scholarly journals Discovery of Novel Leaf Rust Responsive microRNAs in Wheat and Prediction of Their Target Genes

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Dhananjay Kumar ◽  
Dharmendra Singh ◽  
Pulkit Kanodia ◽  
Kumble Vinod Prabhu ◽  
Manish Kumar ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Target Genes ◽  
Sequence Data ◽  
Puccinia Triticina ◽  
Homology Search ◽  
Small Noncoding Rnas ◽  
Cellular Processes ◽  
Novel Mirna ◽  
Transcriptome Sequence Data ◽  
Insight Into

MicroRNAs are endogenous small noncoding RNAs which play critical roles in gene regulation. Few wheat (Triticum aestivumL.) miRNA sequences are available in miRBase repertoire and knowledge of their biological functions related to biotic stress is limited. We identified 52 miRNAs, belonging to 19 families, from next-generation transcriptome sequence data based on homology search. One wheat specific novel miRNA was identified but could not be ascribed or assigned to any known miRNA family. Differentially expressed 22 miRNAs were found between susceptible and resistant wheat near-isogenic lines inoculated with leaf rust pathogenPuccinia triticinaand compared with mock inoculated controls. Most miRNAs were more upregulated in susceptible NIL compared to resistant NIL. We identified 1306 potential target genes for these 52 miRNAs with vital roles in response to stimuli, signaling, and diverse metabolic and cellular processes. Gene ontology analysis showed 66, 20, and 35 target genes to be categorized into biological process, molecular function, and cellular component, respectively. A miRNA-mediated regulatory network revealed relationships among the components of the targetome. The present study provides insight into potential miRNAs with probable roles in leaf rust pathogenesis and their target genes in wheat which establish a foundation for future studies.

scholarly journals Genome-wide Mapping of the Coactivator Ada2p Yields Insight into the Functional Roles of SAGA/ADA Complex inCandida albicans

2009 ◽  
Vol 20 (9) ◽  
pp. 2389-2400 ◽  
Author(s):  
Adnane Sellam ◽  
Christopher Askew ◽  
Elias Epp ◽  
Hugo Lavoie ◽  
Malcolm Whiteway ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resistance Genes ◽  
Target Genes ◽  
Transferase Activity ◽  
Histone Acetyl Transferase ◽  
Functional Roles ◽  
Cellular Processes ◽  
Oxidative Resistance ◽  
Genome Wide ◽  
Insight Into

The SAGA/ADA coactivator complex, which regulates numerous cellular processes by coordinating histone acetylation, is widely conserved throughout eukaryotes, and analysis of the Candida albicans genome identifies the components of this complex in the fungal pathogen. We investigated the multiple functions of SAGA/ADA in C. albicans by determining the genome-wide occupancy of Ada2p using chromatin immunoprecipitation (ChIP). Ada2p is recruited to 200 promoters upstream of genes involved in different stress-response functions and metabolic processes. Phenotypic and transcriptomic analysis of ada2 mutant showed that Ada2p is required for the responses to oxidative stress, as well as to treatments with tunicamycin and fluconazole. Ada2p recruitment to the promoters of oxidative resistance genes is mediated by the transcription factor Cap1p, and coactivator function were also established for Gal4p, which recruits Ada2p to the promoters of glycolysis and pyruvate metabolism genes. Cooccupancy of Ada2p and the drug resistance regulator Mrr1p on the promoters of core resistance genes characterizing drug resistance in clinical strains was also demonstrated. Ada2p recruitment to the promoters of these genes were shown to be completely dependent on Mrr1p. Furthermore, ADA2 deletion causes a decrease in H3K9 acetylation levels of target genes, thus illustrating its importance for histone acetyl transferase activity.

