *Correspondence: Zhanyuan Lu, ; Qiang Zhang, ; Xiaoqing Zhao,
| | - Qiang Zhang
- College of Science, Inner Mongolia Agriculture University, Hohhot, China
- *Correspondence: Zhanyuan Lu, ; Qiang Zhang, ; Xiaoqing Zhao,
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- School of Life Science, Inner Mongolia University, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
- *Correspondence: Zhanyuan Lu, ; Qiang Zhang, ; Xiaoqing Zhao,
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17
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Li R, Song X, Gao S, Peng S. Analysis on the interactions between the first introns and other introns in mitochondrial ribosomal protein genes. Front Microbiol 2022; 13:1091698. [PMID: 36569058 PMCID: PMC9772267 DOI: 10.3389/fmicb.2022.1091698] [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: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
It is realized that the first intron plays a key role in regulating gene expression, and the interactions between the first introns and other introns must be related to the regulation of gene expression. In this paper, the sequences of mitochondrial ribosomal protein genes were selected as the samples, based on the Smith-Waterman method, the optimal matched segments between the first intron and the reverse complementary sequences of other introns of each gene were obtained, and the characteristics of the optimal matched segments were analyzed. The results showed that the lengths and the ranges of length distributions of the optimal matched segments are increased along with the evolution of eukaryotes. For the distributions of the optimal matched segments with different GC contents, the peak values are decreased along with the evolution of eukaryotes, but the corresponding GC content of the peak values are increased along with the evolution of eukaryotes, it means most introns of higher organisms interact with each other though weak bonds binding. By comparing the lengths and matching rates of optimal matched segments with those of siRNA and miRNA, it is found that some optimal matched segments may be related to non-coding RNA with special biological functions, just like siRNA and miRNA, they may play an important role in the process of gene expression and regulation. For the relative position of the optimal matched segments, the peaks of relative position distributions of optimal matched segments are increased during the evolution of eukaryotes, and the positions of the first two peaks exhibit significant conservatism.
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18
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Circulating Long Non-Coding RNAs Could Be the Potential Prognostic Biomarker for Liquid Biopsy for the Clinical Management of Oral Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14225590. [PMID: 36428681 PMCID: PMC9688117 DOI: 10.3390/cancers14225590] [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: 07/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) have little or no coding potential. These transcripts are longer than 200 nucleotides. Since lncRNAs are master regulators of almost all biological processes, recent evidence proves that aberrantly expressed lncRNAs are pathogenic for oral squamous cell carcinoma (OSCC) and other diseases. LncRNAs influence chromatin modifications, transcriptional modifications, post-transcriptional modifications, genomic imprinting, cell proliferation, invasion, metastasis, and apoptosis. Consequently, they have an impact on the disease transformation, progression, and morbidity in OSCC. Therefore, circulating lncRNAs could be the potential cancer biomarker for the better clinical management (diagnosis, prognosis, and monitoring) of OSCC to provide advanced treatment strategies and clinical decisions. In this review, we report and discuss the recent understandings and perceptions of dysregulated lncRNAs with a focus on their clinical significance in OSCC-disease monitoring and treatment. Evidence clearly indicates that a specific lncRNA expression signature could act as an indicator for the early prediction of diagnosis and prognosis for the initiation, progression, recurrence, metastasis and other clinical prognostic-factors (overall survival, disease-free survival, etc.) in OSCC. The present review demonstrates the current knowledge that all potential lncRNA expression signatures are molecular biomarkers for the early prediction of prognosis in OSCC. Finally, the review provides information about the clinical significance, challenges and limitations of the clinical usage of circulating lncRNAs in a liquid biopsy method in early, pre-symptomatic, sub-clinical, accurate OSCC prognostication. More studies on lncRNA are required to unveil the biology of the inherent mechanisms involved in the process of the development of differential prognostic outcomes in OSCC.
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Li J, Wu X, Ma H, Sun G, Ding P, Lu S, Zhang L, Yang P, Peng Y, Fu J, Wang L. New developments in non-exosomal and exosomal ncRNAs in coronary artery disease. Epigenomics 2022; 14:1355-1372. [PMID: 36514887 DOI: 10.2217/epi-2022-0201] [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] [Indexed: 12/15/2022] Open
Abstract
Aim & methods: Non-exosomal and exosomal ncRNAs have been reported to be involved in the regulation of coronary artery disease (CAD). Therefore, to explore the biological effects of non-exosomal/exosomal ncRNAs in CAD, the authors searched for studies published in the last 3 years on these ncRNAs in CAD and summarized their functions and mechanisms. Results: The authors summarized 120 non-exosomal ncRNAs capable of regulating CAD progression. In clinical studies, 47 non-exosomal and nine exosomal ncRNAs were able to serve as biomarkers for the diagnosis of CAD. Conclusion: Non-exosomal/exosomal ncRNAs are not only able to serve as biomarkers for CAD diagnosis but can also regulate CAD progression through ceRNA mechanisms and are a potential target for early clinical intervention in CAD.
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Affiliation(s)
- Jingru Li
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Xinyu Wu
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Haocheng Ma
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Guihu Sun
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Peng Ding
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Si Lu
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Lijiao Zhang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Ping Yang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Yunzhu Peng
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Jingyun Fu
- Department of Endocrinology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Luqiao Wang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
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20
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Hou Z, Li A, Huang C. Genome-wide identification, characterization and expression of HSP 20 gene family in dove. Front Genet 2022; 13:1011676. [PMID: 36267407 PMCID: PMC9576933 DOI: 10.3389/fgene.2022.1011676] [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: 08/04/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Davidia involucrata is a significant living fossil with high abiotic stress tolerance. Although heat shock protein 20 (HSP20) has already been linked to heat stress, nothing is known about HSP20 family protein activities in D. involucrata. The functional dynamics of the D. involucrata HSP20 (DiHSP20) gene family were identified and characterized using a thorough genome-wide investigation. From the genome of D. involucrata, a total of 42 HSP20 genes were identified, which are distributed across 16 chromosomes. The DiHSP20 proteins were grouped into seven separate subfamilies by our phylogenetic analysis, which was validated by the conserved motif composition and gene structure studies. Segmental duplication events were shown to play a crucial role in the expansion of the DiHSP20 gene family. Synteny analysis revealed that 19 DiHSP20 genes of D. involucrata shared a syntenic connection with Arabidopsis genes, 39 with C. acuminata genes, and just 6 with O. sativa genes. Additionally, heat stress differently enhanced the expression levels of D. involucrata HSP20 genes. After 1 hour of heat treatment, the expression levels of most DiHSP20 genes, particularly DiHSP20-7, DiHSP20-29, DiHSP20-30, DiHSP20-32, and DiHSP20-34, were dramatically increased, suggestted that they might be employed as heat tolerance candidate genes. Overall, these findings add to our knowledge of the HSP20 family genes and provide helpful information for breeding heat stress resistance in D. involucrata.
