International Journal of Genomics最新文献

{"title":"circ_0002346 Suppresses Non-Small-Cell Lung Cancer Progression Depending on the Regulation of the miR-582-3p/STXBP6 Axis.","authors":"Weijie Wang,&nbsp;Yi Lin,&nbsp;Guanghui Zhang,&nbsp;Guofu Shi,&nbsp;Yongsheng Jiang,&nbsp;Wentao Hu,&nbsp;Wei Zuo","doi":"10.1155/2021/1565660","DOIUrl":"https://doi.org/10.1155/2021/1565660","url":null,"abstract":"<p><strong>Background: </strong>Accumulating articles have reported the pivotal regulatory roles of circular RNAs (circRNAs) in non-small-cell lung cancer (NSCLC) tumorigenesis. Here, our purpose was to explore the role of circ_0002346 in NSCLC progression and its associated mechanism.</p><p><strong>Methods: </strong>Cell proliferation ability was assessed by a 5-ethynyl-2'-deoxyuridine (EDU) assay and a colony formation assay. Transwell assays were conducted to analyze cell migration and invasion abilities. Cell apoptosis was analyzed by flow cytometry and by using a caspase3 activity assay kit. The glycolysis of NSCLC cells was analyzed using a fluorescence-based glucose/lactate assay kit. A dual-luciferase reporter assay and an RNA pull-down assay were performed to verify the binding relationship between microRNA-582-3p (miR-582-3p) and circ_0002346 or syntaxin-binding protein 6 (STXBP6).</p><p><strong>Results: </strong>circ_0002346 level was prominently downregulated in NSCLC tissues and cell lines. circ_0002346 overexpression significantly suppressed the proliferation, migration, invasion, and glycolysis and triggered the apoptosis of NSCLC cells. circ_0002346 directly interacted with miR-582-3p, and circ_0002346 overexpression-mediated antitumor effects in NSCLC cells were partly reversed by miR-582-3p overexpression. miR-582-3p directly interacted with the 3' untranslated region (3'UTR) of STXBP6, and STXBP6 silencing partly counteracted circ_0002346 overexpression-mediated antitumor influences in NSCLC cells. circ_0002346 can upregulate the expression of STXBP6 by acting as a miR-582-3p sponge in NSCLC cells. circ_0002346 overexpression suppressed xenograft tumor growth <i>in vivo</i>.</p><p><strong>Conclusion: </strong>circ_0002346 overexpression suppressed the malignant properties of NSCLC cells by binding to miR-582-3p to induce the expression of STXBP6.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"1565660"},"PeriodicalIF":2.9,"publicationDate":"2021-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8550861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39580385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Analysis of m⁵C RNA Methylation Regulator Genes in Clear Cell Renal Cell Carcinoma.","authors":"Jiajin Wu,&nbsp;Chao Hou,&nbsp;Yuhao Wang,&nbsp;Zhongyuan Wang,&nbsp;Pu Li,&nbsp;Zengjun Wang","doi":"10.1155/2021/3803724","DOIUrl":"https://doi.org/10.1155/2021/3803724","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Recent research found that N5-methylcytosine (m&lt;sup&gt;5&lt;/sup&gt;C) was involved in the development and occurrence of numerous cancers. However, the function and mechanism of m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation regulators in clear cell renal cell carcinoma (ccRCC) remains undiscovered. This study is aimed at investigating the predictive and clinical value of these m&lt;sup&gt;5&lt;/sup&gt;C-related genes in ccRCC.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Based on The Cancer Genome Atlas (TCGA) database, the expression patterns of twelve m&lt;sup&gt;5&lt;/sup&gt;C regulators and matched clinicopathological characteristics were downloaded and analyzed. To reveal the relationships between the expression levels of m&lt;sup&gt;5&lt;/sup&gt;C-related genes and the prognosis value in ccRCC, consensus clustering analysis was carried out. By univariate Cox analysis and last absolute shrinkage and selection operator (LASSO) Cox regression algorithm, a m&lt;sup&gt;5&lt;/sup&gt;C-related risk signature was constructed in the training group and further validated in the testing group and the entire cohort. Then, the predictive ability of survival of this m&lt;sup&gt;5&lt;/sup&gt;C-related risk signature was analyzed by Cox regression analysis and nomogram. Functional annotation and single-sample Gene Set Enrichment Analysis (ssGSEA) were applied to further explore the biological function and potential signaling pathways. Furthermore, we performed qRT-PCR experiments and measured global m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation level to validate this signature in vitro and tissue samples.