scholarly journals Discovery Function Labels Based On Numerical Features Of MicroRNA Found In Plant

2019 ◽  
Author(s):  
Rongsheng Zhu ◽  
Jinglu Liu ◽  
Dawei Xin ◽  
Zhanguo Zhang ◽  
Zhenbang Hu ◽  
...  
Keyword(s):  
Target Genes ◽  
Biological Function ◽  
Biological Process ◽  
Gc Content ◽  
Mrna Translation ◽  
Non Coding Rnas ◽  
The Difference ◽  
Post Transcriptional Regulation ◽  
Go Terms ◽  
Perl Program

AbstractMicroRNAs(miRNAs),are a class of small endogenous non-coding RNAs that play Important post-transcriptional regulation role by degrading targeted mRNAs or repressing mRNA translation. We screened 84 miRNAs belonging to 21 conserved family from 4014 miRNAs in miRBase database which distributed in 47 plant species. Of the predicted 274 target genes,42 GO terms were found in the Gene Ontology. With the 135 numerical features which extracted by perl program, the difference significantly result of ANOVA (P<0.001) and multiple comparison show that the function labels G…,GC content and Helix in biological process, cellular component and biological function, respectively. Our result have suggested a potential connection between numerical features of miRNAs and the function of target genes of miRNAs.

scholarly journals Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8522 ◽  
Author(s):  
Phongsakorn Chuammitri ◽  
Soulasack Vannamahaxay ◽  
Benjaporn Sornpet ◽  
Kidsadagon Pringproa ◽  
Prapas Patchanee
Keyword(s):  
Target Genes ◽  
Biological Process ◽  
Expression Profiles ◽  
Canine Parvovirus ◽  
Negative Regulation ◽  
Kidney Cells ◽  
B Cell Differentiation ◽  
Go Enrichment ◽  
Go Terms

Background MicroRNAs (miRNAs) play an essential role in gene regulators in many biological and molecular phenomena. Unraveling the involvement of miRNA as a key cellular factor during in vitro canine parvovirus (CPV) infection may facilitate the discovery of potential intervention candidates. However, the examination of miRNA expression profiles in CPV in tissue culture systems has not been fully elucidated. Method In the present study, we utilized high-throughput small RNA-seq (sRNA-seq) technology to investigate the altered miRNA profiling in miRNA libraries from uninfected (Control) and CPV-2c infected Crandell Reese Feline Kidney cells. Results We identified five of known miRNAs (miR-222-5p, miR-365-2-5p, miR-1247-3p, miR-322-5p and miR-361-3p) and three novel miRNAs (Novel 137, Novel 141 and Novel 102) by sRNA-seq with differentially expressed genes in the miRNA repertoire of CPV-infected cells over control. We further predicted the potential target genes of the aforementioned miRNAs using sequence homology algorithms. Notably, the targets of miR-1247-3p exhibited a potential function associated with cellular defense and humoral response to CPV. To extend the probing scheme for gene targets of miR-1247-3p, we explored and performed Gene Ontology (GO) enrichment analysis of its target genes. We discovered 229 putative targets from a total of 38 enriched GO terms. The top over-represented GO enrichment in biological process were lymphocyte activation and differentiation, marginal zone B cell differentiation, negative regulation of cytokine production, negative regulation of programed cell death, and negative regulation of signaling. We next constructed a GO biological process network composed of 28 target genes of miR-1247-3p, of which, some genes, namely BCL6, DLL1, GATA3, IL6, LEF1, LFNG and WNT1 were among the genes with obviously intersected in multiple GO terms. Conclusion The miRNA-1247-3p and its cognate target genes suggested their great potential as novel therapeutic targets or diagnostic biomarkers of CPV or other related viruses.

scholarly journals microRNAs Regulating Human and Mouse Naïve Pluripotency

2019 ◽  
Vol 20 (23) ◽  
pp. 5864 ◽  
Author(s):  
Yuliang Wang ◽  
Abdiasis M. Hussein ◽  
Logeshwaran Somasundaram ◽  
Rithika Sankar ◽  
Damien Detraux ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Meta Analysis ◽  
Regulation Of Gene Expression ◽  
Developmental Pathways ◽  
State Transitions ◽  
Rna Seq ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation ◽  
Human And Mouse

microRNAs are ~22bp nucleotide non-coding RNAs that play important roles in the post-transcriptional regulation of gene expression. Many studies have established that microRNAs are important for cell fate choices, including the naïve to primed pluripotency state transitions, and their intermediate state, the developmentally suspended diapause state in early development. However, the full extent of microRNAs associated with these stage transitions in human and mouse remain under-explored. By meta-analysis of microRNA-seq, RNA-seq, and metabolomics datasets from human and mouse, we found a set of microRNAs, and importantly, their experimentally validated target genes that show consistent changes in naïve to primed transitions (microRNA up, target genes down, or vice versa). The targets of these microRNAs regulate developmental pathways (e.g., the Hedgehog-pathway), primary cilium, and remodeling of metabolic processes (oxidative phosphorylation, fatty acid metabolism, and amino acid transport) during the transition. Importantly, we identified 115 microRNAs that significantly change in the same direction in naïve to primed transitions in both human and mouse, many of which are novel candidate regulators of pluripotency. Furthermore, we identified 38 microRNAs and 274 target genes that may be involved in diapause, where embryonic development is temporarily suspended prior to implantation to uterus. The upregulated target genes suggest that microRNAs activate stress response in the diapause stage. In conclusion, we provide a comprehensive resource of microRNAs and their target genes involved in naïve to primed transition and in the paused intermediate, the embryonic diapause stage.

