Differential Expression Profiles and Function Prediction of tRNA-Derived Fragments in Fibrous Dysplasia

Abstract Background: Fibrous dysplasia (FD) is a benign bone disease which normal bone matrix is replaced by fibrous tissue and immature bone tissue. Transfer RNA (tRNA)-derived RNA fragments (tRFs) and tRNA halves (tiRNAs) are a type of small non-coding RNA in the transcriptome of eukaryotes that produced by specific shearing of mature tRNA. Here, we conducted a comparative analysis of the expression of tRFs/tiRNAs in BMSCs and FD BMSCs using a high‐throughput sequencing technique. Quantitative real‐time polymerase chain reaction (qRT-PCR) was used to validate the differential expressed tRFs/tiRNAs between two samples. Results: The results showed that tRF-34-87R8WP9I1EWJIQ [tDR‐001276] was significantly upregulated in FD BMSCs, and 3 downregulated tDRs (tRNA-derived small RNAs) (tRF-22-8EKSP1852 [tDR‐006826], tRF-18-H9R8B7D2 [tDR‐006049] and tRF-33-86V8WPMN1E8Y0E [tDR‐001271]) were also detected. Prediction of target genes and gene ontology (GO) and KEGG pathway analysis indicated that the upregulated tRF was mainly involved in regulation of immune response and osteoclast differentiation, which may be the underlying mechanism of FD pathological features. The downregulated tRFs/tiRNAs were related to calcium ion transport (tDR-006826), apoptotic signaling pathway and cell proliferation (tDR-006049) and endocrine system development (tDR-001271). The upregulated tRFs/tiRNAs was related to immune response (tDR-001276). The protein-protein interaction network analysis for predicted target genes established by the STRING database showed that PPP2R5A, ADAMTS1, PPARA, and POLR2C were the most frequently interacted proteins in target genes of tDR-006826, tDR-006049, tDR-001271 and tDR-001276, respectively. Conclusions: Our findings provided a comprehensive analysis of the expression of tRFs/tiRNAs in FD BMSCs and BMSCs. These differential expression tRFs/tiRNAs may be novel regulatory factors involved in FD BMSCs, and they could serve as potential therapeutic targets.

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Structure and function prediction of the Brucella abortus P39 protein by comparative modeling with marginal sequence similarities

Protein Engineering Design and Selection ◽

10.1093/protein/12.3.217 ◽

1999 ◽

Vol 12 (3) ◽

pp. 217-223 ◽

Cited By ~ 10

Author(s):

K. de Fays ◽

A. Tibor ◽

C. Lambert ◽

C. Vinals ◽

P. Denoël ◽

...

Keyword(s):

Brucella Abortus ◽

Comparative Modeling ◽

Structure And Function ◽

Function Prediction ◽

And Function ◽

Sequence Similarities

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Hox dosage contributes to flight appendage morphology in Drosophila

Nature Communications ◽

10.1038/s41467-021-23293-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Rachel Paul ◽

Guillaume Giraud ◽

Katrin Domsch ◽

Marilyne Duffraisse ◽

Frédéric Marmigère ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Differential Expression ◽

Hox Genes ◽

Expression Profiles ◽

Fruit Fly ◽

Insect Species ◽

Wing Morphology ◽

Hox Proteins ◽

Spatial Expression ◽

Flying Insects

AbstractFlying insects have invaded all the aerial space on Earth and this astonishing radiation could not have been possible without a remarkable morphological diversification of their flight appendages. Here, we show that characteristic spatial expression profiles and levels of the Hox genes Antennapedia (Antp) and Ultrabithorax (Ubx) underlie the formation of two different flight organs in the fruit fly Drosophila melanogaster. We further demonstrate that flight appendage morphology is dependent on specific Hox doses. Interestingly, we find that wing morphology from evolutionary distant four-winged insect species is also associated with a differential expression of Antp and Ubx. We propose that variation in the spatial expression profile and dosage of Hox proteins is a major determinant of flight appendage diversification in Drosophila and possibly in other insect species during evolution.

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Tentacle Morphological Variation Coincides with Differential Expression of Toxins in Sea Anemones

Toxins ◽

10.3390/toxins13070452 ◽

2021 ◽

Vol 13 (7) ◽

pp. 452

Author(s):

Lauren M. Ashwood ◽

Michela L. Mitchell ◽

Bruno Madio ◽

David A. Hurwood ◽

Glenn F. King ◽

...