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Affiliation(s)
- Zhe Hou
- College of Landscape Engineering, SuZhou Polytechnic Institute of Agriculture, Suzhou, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Ang Li
- College of Landscape Engineering, SuZhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Changbing Huang
- College of Landscape Engineering, SuZhou Polytechnic Institute of Agriculture, Suzhou, China
- *Correspondence: Changbing Huang,
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21
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Gao Y, Li JN, Pu JJ, Tao KX, Zhao XX, Yang QQ. Genome-wide identification and characterization of the HSP gene superfamily in apple snails (Gastropoda: Ampullariidae) and expression analysis under temperature stress. Int J Biol Macromol 2022; 222:2545-2555. [DOI: 10.1016/j.ijbiomac.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/28/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022]
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22
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Amaldoss MJN, Yang JL, Koshy P, Unnikrishnan A, Sorrell CC. Inorganic nanoparticle-based advanced cancer therapies: promising combination strategies. Drug Discov Today 2022; 27:103386. [PMID: 36182068 DOI: 10.1016/j.drudis.2022.103386] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/15/2022] [Accepted: 09/24/2022] [Indexed: 11/17/2022]
Abstract
Inorganic nanoparticles for drug delivery in cancer treatment offer many potential advantages because they can maximize therapeutic effect through targeting ligands while minimizing off-target side-effects through drug adsorption and infiltration. Although inorganic nanoparticles were introduced as drug carriers, they have emerged as having the capacity for combined therapeutic capabilities, including anticancer effects through cytotoxicity, suppression of oncogenes and cancer cell signaling pathway inhibition. The most promising advanced strategies for cancer therapy are as synergistic platforms for RNA interference (siRNA, miRNA, shRNA) and as synergistic drug delivery agents for the inhibition of cancer cell signaling pathways. The present work summarizes relevant current work, the promise of which is suggested by a projected compound annual growth rate of ∼20% for drug delivery alone.
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Affiliation(s)
- Maria John Newton Amaldoss
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia; School of Materials Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia.
| | - Jia-Lin Yang
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Pramod Koshy
- School of Materials Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Charles C Sorrell
- School of Materials Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
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23
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AL-Juhani WS, Alharbi SA, Al Aboud NM, Aljohani AY. Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae. BMC Genomics 2022; 23:626. [PMID: 36045328 PMCID: PMC9434970 DOI: 10.1186/s12864-022-08850-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems.
Results
In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA.
We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs.
Conclusions
The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.
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24
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Wang W, Li N, Wang M, Zhao Y, Wu H, Shi J, Musa M, Chen X. Analysis of ceRNA networks during mechanical tension-induced osteogenic differentiation of periodontal ligament stem cells. Eur J Oral Sci 2022; 130:e12891. [PMID: 35969187 DOI: 10.1111/eos.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Abstract
The molecular mechanisms underlying osteogenic differentiation of periodontal ligament stem cells (PDLSCs) under mechanical tension remain unclear. This study aimed to identify a potential long non-coding ribonucleic acids (lncRNAs)/circular RNAs (circRNAs)-microRNAs (miRNAs)-messenger RNAs (mRNAs) network in mechanical tension-induced osteogenic differentiation of PDLSCs. PDLSCs were isolated from the healthy human periodontal ligament, identified, cultured, and exposed to tensile force. The expression of osteogenic markers was examined, and whole transcriptome sequencing was performed to identify the expression patterns of lncRNA, circRNA, miRNAs, and mRNAs. Enrichment analyses were also performed. Candidate targets of differentially expressed non-coding RNAs (ncRNAs) were predicted, and potential competitive endogenous RNA (ceRNA) networks were constructed by Cytoscape. We found that the osteogenic differentiation of PDLSCs was significantly enhanced under dynamic tension (magnitude: 12%, frequency: 0.7 Hz). Overall, 344 lncRNAs, 57 miRNAs, 41 circRNAs, and 70 mRNAs were differentially expressed in the tension group and the control group. Functional enrichment analysis showed that differentially expressed mRNAs were mainly enriched in osteogenesis-related and mechanical stress-related biological processes and signal transduction pathways (e.g., tumor necrosis factor [TNF] and Hippo signaling pathways). The lncRNA/circRNA-miRNA-mRNA networks were depicted, and potential key ceRNA networks were identified. Our findings may help to further explore the underlying regulatory mechanism of osteogenic differentiation of PDLSCs under mechanical tensile stress.
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Affiliation(s)
- Wenfang Wang
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Ning Li
- Department of Orthodontics, Yantai Stomatological Hospital Affiliated to Binzhou Medical College, Yantai, China
| | - Meijuan Wang
- Department of Anesthesiology, Second Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yunshan Zhao
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Hao Wu
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Jingyi Shi
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Mazen Musa
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xi Chen
- Department of Stomatology, First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, Xi'an, China
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25
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Wan T, Gong Y, Liu Z, Zhou Y, Dai C, Wang Q. Evolution of complex genome architecture in gymnosperms. Gigascience 2022; 11:6659718. [PMID: 35946987 PMCID: PMC9364684 DOI: 10.1093/gigascience/giac078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Gymnosperms represent an ancient lineage that diverged from early spermatophytes during the Devonian. The long fossil records and low diversity in living species prove their complex evolutionary history, which included ancient radiations and massive extinctions. Due to their ultra-large genome size, the whole-genome assembly of gymnosperms has only generated in the past 10 years and is now being further expanded into more taxonomic representations. Here, we provide an overview of the publicly available gymnosperm genome resources and discuss their assembly quality and recent findings in large genome architectures. In particular, we describe the genomic features most related to changes affecting the whole genome. We also highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns. Based on the results of relevant genomic studies of gymnosperms, we suggest additional efforts should be made toward exploring the genomes of medium-sized (5–15 gigabases) species. Lastly, more comparative analyses among high-quality assemblies are needed to understand the genomic shifts and the early species diversification of seed plants.
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Affiliation(s)
- Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China.,Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - Yanbing Gong
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Zhiming Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - YaDong Zhou
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Qingfeng Wang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
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26
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Complete chloroplast genome of the medicinal plant Cleome paradoxa R.Br. ex DC: Comparative Analysis, and Phylogenetic Relationships among the members of Cleomaceae. Gene 2022; 845:146851. [DOI: 10.1016/j.gene.2022.146851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022]
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27
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Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. PLANTS 2022; 11:plants11141869. [PMID: 35890506 PMCID: PMC9317152 DOI: 10.3390/plants11141869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/18/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
The Plicosepalus genus includes hemiparasitic mistletoe and belongs to the Loranthaceae family, and it has several medicinal uses. In the present study, we sequenced the complete plastomes of two species, Plicosepalus acaciae and Plicosepalus curviflorus, and compared them with the plastomes of photosynthetic species (hemiparasites) and nonphotosynthetic species (holoparasites) in the order Santalales. The complete chloroplast genomes of P. acaciae and P. curviflorus are circular molecules with lengths of 120,181 bp and 121,086 bp, respectively, containing 106 and 108 genes and 63 protein-coding genes, including 25 tRNA and 4 rRNA genes for each species. We observed a reduction in the genome size of P. acaciae and P. curviflorus and the loss of certain genes, although this reduction was less than that in the hemiparasite and holoparasitic cp genomes of the Santalales order. Phylogenetic analysis supported the taxonomic state of P. acaciae and P. curviflorus as members of the family Loranthaceae and tribe Lorantheae; however, the taxonomic status of certain tribes of Loranthaceae must be reconsidered and the species that belong to it must be verified. Furthermore, available chloroplast genome data of parasitic plants could help to strengthen efforts in weed management and encourage biotechnology research to improve host resistance.