MicroRNA 299-3p modulates replicative senescence in endothelial cells

2013 ◽  
Vol 45 (7) ◽  
pp. 256-267 ◽  
Author(s):  
Hui-Lan Jong ◽  
Mohd Rais Mustafa ◽  
Paul M. Vanhoutte ◽  
Sazaly AbuBakar ◽  
Pooi-Fong Wong
Keyword(s):  
Endothelial Cells ◽  
Target Genes ◽  
Replicative Senescence ◽  
Umbilical Vein ◽  
Gene Profiling ◽  
Cellular Processes ◽  
Migration Capacity ◽  
Umbilical Vein Endothelial Cells ◽  
Insight Into

MicroRNAs (miRNAs) regulate various cellular processes. While several genes associated with replicative senescence have been described in endothelial cells, miRNAs that regulate these genes remain largely unknown. The present study was designed to identify miRNAs associated with replicative senescence and their target genes in human umbilical vein endothelial cells (HUVECs). An integrated miRNA and gene profiling approach revealed that hsa-miR-299-3p is upregulated in senescent HUVECs compared with the young cells, and one of its target genes could be IGF1. IGF1 was upregulated in senescent compared with young HUVECs, and knockdown of hsa-miR-299-3p dose-dependently increased the mRNA expression of IGF1, more significantly observed in the presenescent cells ( passage 19) compared with the senescent cells ( passage 25). Knockdown of hsa-miR-299-3p also resulted in significant reduction in the percentage of cells positively stained for senescence-associated β-galactosidase and increases in cell viability measured by MTT assay but marginal increases in cell proliferation and cell migration capacity measured by real-time growth kinetics analysis. Moreover, knockdown of hsa-miR-299-3p also increased proliferation of cells treated with H2O2 to induce senescence. These findings suggest that hsa-miR-299-3p may delay or protect against replicative senescence by improving the metabolic activity of the senesced cells but does not stimulate growth of the remaining cells in senescent cultures. Hence, these findings provide an early insight into the role of hsa-miR-299-3p in the modulation of replicative senescence in HUVECs.

scholarly journals Natural Killer Cell Regulation by MicroRNAs in Health and Disease

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Jeffrey W. Leong ◽  
Ryan P. Sullivan ◽  
Todd A. Fehniger
Keyword(s):  
Nk Cells ◽  
Natural Killer ◽  
Nk Cell ◽  
Killer Cell ◽  
Cell Development ◽  
Small Noncoding Rnas ◽  
Cellular Processes ◽  
Health And Disease ◽  
Effector Response ◽  
Insight Into

Natural killer (NK) cells are innate immune lymphocytes that are critical for normal host defense against infections and mediate antitumor immune responses. MicroRNAs (miRNAs) are a family of small, noncoding RNAs that posttranscriptionally regulate the majority of cellular processes and pathways. Our understanding of how miRNAs regulate NK cells biology is limited, but recent studies have provided novel insight into their expression by NK cells, and how they contribute to the regulation of NK cell development, maturation, survival, and effector function. Here, we review the expression of miRNAs by NK cells, their contribution to cell intrinsic and extrinsic control of NK cell development and effector response, and their dysregulation in NK cell malignancies.

scholarly journals Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

2021 ◽  
Vol 22 (13) ◽  
pp. 7153
Author(s):  
Syed Muhammad Muntazir Mehdi ◽  
Sivakumar Krishnamoorthy ◽  
Michal Wojciech Szczesniak ◽  
Agnieszka Ludwików
Keyword(s):  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Plant Responses ◽  
Biological Processes ◽  
Adaptive Responses ◽  
Cellular Processes ◽  
Potential Target ◽  
Novel Mirna

miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5′ RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

scholarly journals Human microRNA similarity in breast cancer

2021 ◽  
Author(s):  
Ying Jing ◽  
Donghai Li
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Mirna Sequence ◽  
Disease Heterogeneity ◽  
Similarity Network ◽  
Novel Mirna ◽  
Functional Classes ◽  
Similarity Networks ◽  
Insight Into

MicroRNAs (miRNAs) play important roles in a variety of human diseases, including breast cancer. A number of miRNAs are up- and down-regulated in breast cancer. However, little is known about miRNA similarity and similarity network in breast cancer. Here, a collection of 272 breast cancer-associated miRNA precursors were utilized to calculate similarities of sequences, target genes, pathways and functions and construct a combined similarity network. Well-characterized miRNAs and their similarity network were highlighted. Interestingly, miRNA sequence-dependent similarity networks were not identified in spite of sequence-target gene association. Similarity networks with minimum and maximum number of miRNAs originate from pathway and mature sequence, respectively. The breast cancer-associated miRNAs were divided into 7 functional classes (classes I-VII) followed by disease enrichment analysis and novel miRNA-based disease similarities were found. The finding would provide insight into miRNA similarity, similarity network and disease heterogeneity in breast cancer.