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;In the TCGA-KIRC cohort, we found significant differences in the expression of m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation-related genes between ccRCC tissues and normal kidney tissues. Consensus cluster analysis was conducted to separate patients into two m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation subtypes. Significantly better outcomes were observed in ccRCC patients in cluster 1 than in cluster 2. m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation-related risk score was calculated to evaluate the prognosis of ccRCC patients by seven screened m&lt;sup&gt;5&lt;/sup&gt;C RNA methylation regulators (NOP2, NSUN2, NSUN3, NSUN4, NSUN5, TET2, and DNMT3B) in the training cohort. The AUC for the 1-, 2-, and 3-year survival in the training cohort were 0.792, 0.675, and 0.709, respectively, indicating that the risk signature had an excellent prognosis prediction in ccRCC. Additionally, univariate and multivariate Cox regression analyses revealed that the risk signature could be an independent prognostic factor in ccRCC. The results of ssGSEA suggested that the immune cells with different infiltration degrees between the high-risk and low-risk groups were T cells including follicular helper T cells, Th1_cells, Th2_cells, and CD8+_T_cells, and the main differences in immune-related functions between the two groups were the interferon response and T cell costimulation. In addition, qRT-PCR experiments confirmed our results in renal cell lines and tissue samples.&lt;/p&gt;&lt;p&gt;&lt;s","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"3803724"},"PeriodicalIF":2.9,"publicationDate":"2021-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8497170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39504238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantile-Dependent Expressivity of Serum Uric Acid Concentrations.","authors":"Paul T Williams","doi":"10.1155/2021/3889278","DOIUrl":"https://doi.org/10.1155/2021/3889278","url":null,"abstract":"<p><strong>Objective: </strong>\"Quantile-dependent expressivity\" occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., serum uric acid) is high or low relative to its distribution. Analyses were performed to test whether serum uric acid heritability is quantile-specific and whether this could explain some reported gene-environment interactions.</p><p><strong>Methods: </strong>Serum uric acid concentrations were analyzed from 2151 sibships and 12,068 offspring-parent pairs from the Framingham Heart Study. Quantile-specific heritability from offspring-parent regression slopes (<i>β</i> _OP, <i>h</i> ² = 2<i>β</i> _OP/(1 + <i>r</i> _spouse)) and full-sib regression slopes (<i>β</i> _FS, <i>h</i> ² = {(1 + 8<i>r</i> _spouse <i>β</i> _FS)^0.5 - 1}/(2<i>r</i> _spouse)) was robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples.</p><p><strong>Results: </strong>Quantile-specific <i>h</i> ² (±SE) increased with increasing percentiles of the offspring's sex- and age-adjusted uric acid distribution when estimated from <i>β</i> _OP (<i>P</i> _trend = 0.001): 0.34 ± 0.03 at the 10^th, 0.36 ± 0.03 at the 25^th, 0.41 ± 0.03 at the 50^th, 0.46 ± 0.04 at the 75^th, and 0.49 ± 0.05 at the 90^th percentile and when estimated from <i>β</i> _FS (<i>P</i> _trend = 0.006). This is consistent with the larger genetic effect size of (1) the <i>SLC2A9</i> rs11722228 polymorphism in gout patients vs. controls, (2) the <i>ABCG2</i> rs2231142 polymorphism in men vs. women, (3) the <i>SLC2A9</i> rs13113918 polymorphism in obese patients prior to bariatric surgery vs. two-year postsurgery following 29 kg weight loss, (4) the <i>ABCG2</i> rs6855911 polymorphism in obese vs. nonobese women, and (5) the <i>LRP2</i> rs2544390 polymorphism in heavier drinkers vs. abstainers. Quantile-dependent expressivity may also explain the larger genetic effect size of an <i>SLC2A9</i>/<i>PKD2</i>/<i>ABCG2</i> haplotype for high vs. low intakes of alcohol, chicken, or processed meats.</p><p><strong>Conclusions: </strong>Heritability of serum uric acid concentrations is quantile-specific.