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28
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Conteduca G, Cangelosi D, Coco S, Malacarne M, Baldo C, Arado A, Pinto R, Testa B, Coviello DA. NSD1 Mutations in Sotos Syndrome Induce Differential Expression of Long Noncoding RNAs, miR646 and Genes Controlling the G2/M Checkpoint. Life (Basel) 2022; 12:life12070988. [PMID: 35888078 PMCID: PMC9324496 DOI: 10.3390/life12070988] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 12/16/2022] Open
Abstract
An increasing amount of evidence indicates the critical role of the NSD1 gene in Sotos syndrome (SoS), a rare genetic disease, and in tumors. Molecular mechanisms affected by NSD1 mutations are largely uncharacterized. In order to assess the impact of NSD1 haploinsufficiency in the pathogenesis of SoS, we analyzed the gene expression profile of fibroblasts isolated from the skin samples of 15 SoS patients and of 5 healthy parents. We identified seven differentially expressed genes and five differentially expressed noncoding RNAs. The most upregulated mRNA was stratifin (SFN) (fold change, 3.9, Benjamini−Hochberg corrected p < 0.05), and the most downregulated mRNA was goosecoid homeobox (GSC) (fold change, 3.9, Benjamini−Hochberg corrected p < 0.05). The most upregulated lncRNA was lnc-C2orf84-1 (fold change, 4.28, Benjamini−Hochberg corrected p < 0.001), and the most downregulated lncRNA was Inc-C15orf57 (fold change, −0.7, Benjamini−Hochberg corrected p < 0.05). A gene set enrichment analysis reported the enrichment of genes involved in the KRAS and E2F signaling pathways, splicing regulation and cell cycle G2/M checkpoints. Our results suggest that NSD1 is involved in cell cycle regulation and that its mutation can induce the down-expression of genes involved in tumoral and neoplastic differentiation. The results contribute to defining the role of NSD1 in fibroblasts for the prevention, diagnosis and control of SoS.
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Affiliation(s)
- Giuseppina Conteduca
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Davide Cangelosi
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Simona Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy;
| | - Michela Malacarne
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Rute Pinto
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Barbara Testa
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
| | - Domenico A. Coviello
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (G.C.); (M.M.); (C.B.); (A.A.); (R.P.); (B.T.)
- Correspondence: ; Tel.: +39-010-5636-3977
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29
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Transcriptome-Guided Identification of Pectin Methyl-Esterase-Related Enzymes and Novel Molecular Processes Effectuating the Hard-to-Cook Defect in Common Bean ( Phaseolus vulgaris L.). Foods 2022; 11:foods11121692. [PMID: 35741889 PMCID: PMC9222787 DOI: 10.3390/foods11121692] [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: 04/27/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023] Open
Abstract
The hard-to-cook defect in common beans is dictated by the ability to achieve cell separation during cooking. Hydrolysis of pectin methyl-esters by the pectin methyl-esterase (PME) enzyme influences cell separation. However, the contributions of the PME enzyme and the cell wall to the hard-to-cook defect have not been studied using molecular tools. We compared relevant molecular processes in fast- and slow-cooking bean varieties to understand the mechanisms underpinning the hard-to-cook defect. A PME spectrophotometric assay showed minor differences in enzyme activity between varieties. Meanwhile, a PME HMMER search in the P. vulgaris genome unveiled 113 genes encoding PMEs and PME inhibitors (PMEIs). Through RNA sequencing, we compared the gene expression of the PME-related genes in both varieties during seed development. A PME (Phvul010g080300) and PMEI gene (Phvul005g007600) showed the highest expression in the fast- and slow-cooking beans, respectively. We further identified 2132 differentially expressed genes (DEGs). Genes encoding cell-wall-related enzymes, mainly glycosylphosphatidylinositol mannosyltransferase, xyloglucan O-acetyltransferase, pectinesterase, and callose synthase, ranked among the top DEGs, indicating novel relations to the hard-to-cook defect. Gene ontology mapping revealed hydrolase activity and protein phosphorylation as functional categories with the most abundant upregulated DEGs in the slow-cooking bean. Additionally, the cell periphery contained 8% of the DEGs upregulated in the slow-cooking bean. This study provides new insights into the role of pectin methyl-esterase-related genes and novel cell wall processes in the occurrence of the hard-to-cook defect.
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30
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Identification of TALE Transcription Factor Family and Expression Patterns Related to Fruit Chloroplast Development in Tomato ( Solanum lycopersicum L.). Int J Mol Sci 2022; 23:ijms23094507. [PMID: 35562896 PMCID: PMC9104321 DOI: 10.3390/ijms23094507] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
The TALE gene family is an important transcription factor family that regulates meristem formation, organ morphogenesis, signal transduction, and fruit development. A total of 24 genes of the TALE family were identified and analyzed in tomato. The 24 SlTALE family members could be classified into five BELL subfamilies and four KNOX subfamilies. SlTALE genes were unevenly distributed on every tomato chromosome, lacked syntenic gene pairs, and had conserved structures but diverse regulatory functions. Promoter activity analysis showed that cis-elements responsive to light, phytohormone, developmental regulation, and environmental stress were enriched in the promoter of SlTALE genes, and the light response elements were the most abundant. An abundance of TF binding sites was also enriched in the promoter of SlTALE genes. Phenotype identification revealed that the green shoulder (GS) mutant fruits showed significantly enhanced chloroplast development and chlorophyll accumulation, and a significant increase of chlorophyll fluorescence parameters in the fruit shoulder region. Analysis of gene expression patterns indicated that six SlTALE genes were highly expressed in the GS fruit shoulder region, and four SlTALE genes were highly expressed in the parts with less-developed chloroplasts. The protein-protein interaction networks predicted interaction combinations among these SlTALE genes, especially between the BELL subfamilies and the KNOX subfamilies, indicating a complex regulatory network of these SlTALE genes in chloroplast development and green fruit shoulder formation. In conclusion, our result provides detailed knowledge of the SlTALE gene for functional research and the utilization of the TALE gene family in fruit quality improvement.
