scholarly journals Characterization of microRNA Profiles in Pasteurella multocida-Infected Rabbits and Identification of miR-29-5p as a Regulator of Antibacterial Immune Response

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiaqing Hu ◽  
Wenqiang Li ◽  
Xibo Qiao ◽  
Wenjie Li ◽  
Kerui Xie ◽  
...  
Keyword(s):  
Immune Response ◽  
Pasteurella Multocida ◽  
Target Genes ◽  
Expression Patterns ◽  
Rabbit Lung ◽  
T Box ◽  
Kegg Pathways ◽  
Small Rna Deep Sequencing ◽  
Epithelial Membrane Protein 2

Pasteurella multocida is the pathogenic agent for a variety of severe diseases in livestock, including rabbits. MicroRNAs (miRNAs) participate in the immune response to the pathogen. Distinct miRNA expression patterns were explored in rabbit lung by small-RNA deep sequencing to assess dysregulated miRNAs during P. multocida infection. Totally, 571 miRNAs were screened, of which, 62 were novel, and 32 exhibited differential expression (DE). Of the 32 known DE-miRNAs, 13 and 15 occurred at 1 day and 3 days post-infection (dpi); and ocu-miR-107-3p and ocu-miR-29b-5p were shared between the two time points. Moreover, 7,345 non-redundant target genes were predicted for the 32 DE-miRNAs. Putative target genes were enriched in diverse GO and KEGG pathways and might be crucial for disease resistance. Interestingly, upregulation of ocu-miR-29-5p suppresses P. multocida propagation and downregulates expression of epithelial membrane protein-2 (EMP2) and T-box 4 (TBX4) genes by binding to their 3′ untranslated region in RK13 cells. Thus, ocu-miR-29-5p may indirectly inhibit P. multocida invasion by modulating genes related to the host immune response, such as EMP2 and TBX4.

scholarly journals Comparison of human and mouse tissues with focus on genes with no 1-to-1 homology

2021 ◽  
Author(s):  
Jieun Jeong ◽  
Manolis Kellis
Keyword(s):  
Immune Response ◽  
Target Genes ◽  
Expression Patterns ◽  
Adaptive Immune Response ◽  
Mouse Skin ◽  
Rna Seq ◽  
Therapy Targets ◽  
Mouse Tissues ◽  
Tissues Expression ◽  
Human And Mouse

We assembled a panel of 28 tissue pairs of human and mouse with RNA-Seq data on gene expression. We focused on genes with no 1-to-1 homology, because they pose special challenges. In this way, we identified expression patterns that identify and explain differences between the two species and suggest target genes for therapeutic applications. Here we mention three examples. One pattern is observed by defining the aggregate expression of immunoglobulin genes (which have no homology) as a measure of different levels of an immune response. In Lung, we used this statistic to find genes that have significantly higher expression in low/moderate response, and thus they may be therapy targets: increasing their expression or mimicking their function with medications may help in recovery from inflammation in the lungs. Some of the observed associations are common to human and mouse; other associations involve genes involved in cell-to-cell signaling or in regeneration but were not known to be important in Lung. Second pattern is that in the Small Intestine, mouse expresses much less antimicrobial defensins, while it has much higher expression of enzymes that are found to improve adaptive immune response. Such enzymes may be tested if they improve probiotic supplements that help in gut inflammation and other diseases. Another pattern involves a many-to-many homology group of defensins that did not have a described function. In human tissues, expression of its genes was found only in a study of a disease of hair covered skin, but several of its genes are highly expressed in two tissues of our panel: mouse Skin and to a lesser degree mouse Vagina. This suggests that those genes or their homologs in other species may provide non-antibiotic medications for hair covered skin and other tissues with microbiome that includes fungi.

scholarly journals Potential role of miR-155-5p in fat deposition and skeletal muscle development of chicken

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Sifan Xu ◽  
Yang Chang ◽  
Guanxian Wu ◽  
Wanting Zhang ◽  
Chaolai Man
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Fat Deposition ◽  
Skeletal Muscle Development ◽  
Stem Loop ◽  
Related Target ◽  
Kegg Pathways