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"3889278"},"PeriodicalIF":2.9,"publicationDate":"2021-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8448993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39434901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulation of the Wound Healing through Noncoding RNA Interplay and GSK-3<i>β</i>/NF-<i>κ</i>B Signaling Interaction.","authors":"Xianyi Wang,&nbsp;Wanqiu Li,&nbsp;Shengdi Lu,&nbsp;Zhongliang Ma","doi":"10.1155/2021/9709290","DOIUrl":"https://doi.org/10.1155/2021/9709290","url":null,"abstract":"<p><p>Diabetic foot ulcers are seriously endangering the physical and mental health of patients. Due to the long duration of inflammation, the treatment of nonhealing wounds in diabetes is one of the most prominent healthcare problems in the world. The nuclear factor kappa B (NF-<i>κ</i>B) signaling pathway, a classical pathway that triggers inflammatory response, is regulated by many regulators, such as glycogen synthase kinase 3 beta (GSK-3<i>β</i>). Noncoding RNAs, a large class of molecules that regulate gene expression at the posttranscriptional or posttranslational level, play an important role in various stages of wound healing, especially in the stage of inflammation. Herein, we summarized the roles of noncoding RNAs in the NF-<i>κ</i>B/GSK-3<i>β</i> signaling, which might provide new ideas for the treatment of diabetic wound healing.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"9709290"},"PeriodicalIF":2.9,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8413067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39386717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor (<i>ARF</i>) Genes in Foxtail Millet (<i>Setaria italica</i> L.).","authors":"You Chen,&nbsp;Bin Liu,&nbsp;Yujun Zhao,&nbsp;Wenzhe Yu,&nbsp;Weina Si","doi":"10.1155/2021/2590665","DOIUrl":"https://doi.org/10.1155/2021/2590665","url":null,"abstract":"<p><p>Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of <i>ARF</i> genes was seldom investigated in <i>Setaria italica</i>, an important crop and C₄ model plant. In the present study, genome-wide evolutionary analysis of <i>ARFs</i> was performed in <i>S. italica</i>. Twenty-four <i>SiARF</i> genes were identified and unevenly distributed on eight of the nine chromosomes in <i>S. italica</i>. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of <i>SiARFs</i> under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of <i>SiARFs</i> and benefit for further functional characterization.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"2590665"},"PeriodicalIF":2.9,"publicationDate":"2021-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39328714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome and Metabolome Analysis Unveil Anthocyanin Metabolism in Pink and Red Testa of Peanut (<i>Arachis hypogaea</i> L.).","authors":"Qiqin Xue,&nbsp;Xiurong Zhang,&nbsp;Hui Yang,&nbsp;Huadong Li,&nbsp;Yuying Lv,&nbsp;Kun Zhang,&nbsp;Yongguang Liu,&nbsp;Fengzhen Liu,&nbsp;Yongshan Wan","doi":"10.1155/2021/5883901","DOIUrl":"https://doi.org/10.1155/2021/5883901","url":null,"abstract":"<p><p>Peanut (<i>Arachis hypogaea</i> L.) is an important source of oil and food around the world, and the testa color affects its appearance and commercial value. However, few studies focused on the mechanism of pigment formation in peanut testa. In this study, cultivars Shanhua 15 with pink testa and Zhonghua 12 with red testa were used as materials to perform the combined analysis of transcriptome and metabolome. A total of 198 flavonoid metabolites were detected, among which petunidin 3-O-glucoside and cyanidin O-acetylhexoside in Zhonghua12 were 15.23 and 14.72 times higher than those of Shanhua 15 at the R7 stage, revealing the anthocyanins underlying the red testa. Transcriptome analysis showed that there were 6059 and 3153 differentially expressed genes between Shanhua 15 and Zhonghua 12 in different growth periods, respectively. These differentially expressed genes were significantly enriched in the flavonoid biosynthesis, biosynthesis of secondary metabolites, and metabolic pathways. Integrated analysis of transcriptome and metabolome indicated CHS gene (<i>arahy.CM90T6</i>), F3'H genes (<i>arahy. 