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Liu RJ, Xu ZP, Li SY, Yu JJ, Feng NH, Xu B, Chen M. BAP1-Related ceRNA (NEAT1/miR-10a-5p/SERPINE1) Promotes Proliferation and Migration of Kidney Cancer Cells. Front Oncol 2022; 12:852515. [PMID: 35425712 PMCID: PMC9004599 DOI: 10.3389/fonc.2022.852515] [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: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 01/09/2023] Open
Abstract
Background BAP1 is an important tumor suppressor involved in various biological processes and is commonly lost or inactivated in clear-cell renal cell carcinoma (ccRCC). However, the role of the BAP1-deficient tumor competing endogenous RNA (ceRNA) network involved in ccRCC remains unclear. Thus, this study aims to investigate the prognostic BAP1-related ceRNA in ccRCC. Methods Raw data was obtained from the TCGA and the differentially expressed genes were screened to establish a BAP1-related ceRNA network. Subsequently, the role of the ceRNA axis was validated using phenotypic experiments. Dual-luciferase reporter assays and fluorescence in situ hybridization (FISH) assays were used to confirm the ceRNA network. Results Nuclear enriched abundant transcript 1 (NEAT1) expression was significantly increased in kidney cancer cell lines. NEAT1 knockdown significantly inhibited cell proliferation and migration, which could be reversed by miR-10a-5p inhibitor. Dual-luciferase reporter assay confirmed miR-10a-5p as a common target of NEAT1 and Serine protease inhibitor family E member 1 (SERPINE1). FISH assays revealed the co-localization of NEAT1 and miR-10a-5p in the cytoplasm. Additionally, the methylation level of SERPINE1 in ccRCC was significantly lower than that in normal tissues. Furthermore, SERPINE1 expression was positively correlated with multiple immune cell infiltration levels. Conclusions In BAP1-deficient ccRCC, NEAT1 competitively binds to miR-10a-5p, indirectly upregulating SERPINE1 expression to promote kidney cancer cell proliferation. Furthermore, NEAT1/miR-10a-5p/SERPINE1 were found to be independent prognostic factors of ccRCC.
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Affiliation(s)
- Rui-Ji Liu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Zhi-Peng Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Shu-Ying Li
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Cancer Hospital affiliate to School of Medicine, UESTC, Chengdu, China
| | - Jun-Jie Yu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Ning-Han Feng
- Department of Urology, Wuxi No.2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China.,Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China.,Nanjing Lishui District People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
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32
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Wang X, Dorjee T, Chen Y, Gao F, Zhou Y. The complete chloroplast genome sequencing analysis revealed an unusual IRs reduction in three species of subfamily Zygophylloideae. PLoS One 2022; 17:e0263253. [PMID: 35108324 PMCID: PMC8809528 DOI: 10.1371/journal.pone.0263253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
Tetraena mongolica, Zygophyllum xanthoxylon, and Z. fabago are three typical dryland plants with important ecological values in subfamily Zygophylloideae of Zygophyllaceae. Studies on the chloroplast genomes of them are favorable for understanding the diversity and phylogeny of Zygophyllaceae. Here, we sequenced and assembled the whole chloroplast genomes of T. mongolica, Z. xanthoxylon, and Z. fabago, and performed comparative genomic and phylogenetic analysis. The total size, structure, gene content and orders of these three chloroplast genomes were similar, and the three chloroplast genomes exhibited a typical quadripartite structure with a large single-copy region (LSC; 79,696–80,291 bp), a small single-copy region (SSC; 16,462–17,162 bp), and two inverted repeats (IRs; 4,288–4,413 bp). A total of 107 unique genes were identified from the three chloroplast genomes, including 70 protein-coding genes, 33 tRNAs, and 4 rRNAs. Compared with other angiosperms, the three chloroplast genomes were significantly reduced in overall length due to an unusual 16–24 kb shrinkage of IR regions and loss of the 11 genes which encoded subunits of NADH dehydrogenase. Genome-wide comparisons revealed similarities and variations between the three species and others. Phylogenetic analysis based on the three chloroplast genomes supported the opinion that Zygophyllaceae belonged to Zygophyllales in Fabids, and Z. xanthoxylon and Z. fabago belonged to Zygophyllum. The genome-wide comparisons revealed the similarity and variations between the chloroplast genomes of the three Zygophylloideae species and other plant species. This study provides a valuable molecular biology evidence for further studies of phylogenetic status of Zygophyllaceae.
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Affiliation(s)
- Xiaoyang Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Tashi Dorjee
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yiru Chen
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
| | - Yijun Zhou
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- * E-mail: (FG); (YZ)
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Ramakrishna G, Singh A, Kaur P, Yadav SS, Sharma S, Gaikwad K. Genome wide identification and characterization of small heat shock protein gene family in pigeonpea and their expression profiling during abiotic stress conditions. Int J Biol Macromol 2022; 197:88-102. [PMID: 34902444 DOI: 10.1016/j.ijbiomac.2021.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/26/2022]
Abstract
Small heat shock proteins as large multigene family are present ubiquitously among Archaea to Eukaryota. The sHSPs are molecular chaperones that maintain the proper protein folding and disaggregation of denatured proteins during stress conditions. In the present study, out of identified 38 sHSPs in the pigeonpea genome, the 20 are distributed across seven chromosomes while the remaining are located on unassembled scaffolds. These Cc_sHSPs are classified into 16 subfamilies. The cytoplasmic class-II is the largest sub-family with five Cc_sHSPs. The gene structure analysis revealed that Cc_sHSP genes specifically containing no or very few introns. The promoter analysis revealed the presence of various cis-acting elements responsible for developmental, biotic, and abiotic stress specific-induction of Cc_sHSPs. A total of one segmental duplication and four tandem duplication events are identified for Cc_sHSPs. The qRT-PCR based expression analysis of all 38 Cc_sHSP genes was conducted for diverse abiotic stress conditions. The Cc_sHSP genes are highly induced by heat, drought, cold, and salt stresses indicating a key role in mitigating the various abiotic stress responses. The divergence time of paralogous Cc_sHSPs ranged from 8.66 to 191.82 MYA. The present study can be a strong basis for the functional characterization of Cc_sHSPs.