SCREENING OF WHEAT LR-GENES FOR RESISTANCE TO PUCCINIA TRITICINA IN THE NORTH CAUCASUS REGION CONDITIONS

1970 ◽  
pp. 54-56
Author(s):  
G. V. Volkova ◽  
O. A. Kudinova ◽  
O. F. Vaganova
Keyword(s):  
Winter Wheat ◽  
Leaf Rust ◽  
Puccinia Triticina ◽  
North Caucasus ◽  
Breeding Programs ◽  
Lr Genes ◽  
Caucasus Region ◽  
Highly Efficient ◽  
The North ◽  
Wheat Rust

Currently, more than 70 wheat rust resistance genes are known, but few of them are effective. The purpose of this work is to screen lines of Lr gene carriers for resistance to leaf rust under conditions of the North Caucasus region. Investigations were carried out in 2016-2018 at the infectious site of VNIIBZR. Research material was 49 near isogenic lines of winter wheat cultivar Thatcher. Infectious material was the combined populations of P. triticina, obtained as a result of route surveys of industrial and breeding crops of winter wheat in the areas of the Krasnodar, Stavropol Territories and the Rostov Region, conducted in 2016-2018. According to the assessment, the genes are ranked as follows: - highly efficient genes (plants with no signs of damage): Lr9, Lr42, Lr43 + 24 and Lr50; effective (1R-5R) Lr genes: 19, 24, 29, 36, 37, 38, 45, 47; moderately effective (10MR-20MR) Lr genes: 17, 18, 21, 22a, 28, 32, 41, 52. The remaining Lr-lines were susceptible to P. triticina (25 MR - 90S) to varying degrees. Highly efficient and effective genes Lr9, Lr19, Lr24, Lr29, Lr38, Lr42, Lr43 + 24, Lr47 and Lr50 showed resistance in the seedling phase and can be recommended for inclusion in breeding programs to protect wheat from leaf rust in different phases of plant ontogenesis in the North Caucasus region.

MiRNA-145 and Its Direct Downstream Targets in Digestive System Cancers: A Promising Therapeutic Target

2020 ◽  
Vol 26 ◽  
Author(s):  
Yini Ma ◽  
Xiu Cao ◽  
Guojuan Shi ◽  
Tianlu Shi
Keyword(s):  
Digestive System ◽  
Target Genes ◽  
Malignant Neoplasm ◽  
Vital Role ◽  
Diagnostic Biomarkers ◽  
Cellular Processes ◽  
Promising Therapeutic Target ◽  
Direct Target ◽  
Potential Strategy

: MicroRNAs (miRNAs) play a vital role in the onset and development of many diseases, including cancers. Emerging evidence shows that numerous miRNAs have the potential to be used as diagnostic biomarkers for cancers, and miRNA-based therapy may be a promising therapy for the treatment of malignant neoplasm. MicroRNA-145 (miR-145) has been considered to play certain roles in various cellular processes, such as proliferation, differentiation and apoptosis, via modulating expression of direct target genes. Recent reports show that miR-145 participates in the progression of digestive system cancers, and plays crucial and novel roles for cancer treatment. In this review, we summarize the recent knowledge concerning the function of miR-145 and its direct targets in digestive system cancers. We discuss the potential role of miR-145 as valuable biomarkers for digestive system cancers and how miR-145 regulates these digestive system cancers via different targets to explore the potential strategy of targeting miR-145.

scholarly journals Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 408 ◽  
Author(s):  
Jing-Yao Yu ◽  
Zhan-Guo Zhang ◽  
Shi-Yu Huang ◽  
Xue Han ◽  
Xin-Yu Wang ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Small Rna ◽  
Target Genes ◽  
Soybean Seed ◽  
Regulatory Genes ◽  
Small Rna Sequencing ◽  
Grain Development ◽  
Regulatory Relationship ◽  
Novel Mirna

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

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