8F7PE4</i> and <i>arahy. K8H9R8</i>), and DFR genes (<i>arahy. LDV9QN</i> and <i>arahy. X8EVF3</i>) may be the key functional genes controlling the formation of pink and red testa in peanut. Transcription factors MYB (<i>arahy.A2IWKV</i>, <i>arahy.US2SKM</i>, <i>arahy.SJGE27</i>, <i>arahy.H8DJRL</i>, and <i>arahy.PR7AYB</i>), bHLH (<i>arahy.26781</i>N, <i>arahy.HM1IVV</i>, and <i>arahy.MP3D3D</i>), and WD40 (<i>arahy.L6JJW9</i>) in the biosynthetic pathway of anthocyanin were significantly upregulated in Zhonghua 12 which may be the key regulatory genes in testa pigment formation. This is a comprehensive analysis on flavonoid metabolites and related genes expression in peanut testa, providing reference for revealing the regulatory mechanism of pigment accumulation in peanut testa.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"5883901"},"PeriodicalIF":2.9,"publicationDate":"2021-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39313975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genes Encoding Teleost Orthologs of Human Haploinsufficient and Monoallelically Expressed Genes Remain in Duplicate More Frequently Than the Whole Genome.","authors":"Floriane Picolo,&nbsp;Anna Grandchamp,&nbsp;Benoît Piégu,&nbsp;Antoine D Rolland,&nbsp;Reiner A Veitia,&nbsp;Philippe Monget","doi":"10.1155/2021/9028667","DOIUrl":"https://doi.org/10.1155/2021/9028667","url":null,"abstract":"<p><p>Gene dosage is an important issue both in cell and evolutionary biology. Most genes are present in two copies or alleles in diploid eukariotic cells. The most outstanding exception is monoallelic gene expression (MA) that concerns genes localized on the X chromosome or in regions undergoing parental imprinting in eutherians, and many other genes scattered throughout the genome. In diploids, haploinsufficiency (HI) implies that a single functional copy of a gene in a diploid organism is insufficient to ensure a normal biological function. One of the most important mechanisms ensuring functional innovation during evolution is whole genome duplication (WGD). In addition to the two WGDs that have occurred in vertebrate genomes, the teleost genomes underwent an additional WGD, after their divergence from tetrapods. In the present work, we have studied on 57 teleost species whether the orthologs of human MA or HI genes remain more frequently in duplicates or returned more frequently in singleton than the rest of the genome. Our results show that the teleost orthologs of HI human genes remained more frequently in duplicate than the rest of the genome in all of the teleost species studied. No signal was observed for the orthologs of genes mapping to the human X chromosome or subjected to parental imprinting. Surprisingly, the teleost orthologs of the other human MA genes remained in duplicate more frequently than the rest of the genome for most teleost species. These results suggest that the teleost orthologs of MA and HI human genes also undergo selective pressures either related to absolute protein amounts and/or of dosage balance issues. However, these constraints seem to be different for MA genes in teleost in comparison with human genomes.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"9028667"},"PeriodicalIF":2.9,"publicationDate":"2021-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39292589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Association Studies for <i>Striga asiatica</i> Resistance in Tropical Maize.","authors":"Arthur Pfunye,&nbsp;Rwafa Rwafa,&nbsp;Stanford Mabasa,&nbsp;Edmore Gasura","doi":"10.1155/2021/9979146","DOIUrl":"https://doi.org/10.1155/2021/9979146","url":null,"abstract":"<p><p><i>Striga asiatica</i> L. is a parasitic weed in cereal crops including maize leading to tremendous yield losses up to 100% under severe infestation. The available <i>S. asiatica</i> control methods include cultural control options such as uprooting and burning the <i>Striga</i> plants before they flower, field sanitation, crop rotation, intercropping, organic matter usage, improved fallows, and application of herbicides. Resource limitation among smallholder farmers renders almost all of the control methods impossible. Development and use of <i>Striga</i> resistant genotypes are seen as the most feasible management option. Marker identification formulates tools that are faster, cheaper, and easier to utilise in breeding for <i>S. asiatica</i> resistance which has low heritability. The objective of this study was