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Affiliation(s)
- G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Anupam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Parampreet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sunishtha S Yadav
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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Zaynab M, Peng J, Sharif Y, Albaqami M, Al-Yahyai R, Fatima M, Nadeem MA, Khan KA, Alotaibi SS, Alaraidh IA, Shaikhaldein HO, Li S. Genome-Wide Identification and Expression Profiling of DUF221 Gene Family Provides New Insights Into Abiotic Stress Responses in Potato. FRONTIERS IN PLANT SCIENCE 2022; 12:804600. [PMID: 35126430 PMCID: PMC8811145 DOI: 10.3389/fpls.2021.804600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The domain of the unknown function 221 proteins regulate several processes in plants, including development, growth, hormone transduction mechanism, and abiotic stress response. Therefore, a comprehensive analysis of the potato genome was conducted to identify the deafness-dystonia peptide (DDP) proteins' role in potatoes. In the present study, we performed a genome-wide analysis of the potato domain of the unknown function 221 (DUF221) genes, including phylogenetic inferences, chromosomal locations, gene duplications, gene structures, and expression analysis. In our results, we identified 10 DDP genes in the potato genome. The phylogenetic analysis results indicated that StDDPs genes were distributed in all four clades, and clade IV was the largest clade. The gene duplication under selection pressure analysis indicated various positive and purifying selections in StDDP genes. The putative stu-miRNAs from different families targeting StDDPs were also predicted in the present study. Promoter regions of StDDP genes contain different cis-acting components involved in multiple stress responses, such as phytohormones and abiotic stress-responsive factors. The analysis of the tissue-specific expression profiling indicated the StDDPs gene expression in stem, root, and leaf tissues. We subsequently observed that StDDP4, StDDP5, and StDDP8 showed higher expressions in roots, stems, and leaves. StDDP5 exhibited high expression against heat stress response, and StDDP7 showed high transcript abundance against salt stress in potatoes. Under abscisic acid (ABA) and indole acetic acid (IAA) treatments, seven StDDP genes' expressions indicated that ABA and IAA performed important roles in immunity response. The expression profiling and real-time qPCR of stems, roots, and leaves revealed StDDPs' significant role in growth and development. These expression results of DDPs are primary functional analysis and present basic information for other economically important crops.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiaofeng Peng
- Instrument Analysis Center, Shenzhen University, Shenzhen, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rashid Al-Yahyai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Ibrahim A. Alaraidh
- Botany & Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Botany & Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Petschner P, Baksa D, Hullam G, Torok D, Millinghoffer A, Deakin JFW, Bagdy G, Juhasz G. A replication study separates polymorphisms behind migraine with and without depression. PLoS One 2021; 16:e0261477. [PMID: 34972135 PMCID: PMC8719675 DOI: 10.1371/journal.pone.0261477] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
The largest migraine genome-wide association study identified 38 candidate loci. In this study we assessed whether these results replicate on a gene level in our European cohort and whether effects are altered by lifetime depression. We tested SNPs of the loci and their vicinity with or without interaction with depression in regression models. Advanced analysis methods such as Bayesian relevance analysis and a neural network based classifier were used to confirm findings. Main effects were found for rs2455107 of PRDM16 (OR = 1.304, p = 0.007) and five intergenic polymorphisms in 1p31.1 region: two of them showed risk effect (OR = 1.277, p = 0.003 for both rs11209657 and rs6686879), while the other three variants were protective factors (OR = 0.4956, p = 0.006 for both rs12090642 and rs72948266; OR = 0.4756, p = 0.005 for rs77864828). Additionally, 26 polymorphisms within ADGRL2, 2 in REST, 1 in HPSE2 and 33 mostly intergenic SNPs from 1p31.1 showed interaction effects. Among clumped results representing these significant regions, only rs11163394 of ADGRL2 showed a protective effect (OR = 0.607, p = 0.002), all other variants were risk factors (rs1043215 of REST with the strongest effect: OR = 6.596, p = 0.003). Bayesian relevance analysis confirmed the relevance of intergenic rs6660757 and rs12128399 (p31.1), rs1043215 (REST), rs1889974 (HPSE2) and rs11163394 (ADGRL2) from depression interaction results, and the moderate relevance of rs77864828 and rs2455107 of PRDM16 from main effect analysis. Both main and interaction effect SNPs could enhance predictive power with the neural network based classifier. In summary, we replicated p31.1, PRDM16, REST, HPSE2 and ADGRL2 genes with classic genetic and advanced analysis methods. While the p31.1 region and PRDM16 are worthy of further investigations in migraine in general, REST, HPSE2 and ADGRL2 may be prime candidates behind migraine pathophysiology in patients with comorbid depression.
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Affiliation(s)
- Peter Petschner
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
- MTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Daniel Baksa
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
- SE-NAP2 Genetic Brain Imaging Migraine Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary
| | - Gabor Hullam
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Dora Torok
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
| | - Andras Millinghoffer
- MTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
- NAP-2-SE New Antidepressant Target Research Group, Semmelweis University, Budapest, Hungary
| | - J. F. William Deakin
- Neuroscience and Psychiatry Unit, Division of Neuroscience and Experimental Psychology, The University of Manchester and Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Gyorgy Bagdy
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
- MTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
- NAP-2-SE New Antidepressant Target Research Group, Semmelweis University, Budapest, Hungary
| | - Gabriella Juhasz
- Department of Pharmacodynamics, Faculty of Pharmacy, Semmelweis University, Budapest, Hungary
- MTA-SE Neuropsychopharmacology and Neurochemistry Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
- SE-NAP2 Genetic Brain Imaging Migraine Research Group, Hungarian Brain Research Program, Semmelweis University, Budapest, Hungary
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Zhang R, Zhong Y, Long SY, Yang QN, Zhou B, Rao L. Association between CDK8 gene polymorphisms and dilated cardiomyopathy in a Chinese Han population. Cardiovasc Diagn Ther 2021; 11:1036-1046. [PMID: 34815954 DOI: 10.21037/cdt-21-323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/30/2021] [Indexed: 02/05/2023]
Abstract
Background Dilated cardiomyopathy (DCM) is one of the most common types of cardiomyopathies. Various genes have been verified to be related to DCM, but the pathogenesis remains unclear. Cyclin-dependent-kinase 8 (CDK8), encoded by the CDK8 gene, is a transcriptional factor that regulates the phosphorylation of RNA polymerase II. It plays an important role in the transcription process and different signaling pathways. This study aimed to investigate the potential role of CDK8 gene polymorphisms in DCM susceptibility and prognosis in a Chinese Han population. Methods Two single nucleotide polymorphisms (SNPs) of CDK8, rs17083838 (A/G) and rs7992670 (A/G), were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 341 DCM patients and 381 healthy controls. Survival analysis was performed using Kaplan-Meier curves and Cox regression analysis. Results The frequencies of allele A of both SNPs rs17083838 and rs7992670 were increased in DCM patients compared to healthy controls (P<0.05). Genotypic frequencies of rs17083838 and rs7992670 were associated with the susceptibility to DCM in the codominant, and recessive models (P<0.05), and AA/AG genotypes of rs17083838 were also related to DCM susceptibility in the dominant model. AA/AG genotypes of rs17083838 and the AA genotype of rs7992670 in the dominant and recessive genetic models presented a correlation with the poor prognosis of DCM patients in both univariate (P<0.05) and multivariate analyses (P<0.05) after adjusting for age, gender, left ventricular end-diastolic diameter (LVEDD), and left ventricular ejection fraction (LVEF). Conclusions This research is the first to reveal that CDK8 gene polymorphisms might be related to DCM susceptibility and prognosis in the Chinese Han population.
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Affiliation(s)
- Ran Zhang
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, China
| | - Yue Zhong
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, China
| | - Si-Yu Long
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qin-Ni Yang
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Bin Zhou
- Laboratory of Molecular Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Center of Translational Medicine, Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Li Rao
- Department of Cardiology, West China Hospital of Sichuan University, Chengdu, China
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Zaynab M, Peng J, Sharif Y, Al-Yahyai R, Jamil A, Hussain A, Khan KA, Alotaibi SS, Li S. Expression profiling of pathogenesis-related Protein-1 (PR-1) genes from Solanum tuberosum reveals its critical role in phytophthora infestans infection. Microb Pathog 2021; 161:105290. [PMID: 34808276 DOI: 10.1016/j.micpath.2021.105290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 11/19/2022]
Abstract
Pathogen-related (PR) proteins are an integral part of plants' defense mechanisms against various types of biotic and abiotic stresses. A little is known about the importance of these PR proteins in potato defense mechanisms. In the current study, a total of 22 pathogenesis-related 1 genes were identified in the potato genome. All identified proteins possessed the CAP superfamily domain with some other motifs. The cis-acting elements analysis identified several stress-responsive elements, including MYB, ABRE, and MeJRE. The gene duplication events demonstrated purifying and positive selection pressure. Expression profiling showed high transcripts level in root compared to other tissues; however, some genes have tissue-specific expression. Furthermore, the PR-1-5 gene is transcriptionally induced under Phytophthora infestans stress and hormonal (ABA and IAA) treatments. The Real-Time qPCR analysis also validated the RNA-seq data results of genes with maximum expression in roots compared to leaves and stems. The current study results provided basic data for functional characterization and can also use as a reference study for other important crops.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 51807, China
| | - Jiaofeng Peng
- Instrument Analysis Center, Shenzhen University, Shenzhen, Guangdong, 51807, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Rashid Al-Yahyai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, PO Box 34, Al-Khod 123, Muscat, Oman
| | - Atka Jamil
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan
| | - Athar Hussain
- Genomics Lab, Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science(RCAMS), King Khalid University, P.O. Box9004, Abha61413, Saudi Arabia; Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box9004, Abha61413, Saudi Arabia; Department, Faculty of Science, King Khalid University, P.O. Box9004, Abha61413, Saudi Arabia
| | - Saqer S Alotaibi
- Department of Biotechnology, College of Science, Taif University, P.O.BOX 11099, Taif, 21944, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 51807, China.