Abstract miR-155 has multiple functions in many physiological and pathological processes. However, little is known about the expression characteristics of avian miR-155. In the present study, partial pri-miR-155 sequences were cloned from AA+ broiler, Sanhuang broiler and Hy-Line Brown layer, respectively. Stem–loop qRT-PCR was performed to detect the miR-155-5p spatiotemporal expression profiles of each chicken breed, and the target genes of miR-155-5p were predicted in Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The results showed that the partial pri-miR-155 sequences of different breeds of chicken were high conserved. The expression patterns of miR-155-5p between broiler and layer were basically similar, and miR-155-5p was expressed highly in immune related tissues (spleen, thymus and bursa). In the same old chicken (14 days old), miR-155-5p expression activity of fat tissue all had higher level in the three chicken breeds, but the expression activities in skeletal muscle of broilers were significantly lower than that of layer (P<0.05). In different development stages of Hy-Line Brown layer, miR-155-5p expression activities in skeletal muscle of 14-day-old and 10-month-old layers were significantly lower than that of 24-month-old layer (P<0.05). Fat related target genes (ACOX1, ACOT7, FADS1, SCD and HSD17B12) and skeletal muscle related target genes (CCNT2, DMD, CFL2, MAPK14, FLNB, ZBTB18 and CDK5) of miR-155-5p were predicted, respectively. The results indicate that miR-155-5p may be an important factor inhibiting the fat deposition and skeletal muscle development in chicken.

scholarly journals Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169

2019 ◽  
Vol 20 (14) ◽  
pp. 3448
Author(s):  
Runqing Yang ◽  
Gu Chen ◽  
Huifeng Peng ◽  
Dong Wei
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Acid Metabolism ◽  
Biofuel Production ◽  
Transcriptional Level ◽  
Alpha Linolenic Acid ◽  
Kegg Pathways ◽  
Coccomyxa Subellipsoidea ◽  
Potential Impact

Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO2 supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO2 revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs’ target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.

scholarly journals Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. Results Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. Conclusions In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Genome-Wide Identification and Characterization of the AREB/ABF/ABI5 Subfamily Members from Solanum tuberosum

2019 ◽  
Vol 20 (2) ◽  
pp. 311 ◽  
Author(s):  
Tengfei Liu ◽  
Tingting Zhou ◽  
Meiting Lian ◽  
Tiantian Liu ◽  
Juan Hou ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Leucine Zipper ◽  
Target Genes ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Mobility Shift ◽  
Potato Genome

Abscisic acid (ABA) plays crucial roles in plant development and adaption to environmental stresses. The ABA-responsive element binding protein/ABRE-binding factor and ABA INSENSITIVE 5 (AREB/ABF/ABI5) gene subfamily members, which belong to the basic domain/leucine zipper (bZIP) transcription factors family, participate in the ABA-mediated signaling pathway by regulating the expression of their target genes. However, information about potato (Solanum tuberosum) AREB/ABF/ABI5 subfamily members remains scarce. Here, seven putative AREB/ABF/ABI5 members were identified in the potato genome. Sequences alignment revealed that these members shared high protein sequence similarity, especially in the bZIP region, indicating that they might possess overlapping roles in regulating gene expression. Subcellular localization analysis illustrated that all seven AREB/ABF/ABI5 members were localized in the nucleus. Transactivation activity assays in yeast demonstrated that these AREB/ABF/ABI5 members possessed distinct transcriptional activity. Electrophoretic mobility shift assays (EMSA) confirmed that all of these AREB/ABF/ABI5 members could have an affinity to ABRE in vitro. The expression patterns of these AREB/ABF/ABI5 genes showed that they were in response to ABA or osmotic stresses in varying degrees. Moreover, most AREB/ABF/ABI5 genes were induced during stolon swelling. Overall, these results provide the first comprehensive identification of the potato AREB/ABF/ABI5 subfamily and would facilitate further functional characterization of these subfamily members in future work.

scholarly journals Transcription factors Aryl hydrocarbon receptor and TGF-inducible early gene are involved in an axis modulating immune response in mosquitoes