to identify single nucleotide polymorphism (SNP) markers for <i>Striga</i> resistance using the genome-wide association study (GWAS). Genotyping by sequencing was done on tropical maize inbred lines followed by their evaluation for <i>Striga</i> resistance. Analysis of variance showed significant (<i>p</i> < 0.05) variation among evaluated genotypes for <i>Striga</i> resistance traits such as germination distance, germination percentage, haustoria root attachments, total <i>Striga</i> plants emerged, total biomass, and growth rate. There were also significant differences (<i>p</i> < 0.05) for cobs, leaves, stems, and roots weight. The broad sense heritability was fairly high (up to 61%) for most traits. The means for derived traits on stress tolerance indices were subjected to a <i>t</i>-test, and significant differences (<i>p</i> < 0.05) were found for leaves, stem, roots, shoots, and total biomass. The Manhattan plots from GWAS showed the presence of three SNP markers on chromosome numbers 5, 6, and 7 for total <i>Striga</i> plants emerged. The identified markers for resistance to <i>S. asiatica</i> should be validated and utilised to breed for <i>Striga</i> resistance in tropical maize.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"9979146"},"PeriodicalIF":2.9,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39166583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of lncRNA, miRNA, and mRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages.","authors":"Congcong Li, Haoyuan Han, Xiuling Li, Jiao Wu, Xinfeng Li, Hui Niu, Wantao Li","doi":"10.1155/2021/6666160","DOIUrl":"10.1155/2021/6666160","url":null,"abstract":"<p><p>Current data is scarce regarding the function of noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in the interferon- (IFN-) mediated immune response. This is a comprehensive study that analyzes the lncRNA and miRNA expression profiles of the type I IFN and type II IFN in porcine alveolar macrophages using RNA sequencing. There was a total of 152 overexpressed differentially expressed (DE) lncRNAs and 21 DE miRNAs across type I IFN and type II IFN in porcine alveolar macrophages. Subsequent lncRNA-miRNA-mRNA network construction revealed the involvement of 36 DE lncRNAs and 12 DE miRNAs. LncRNAs such as the XLOC_211306, XLOC_100516, XLOC_00695, XLOC_149196, and XLOC_014459 were expressed at a higher degree in the type I IFN group, while XLOC_222640, XLOC_047290, XLOC_147777, XLOC_162298, XLOC_220210, and XLOC_165237 were expressed at a higher degree in the type II IFN group. These lncRNAs were found to act as \"sponges\" for miRNAs such as miR-34a, miR-328, miR-885-3p, miR-149, miR-30c-3p, miR-30b-5p, miR-708-5p, miR-193a-5p, miR-365-5p, and miR-7. Their target genes FADS2, RPS6KA1, PIM1, and NOD1 were found to be associated with several immune-related signaling pathways including the NOD-like receptor, Jak-STAT, mTOR, and PPAR signaling pathways. These experiments provide a comprehensive profile of overexpressed noncoding RNAs in porcine alveolar macrophages, providing new insights regarding the IFN-mediated immune response.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"6666160"},"PeriodicalIF":2.9,"publicationDate":"2021-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39150206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment.","authors":"Yuntian Ye,&nbsp;Yongqiang Liu,&nbsp;Xiaolong Li,&nbsp;Qing Chen,&nbsp;Yong Zhang,&nbsp;Ya Luo,&nbsp;Zejing Liu,&nbsp;Yan Wang,&nbsp;Yuanxiu Lin,&nbsp;Yunting Zhang,&nbsp;Xiaorong Wang,&nbsp;Haoru Tang","doi":"10.1155/2021/5572076","DOIUrl":"https://doi.org/10.1155/2021/5572076","url":null,"abstract":"<p><p>Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (<i>Fragaria × ananassa</i> Duch.) \"Benihoppe\" were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (<i>PhyB</i>, <i>PIF</i>s, and <i>HY5</i>) and circadian rhythm (<i>FKF1</i>, <i>CCA1</i>, <i>LHY</i>, and <i>CO</i>) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the <i>FaBBX29</i>, one of strawberry's BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.</p>","PeriodicalId":13988,"journal":{"name":"International Journal of Genomics","volume":"2021 ","pages":"5572076"},"PeriodicalIF":2.9,"publicationDate":"2021-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39162684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}