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Hu Y, Zhang T, Liu Y, Li Y, Wang M, Zhu B, Liao D, Yun T, Huang W, Zhang W, Zhou Y. Pumpkin ( Cucurbita moschata) HSP20 Gene Family Identification and Expression Under Heat Stress. Front Genet 2021; 12:753953. [PMID: 34721541 PMCID: PMC8553033 DOI: 10.3389/fgene.2021.753953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Pumpkin (Cucurbita moschata) is an important cucurbit vegetable crop that has strong resistance to abiotic stress. While heat shock protein 20 (HSP20) has been implicated in vegetable response to heat stress, little is known regarding activity of HSP20 family proteins in C. moschata. Here, we performed a comprehensive genome-wide analysis to identify and characterize the functional dynamics of the Cucurbita moschata HSP20 (CmoHSP20) gene family. A total of 33 HSP20 genes distributed across 13 chromosomes were identified from the pumpkin genome. Our phylogenetic analysis determined that the CmoHSP20 proteins fell into nine distinct subfamilies, a division supported by the conserved motif composition and gene structure analyses. Segmental duplication events were shown to play a key role in expansion of the CmoHSP20 gene family. Synteny analysis revealed that 19 and 18 CmoHSP20 genes were collinear with those in the cucumber and melon genomes, respectively. Furthermore, the expression levels of pumpkin HSP20 genes were differentially induced by heat stress. The transcript level of CmoHSP20-16, 24 and 25 were down-regulated by heat stress, while CmoHSP20-7, 13, 18, 22, 26 and 32 were up-regulated by heat stress, which could be used as heat tolerance candidate genes. Overall, these findings contribute to our understanding of vegetable HSP20 family genes and provide valuable information that can be used to breed heat stress resistance in cucurbit vegetable crops.
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Affiliation(s)
- Yanping Hu
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Tingting Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Ying Liu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Yuxin Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Min Wang
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Baibi Zhu
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Daolong Liao
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Tianhai Yun
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Wenfeng Huang
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Wen Zhang
- Key Laboratory of Vegetable Biology of Hainan Province, Hainan Vegetable Breeding Engineering Technology Research Center, The Institute of Vegetables, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Yang Zhou
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
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Mehta SL, Chokkalla AK, Vemuganti R. Noncoding RNA crosstalk in brain health and diseases. Neurochem Int 2021; 149:105139. [PMID: 34280469 PMCID: PMC8387393 DOI: 10.1016/j.neuint.2021.105139] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
The mammalian brain expresses several classes of noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). These ncRNAs play vital roles in regulating cellular processes by RNA/protein scaffolding, sponging and epigenetic modifications during the pathophysiological conditions, thereby controlling transcription and translation. Some of these functions are the result of crosstalk between ncRNAs to form a competitive endogenous RNA network. These intricately organized networks comprise lncRNA/miRNA, circRNA/miRNA, or lncRNA/miRNA/circRNA, leading to crosstalk between coding and ncRNAs through miRNAs. The miRNA response elements predominantly mediate the ncRNA crosstalk to buffer the miRNAs and thereby fine-tune and counterbalance the genomic changes and regulate neuronal plasticity, synaptogenesis and neuronal differentiation. The perturbed levels and interactions of the ncRNAs could lead to pathologic events like apoptosis and inflammation. Although the regulatory landscape of the ncRNA crosstalk is still evolving, some well-known examples such as lncRNA Malat1 sponging miR-145, circRNA CDR1as sponging miR-7, and lncRNA Cyrano and the circRNA CDR1as regulating miR-7, has been shown to affect brain function. The ability to manipulate these networks is crucial in determining the functional outcome of central nervous system (CNS) pathologies. The focus of this review is to highlights the interactions and crosstalk of these networks in regulating pathophysiologic CNS function.
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Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA; William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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Zaynab M, Wang Z, Hussain A, Bahadar K, Sajid M, Sharif Y, Azam M, Sughra K, Raza MA, Khan KA, Li S. ATP-binding cassette transporters expression profiling revealed its role in the development and regulating stress response in Solanum tuberosum. Mol Biol Rep 2021; 49:5251-5264. [PMID: 34480688 DOI: 10.1007/s11033-021-06697-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
The ATP-binding cassette (ABC) transporter gene family plays a vital role in substance transportation, including secondary metabolites, and phytohormones across membranous structures. It is still uncovered in potato (Solanum tuberosum), grown worldwide as a 3rd important food crop. The current study identified a total of 54 Stabc genes in potato genome. The accumulative phylogenetic tree of Stabc with arabidopsis, divided into eight groups (ABCA to ABCH). ABCG was the most prominent group covering 90% of Stabc genes, followed by ABCB group. The number and architecture of exon-intron varied from gene to gene. In addition, the presence of stress-responsive elements in the regulatory regions depicted their role in environmental stress. Furthermore, the tissue-specific and stress-specific expression profiling of Stabc genes and their validation through real-time-qPCR analysis revealed their role in development and stress. The presented results provided useful information for further functional analysis of Stabc genes and can also use as a reference study for other important crops.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China
| | - Zongkang Wang
- Shenzhen Batian Ecotypic Engineering Company Limited, Shenzhen, 518105, China
| | - Athar Hussain
- Genomics Lab, Department of Life Science, University of Management and Technology (UMT), Lahore, 54770, Pakistan
| | - Khalida Bahadar
- National Agriculture Research Center, PARC Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
| | - Mateen Sajid
- Department of Horticulture, Ghazi University, Dera Ghazi Khan, 32200, Pakistan
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Muhammad Azam
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Kalsoom Sughra
- Department of Biochemistry & Biotechnology, Hafiz Hayat Campus University of Gujrat, Gujrat City, Pakistan
| | - Muhammad Ammar Raza
- Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia.,Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, Guangdong, China.