2020 ◽  
Author(s):  
Aditi Kulkarni ◽  
Ashmita Pandey ◽  
Patrick Trainor ◽  
Samantha Carlisle ◽  
Wanqin Yu ◽  
...  
Keyword(s):  
Adverse Effect ◽  
Immune Response ◽  
Transcription Factors ◽  
Immune Suppression ◽  
Target Genes ◽  
Expression Patterns ◽  
Early Gene ◽  
Immune Homeostasis ◽  
Aryl Hydrocarbon ◽  
Imd Pathway

AbstractImmune homeostasis balances effective defense against pathogens with avoiding the adverse effect of immune overactivation. AhR is a ligand activated transcription factor that transduces chemical signals into transcription of a variety of target genes. In this study, we demonstrate that mosquito AhR and TIEG mediate a transcriptional axis modulating immune response negatively. When AhR was activated by diet delivery of agonist kynurenine, the anti-bacterial immunity was compromised with a reduced survival at 24hr post bacterial challenge. In contrast, when AhR was inhibited by antagonists, CH223191 or SR1, the immunity was enhanced with increased survival. The observed immune enhancement via AhR antagonist was corroborated by AhR gene silencing via RNAi, which resulted in increased survival upon the infection. Exploration of transcriptomes following AhR inactivation, either pharmacologically or genetically, highlighted a set of genes that are infection inducible and AhR dependent, including genes that may mediate immune suppressive functions. One of the genes, TIEG (TGF-β inducible early gene), a member of the Krüppel -like factor family of transcription factors, was further studied. TIEG is required for AhR mediated immune suppression. Silencing TIEG increased the survival and reversed the immune suppression mediated by kynurenine activation of AhR. Moreover, the mosquito cohorts with AhR or TIEG knockdown demonstrated similar transcriptomic responses upon infection. There were co-expression patterns shared between the respective cohorts treated with AhR antagonist or AhR and TIEG silencing. In the naïve mosquitoes where the IMD pathway was overactivated by silencing the inhibitor gene Caspar, co-silencing Caspar with AhR or TIEG resulted in a reduced survival, indicating the AhR-TIEG axis is required to prevent the adverse effect of overactivation of IMD without an infection. Together, AhR and TIEG are involved in a transcriptional axis that is critical for maintaining immune homeostasis.

Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background: As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.Results: Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.Conclusions: In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Identification and in Silico Characterization of Novel and Conserved MicroRNAs in Methyl Jasmonate-Stimulated Scots Pine (Pinus sylvestris L.) Needles

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 384
Author(s):  
Baiba Krivmane ◽  
Ilze Šņepste ◽  
Vilnis Šķipars ◽  
Igor Yakovlev ◽  
Carl Gunnar Fossdal ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Scots Pine ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Stem Loop ◽  
Protein Coding ◽  
Stem Loop Structure ◽  
In Silico Characterization ◽  
Potential Precursor

MicroRNAs (miRNAs) are non-protein coding RNAs of ~20–24 nucleotides in length that play an important role in many biological and metabolic processes, including the regulation of gene expression, plant growth and developmental processes, as well as responses to stress and pathogens. The aim of this study was to identify and characterize novel and conserved microRNAs expressed in methyl jasmonate-treated Scots pine needles. In addition, potential precursor sequences and target genes of the identified miRNAs were determined by alignment to the Pinus unigene set. Potential precursor sequences were identified using the miRAtool, conserved miRNA precursors were also tested for the ability to form the required stem-loop structure, and the minimal folding free energy indexes were calculated. By comparison with miRBase, 4975 annotated sequences were identified and assigned to 173 miRNA groups, belonging to a total of 60 conserved miRNA families. A total of 1029 potential novel miRNAs, grouped into 34 families were found, and 46 predicted precursor sequences were identified. A total of 136 potential target genes targeted by 28 families were identified. The majority of previously reported highly conserved plant miRNAs were identified in this study, as well as some conserved miRNAs previously reported to be monocot specific. No conserved dicot-specific miRNAs were identified. A number of potential gymnosperm or conifer specific miRNAs were found, shared among a range of conifer species.

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