Keyword(s):

Differential Expression ◽

Morphological Variation ◽

Expression Profiles ◽

The Body ◽

Sea Anemones ◽

Tissue Specific ◽

Venom Composition ◽

Specific Manner ◽

Branched Structures ◽

Morphological Variants

Phylum Cnidaria is an ancient venomous group defined by the presence of cnidae, specialised organelles that serve as venom delivery systems. The distribution of cnidae across the body plan is linked to regionalisation of venom production, with tissue-specific venom composition observed in multiple actiniarian species. In this study, we assess whether morphological variants of tentacles are associated with distinct toxin expression profiles and investigate the functional significance of specialised tentacular structures. Using five sea anemone species, we analysed differential expression of toxin-like transcripts and found that expression levels differ significantly across tentacular structures when substantial morphological variation is present. Therefore, the differential expression of toxin genes is associated with morphological variation of tentacular structures in a tissue-specific manner. Furthermore, the unique toxin profile of spherical tentacular structures in families Aliciidae and Thalassianthidae indicate that vesicles and nematospheres may function to protect branched structures that host a large number of photosynthetic symbionts. Thus, hosting zooxanthellae may account for the tentacle-specific toxin expression profiles observed in the current study. Overall, specialised tentacular structures serve unique ecological roles and, in order to fulfil their functions, they possess distinct venom cocktails.

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Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

Scientific Reports ◽

10.1038/s41598-021-81189-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaoqian Zhang ◽

Chang Li ◽

Bingzhou Zhang ◽

Zhonghua Li ◽

Wei Zeng ◽

...

Keyword(s):

Differential Expression ◽

Porcine Epidemic Diarrhea Virus ◽

Expression Profiles ◽

Expression Patterns ◽

Bacterial Invasion ◽

Sequencing Data ◽

Diarrhea Virus ◽

Comparison Groups ◽

Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

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Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells

Allergy Asthma & Clinical Immunology ◽

10.1186/s13223-021-00584-9 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Jan K. Nowak ◽

Marzena Dworacka ◽

Nazgul Gubaj ◽

Arystan Dossimov ◽

Zhumabek Dossimov ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Differential Expression ◽

Expression Profiles ◽

Differential Expression Analysis ◽

Goblet Cells ◽

Ileal Mucosa ◽

Significant Differential Expression ◽

Immune Genes ◽

Asthma Patients

Abstract Background The expression profiles of the intestinal mucosa have not been comprehensively investigated in asthma. We aimed to explore this in the Correlated Expression and Disease Association Research (CEDAR) patient cohort. Methods Differential expression analysis of ileal, transverse colon, and rectal biopsies were supplemented by a comparison of transcriptomes from platelets and leukocytes subsets, including CD4+, CD8+, CD14+, CD15+, and CD19+ cells. Asthma patients (n = 15) and controls (n = 15) had similar age (p = 0.967), body mass index (p = 0.870), similar numbers of females (80%) and smoking rates (13.3%). Results Significant differential expression was found in the ileum alone, and not in any other cell/tissue types. More genes were found to be overexpressed (1,150) than under-expressed (380). The most overexpressed genes included Fc Fragment of IgG Binding Protein (FCGBP, logFC = 3.01, pFDR = 0.015), Mucin 2 (MUC2, logFC = 2.78, pFDR = 0.015), and Alpha 1B Defensin (DEFA1B, logFC = 2.73, pFDR = 0.024). Gene ontology implicated the immune system, including interleukins 4 and 13, as well as antimicrobial peptides in this overexpression. There was concordance of gene over- (STAT1, XBP1) and underexpression (NELF, RARA) in asthma and Crohn’s disease ileum when our results were compared to another dataset (p = 3.66 × 10–7). Conclusion Ileal mucosa in asthma exhibits a specific transcriptomic profile, which includes the overexpression of innate immune genes, mostly characteristic of Paneth and goblet cells, in addition to other changes that may resemble Crohn’s disease.

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Identification and function prediction of iron-deficiency-responsive microRNAs in citrus leaves

3 Biotech ◽

10.1007/s13205-021-02669-z ◽

2021 ◽

Vol 11 (3) ◽

Author(s):

Long-Fei Jin ◽

Rajesh Yarra ◽

Xin-Xing Yin ◽

Yong-Zhong Liu ◽

Hong-Xing Cao

Keyword(s):

Iron Deficiency ◽

Function Prediction ◽

Citrus Leaves ◽

And Function

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Differential expression profiles of microRNA in mice internally exposed to tritiated water

Toxicological and Environmental Chemistry ◽

10.1080/02772248.2011.557478 ◽

2011 ◽

Vol 93 (4) ◽

pp. 738-751 ◽

Cited By ~ 2

Author(s):

Feng-Mei Cui ◽

Xiu-Jin Sun ◽

Xiang Ding ◽

Qiu Chen ◽

Jian-Ping Cao ◽

...

Keyword(s):

Differential Expression ◽

Expression Profiles ◽

Tritiated Water

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Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids

Plants ◽

10.3390/plants10040655 ◽

2021 ◽

Vol 10 (4) ◽

pp. 655

Author(s):

Hongmei Du ◽

Shah Zaman ◽

Shuiqingqing Hu ◽

Shengquan Che

Keyword(s):

Fatty Acids ◽

Differential Expression ◽

Single Molecule ◽

Unsaturated Fatty Acids ◽

Average Length ◽

Expression Profiles ◽

Portulaca Oleracea ◽

Pcr Analysis ◽

Sequence Information ◽

Leaves And Roots

This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

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