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Bhatti GK, Khullar N, Sidhu IS, Navik US, Reddy AP, Reddy PH, Bhatti JS. Emerging role of non-coding RNA in health and disease. Metab Brain Dis 2021; 36:1119-1134. [PMID: 33881724 PMCID: PMC8058498 DOI: 10.1007/s11011-021-00739-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Human diseases have always been a significant turf of concern since the origin of mankind. It is cardinal to know the cause, treatment, and cure for every disease condition. With the advent and advancement in technology, the molecular arena at the microscopic level to study the mechanism, progression, and therapy is more rational and authentic pave than a macroscopic approach. Non-coding RNAs (ncRNAs) have now emerged as indispensable players in the diagnosis, development, and therapeutics of every abnormality concerning physiology, pathology, genetics, epigenetics, oncology, and developmental diseases. This is a comprehensive attempt to collate all the existing and proven strategies, techniques, mechanisms of genetic disorders including Silver Russell Syndrome, Fascio- scapula humeral muscular dystrophy, cardiovascular diseases (atherosclerosis, cardiac fibrosis, hypertension, etc.), neurodegenerative diseases (Spino-cerebral ataxia type 7, Spino-cerebral ataxia type 8, Spinal muscular atrophy, Opitz-Kaveggia syndrome, etc.) cancers (cervix, breast, lung cancer, etc.), and infectious diseases (viral) studied so far. This article encompasses discovery, biogenesis, classification, and evolutionary prospects of the existence of this junk RNA along with the integrated networks involving chromatin remodelling, dosage compensation, genome imprinting, splicing regulation, post-translational regulation and proteomics. In conclusion, all the major human diseases are discussed with a facilitated technology transfer, advancements, loopholes, and tentative future research prospects have also been proposed.
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Affiliation(s)
- Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab India
| | | | - Uma Shanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | | | - P. Hemachandra Reddy
- Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Cell Biology & Biochemistry, Neuroscience & Pharmacology, Neurology, Public Health, School of Health Professions, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430 USA
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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Yang XM, Liang Y, Zhong ZJ, Tao X, Yang YK, Zhang P, Wang Y, Lei YF, Chen XH, Zeng K, Gong JJ, Ying SC, Zhang JL, Pang JH, Lv XB, Gu YR, He ZP. Comparison of long non-coding RNAs in adipose and muscle tissues between seven indigenous Chinese and the Yorkshire pig breeds. Anim Genet 2021; 52:645-655. [PMID: 34324723 DOI: 10.1111/age.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/01/2022]
Abstract
lncRNAs play crucial roles in fat metabolism in animals. Previously, we have compared the mRNA transcriptome profiles between seven fat-type Chinese pig breeds and one lean-type Western breed (Yorkshire, YY). The associations between differentially expressed (DE) genes and phenotypical traits were investigated. In the present study, to further explore the underlying regulatory mechanisms, lncRNAs were sequenced and compared between YY and Chinese indigenous breeds. The results showed 9114 and 7538 DE lncRNAs between at least one Chinese breed and the YY breed in the adipose and muscle tissue respectively. KEGG enrichment analysis revealed that the target genes of these DE lncRNAs mainly influenced the glucolipid metabolism, which is an important process affecting meat quality. Correlation analyses between the DE lncRNA and DE mRNA genes related to meat quality and growth traits were performed. The results showed that LTCONS_00073280 was associated with intramuscular fat content. Four lncRNAs (LTCONS_00101781, LTCONS_00037879, LTCONS_00088260 and LTCONS-00128343) might mediate backfat thickness. Overall, this study provides candidate lncRNAs that potentially affect meat quality, which might be useful for molecular breeding of pig breeds in future.
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Affiliation(s)
- X-M Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-J Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-K Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - P Zhang
- Chengdu Agricultural Technology Vocational College, Chengdu, Sichuan, 610000, China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-F Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X-H Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - S-C Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-L Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-H Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, 610000, China
| | - X-B Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-R Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-P He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
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Zaynab M, Hussain A, Sharif Y, Fatima M, Sajid M, Rehman N, Yang X, Khan KA, Ghramh HA, Li S. Mitogen-Activated Protein Kinase Expression Profiling Revealed Its Role in Regulating Stress Responses in Potato ( Solanum tuberosum). PLANTS 2021; 10:plants10071371. [PMID: 34371574 PMCID: PMC8309457 DOI: 10.3390/plants10071371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are the universal signal transduction networks that regulate cell growth and development, hormone signaling, and other environmental stresses. However, their essential contribution to plant tolerance is very little known in the potato (Solanum tuberosum) plant. The current study carried out a genome-wide study of StMAPK and provided a deep insight using bioinformatics tools. In addition, the relative expression of StMAPKs was also assessed in different plant tissues. The similarity search results identified a total of 22 StMAPK genes in the potato genome. The sequence alignment also showed conserved motif TEY/TDY in most StMAPKs with conserved docking LHDXXEP sites. The phylogenetic analysis divided all 22 StMAPK genes into five groups, i.e., A, B, C, D, and E, showing some common structural motifs. In addition, most of the StMAPKs were found in a cluster form at the terminal of chromosomes. The promoter analysis predicted several stress-responsive Cis-acting regulatory elements in StMAPK genes. Gene duplication under selection pressure also indicated several purifying and positive selections in StMAPK genes. In potato, StMAPK2, StMAPK6, and StMAPK19 showed a high expression in response to heat stress. Under ABA and IAA treatment, the expression of the total 20 StMAPK genes revealed that ABA and IAA played an essential role in this defense process. The expression profiling and real-time qPCR (RT-qPCR) exhibited their high expression in roots and stems compared to leaves. These results deliver primary data for functional analysis and provide reference data for other important crops.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 51807, China; (M.Z.); (X.Y.)
| | - Athar Hussain
- Genomics Lab, Department of Life Science, University of Management and Technology (UMT), Lahore 54770, Pakistan;
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Mateen Sajid
- Department of Horticulture, Ghazi University, Dera Ghazi Khan 32200, Pakistan;
| | - Nazia Rehman
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad 44000, Pakistan;
| | - Xuewei Yang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 51807, China; (M.Z.); (X.Y.)
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science(RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (K.A.K.); (H.A.G.)
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hamed A. Ghramh
- Research Center for Advanced Materials Science(RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia; (K.A.K.); (H.A.G.)
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 51807, China; (M.Z.); (X.Y.)
- Correspondence:
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Wang J, Wang Z, Jia C, Miao H, Zhang J, Liu J, Xu B, Jin Z. Genome-Wide Identification and Transcript Analysis of TCP Gene Family in Banana (Musa acuminata L.). Biochem Genet 2021; 60:204-222. [PMID: 34156635 DOI: 10.1007/s10528-021-10100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) gene family has versatile functions in diverse aspects of plants. However, less research on banana TCPs was done comprehensively. Accordingly, 48 banana TCP genes were characterized on aspects of gene structure, conserved motifs, phylogenetic relationship, and expression patterns. Members of the MaTCP gene family were unevenly distributed among 11 chromosomes and purification selection was the driving force of the MaTCP gene family. Gene duplication analysis indicated that segmental duplication is the major contributor to family expansion. Promoter analysis showed that MaTCPs might be involved in banana growth, development, and abiotic stress responses. Further, the expression of 12 MaTCPs was analyzed by real-time quantitative RT-PCR, and the protein interaction analysis showed that MaPCF10 and MaPCF13 may have an important function in banana fruit development and ripening. These results lay the foundation for further study of the functions of TCP genes in banana.
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Affiliation(s)
- Jingyi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Hongxia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Jianbin Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China
| | - Juhua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China. .,Hainan Key Laboratory for Protection and Utilization of Tropical Bioresource, Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, 571101, China.
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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46
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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Li Y, Deng L, Pan X, Liu C, Fu R. The Role of lncRNA AF117829.1 in the Immunological Pathogenesis of Severe Aplastic Anaemia. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5587921. [PMID: 37600601 PMCID: PMC10435305 DOI: 10.1155/2021/5587921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/20/2021] [Accepted: 03/03/2021] [Indexed: 08/22/2023]
Abstract
Objective Severe aplastic anaemia (SAA) is an autoimmune disease with immune tolerance dysfunction mediated by hyperactivated T lymphocytes that target the haematopoietic system. Numerous studies suggest that long noncoding RNAs (lncRNAs) play a significant role in almost every level of gene function/regulation. However, their specific mechanisms in SAA remain undetermined. This study is aimed at determining the role of key lncRNAs in CD8+ T lymphocytes in the mechanisms of SAA. Methods RNA-seq was performed to detect all lncRNAs and mRNAs in peripheral CD8+ T lymphocytes from SAA patients and healthy controls. The lncRNA targets were predicted by bioinformatics, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. RT-qPCR was used to verify the expression of key lncRNAs and their predicted targets. We screened lncRNA AF117829.1, which was correlated with autoimmune diseases and downregulated in CD8+ T lymphocytes, and further validated its effects on CD8+ T lymphocytes from SAA patients. Results We systematically described the lncRNA/mRNA expression changes in CD8+ T lymphocytes in SAA patients and assessed their possible biological functions and signalling pathways. A total of 194 lncRNAs and 2099 mRNAs were changed in SAA patients versus healthy controls. These differentially expressed lncRNAs/mRNAs were associated with organelle components, catalytic activity, the response to stimulation, signal transduction, the immune system and metabolic processes. The downregulated expression of one altered factor, lncRNA AF117829.1, in CD8+ T lymphocytes from SAA patients increased CD8+ T lymphocyte immune function by promoting RIP2 expression. lncRNA AF117829.1 overexpression in CD8+ T lymphocytes reduced perforin and granzyme B expression. The same effect was achieved with GSK583, a RIP2 kinase inhibitor. Conclusions The proliferation and overactivation of CD8+ T lymphocytes, also known as cytotoxic T cells (CTLs), directly induce bone marrow (BM) failure in SAA patients, but the specific mechanism remains unclear. We found that lncRNA AF117829.1 and its target genes were associated with T cell proliferation, differentiation, and immune dysregulation and that lncRNA AF117829.1 regulated CD8+ T lymphocyte function in SAA patients by promoting RIP2 expression. These findings improve our understanding of the molecular mechanism of immune pathogenesis and provide potential targets for SAA diagnosis and treatment.
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Affiliation(s)
- Yang Li
- Department of Haematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ling Deng
- Department of Haematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Xiaofeng Pan
- Department of Haematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chunyan Liu
- Department of Haematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Rong Fu
- Department of Haematology, Tianjin Medical University General Hospital, Tianjin 300052, China
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Malayaperumal S, Sriramulu S, Jothimani G, Banerjee A, Pathak S. A Review of AEG-1 Oncogene Regulating MicroRNA Expression in Colon Cancer Progression. Endocr Metab Immune Disord Drug Targets 2021; 21:27-34. [PMID: 32552658 DOI: 10.2174/1871530320666200618104116] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/19/2019] [Accepted: 03/24/2020] [Indexed: 11/22/2022]
Abstract
MicroRNAs are a class of small non-coding RNAs that perform a crucial function in posttranscriptional gene regulation. Dysregulation of these microRNAs is associated with many types of cancer progression. In tumorigenesis, downregulated microRNAs might function as a tumour suppressor by repressing oncogenes, whereas overexpressed miRs might function as oncogenes by suppressing tumour suppressor. Similarly, Metadherin (also known as AEG-1/ LYRIC), is an oncogene, the levels of which are found to be very high in various cancers and play a crucial role in the proliferation of cells and invasion. Our review focuses on the study, which shows the alteration of microRNA expression profile and suppression of carcinogenesis when MTDH/AEG-1 is targeted. It summarises the studies where downregulation and upregulation of AEG-1 and microRNAs, respectively, alter the biological functions of the cell, such as proliferation and apoptosis. Studies have reported that AEG-1 can be direct or indirect target of microRNA, which could provide a new-insight to know the underlying molecular mechanism and might contribute to the progress of new therapeutic strategies for the disease.
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Affiliation(s)
- Sarubala Malayaperumal
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Sushmitha Sriramulu
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Ganesan Jothimani
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai 603103, Tamil Nadu, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam, Chennai 603103, Tamil Nadu, India
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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Zaynab M, Peng J, Sharif Y, Fatima M, Albaqami M, Al-Yahyai R, Khan KA, Alotaibi SS, Alaraidh IA, Shaikhaldein HO, Li S. Genome-Wide Identification and Expression Profiling of Germin-Like Proteins Reveal Their Role in Regulating Abiotic Stress Response in Potato. FRONTIERS IN PLANT SCIENCE 2021; 12:831140. [PMID: 35251067 PMCID: PMC8891383 DOI: 10.3389/fpls.2021.831140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 12/31/2021] [Indexed: 05/05/2023]
Abstract
Germin and germin-like proteins (GLPs) perform a significant role in plants against biotic and abiotic stress. To understand the role of GLPs in potato, a comprehensive genome-wide analysis was performed in the potato genome. This study identified a total of 70 StGLPs genes in the potato genome, distributed among 11 chromosomes. Phylogenetic analysis exhibited that StGLPs were categorized into six groups with high bootstrap values. StGLPs gene structure and motifs analysis showed a relatively well-maintained intron-exon and motif formation within the cognate group. Additionally, several cis-elements in the promoter regions of GLPs were hormones, and stress-responsive and different families of miRNAs target StGLPs. Gene duplication under selection pressure also exhibited positive and purifying selections in StGLPs. In our results, the StGLP5 gene showed the highest expression in response to salt stress among all expressed StGLPs. Totally 19 StGLPs genes were expressed in response to heat stress. Moreover, three genes, StGLP30, StGLP17, and StGLP14, exhibited a relatively higher expression level in the potato after heat treatment. In total, 22 genes expressed in response to abscisic acid (ABA) treatment indicated that ABA performed an essential role in the plant defense or tolerance mechanism to environmental stress. RNA-Seq data validated by RT-qPCR also confirm that the StGLP5 gene showed maximum expression among selected genes under salt stress. Concisely, our results provide a platform for further functional exploration of the StGLPs against salt and heat stress conditions.
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Affiliation(s)
- Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiaofeng Peng
- Instrument Analysis Center, Shenzhen University, Shenzhen, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mahpara Fatima
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rashid Al-Yahyai
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Ibrahim A. Alaraidh
- Botany and Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Hassan O. Shaikhaldein
- Botany and Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Shuangfei Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Shuangfei Li,
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