scholarly journals Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions

2019 ◽  
Vol 5 (1) ◽  
pp. 18 ◽  
Author(s):  
Shengqian Dou ◽  
Yirong Wang ◽  
Jian Lu
Keyword(s):  
Small Rnas ◽  
Mrna Translation ◽  
Evolutionary Genomics ◽  
Biological Processes ◽  
Domains Of Life ◽  
Conservation Patterns ◽  
Fundamental Biology ◽  
Non Coding Rnas ◽  
Regulatory Functions ◽  
Post Transcriptional Regulation

Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional and evolutionary genomics, with a focus on the tsRNA biology of Drosophila. We first summarize our current understanding of the biogenesis mechanisms of different categories of tsRNAs that are generated under physiological or stressed conditions. Next, we review the conservation patterns of tsRNAs in all domains of life, with an emphasis on the conservation of tsRNAs between two Drosophila species. Then, we elaborate the currently known regulatory functions of tsRNAs in mRNA translation that are independent of, or dependent on, Argonaute (AGO) proteins. We also highlight some issues related to the fundamental biology of tsRNAs that deserve further study.

scholarly journals Regulation of long non-coding RNAs and circular RNAs in spermatogonial stem cells

Reproduction ◽  
2019 ◽  
Vol 158 (1) ◽  
pp. R15-R25 ◽  
Author(s):  
Fan Zhou ◽  
Wei Chen ◽  
Yiqun Jiang ◽  
Zuping He
Keyword(s):  
Stem Cells ◽  
Biological Function ◽  
Spermatogonial Stem Cells ◽  
Circular Rnas ◽  
Biological Functions ◽  
Self Renewal ◽  
Coordinated Expression ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Spermatogonial stem cells (SSCs) are one of the most significant stem cells with the potentials of self-renewal, differentiation, transdifferentiation and dedifferentiation, and thus, they have important applications in reproductive and regenerative medicine. They can transmit the genetic and epigenetic information across generations, which highlights the importance of the correct establishment and maintenance of epigenetic marks. Accurate transcriptional and post-transcriptional regulation is required to support the highly coordinated expression of specific genes for each step of spermatogenesis. Increasing evidence indicates that non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play essential roles in controlling gene expression and fate determination of male germ cells. These ncRNA molecules have distinct characteristics and biological functions, and they independently or cooperatively modulate the proliferation, apoptosis and differentiation of SSCs. In this review, we summarized the features, biological function and fate of mouse and human SSCs, and we compared the characteristics of lncRNAs and circRNAs. We also addressed the roles and mechanisms of lncRNAs and circRNAs in regulating mouse and human SSCs, which would add novel insights into the epigenetic mechanisms underlying mammalian spermatogenesis and provide new approaches to treat male infertility.

scholarly journals miRinGO: Prediction of biological processes indirectly targeted by human microRNAs

2020 ◽  
Author(s):  
Mohammed Sayed ◽  
Juw Won Park
Keyword(s):  
Target Genes ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Go Enrichment ◽  
R Shiny ◽  
Canonical Approach ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation ◽  
Go Enrichment Analysis ◽  
Shiny Application

AbstractMicroRNAs are small non-coding RNAs that are known for their role in post-transcriptional regulation of target genes. Typically, their functions are predicted by first identifying their target genes and then finding biological processes enriched in these targets. Current tools for miRNA functional analysis use only genes with physical binding sites as their targets and exclude other genes that are indirectly targeted transcriptionally through transcription factors. Here, we introduce a method to predict gene ontology (GO) annotations indirectly targeted by microRNAs. The proposed method resulted in better performance in predicting known miRNA-GO term associations compared to the canonical approach. To facilitate miRNA GO enrichment analysis, we developed an R Shiny application, miRinGO, that is freely available from GitHub at https://github.com/Fadeel/miRinGO

scholarly journals Genome-Wide Identification and Characterization of Fusarium circinatum-Responsive lncRNAs in Pinus radiata

2021 ◽  
Author(s):  
Cristina Zamora-Ballesteros ◽  
Jorge Martin-Garcia ◽  
Aroa Suarez-Vega ◽  
Julio Diez
Keyword(s):  
Cell Wall ◽  
Pinus Radiata ◽  
Target Genes ◽  
Early Stage ◽  
Gc Content ◽  
Fusarium Circinatum ◽  
Protein Coding ◽  
Biotic Stresses ◽  
Non Coding Rnas

One of the most promising strategies of Pine Pitch Canker (PPC) management is the use of reproductive plant material resistant to the disease. Understanding the complexity of plant transcriptome that underlies the defence to the causal agent Fusarium circinatum, would greatly facilitate the development of an accurate breeding program. Long non-coding RNAs (lncRNAs) are emerging as important transcriptional regulators under biotic stresses in plants. However, to date, characterization of lncRNAs in conifer trees has not been reported. In this study, transcriptomic identification of lncRNAs was carried out using strand-specific paired-end RNA sequencing, from Pinus radiata samples inoculated with F. circinatum at an early stage of infection. Overall, 13,312 lncRNAs were predicted through a bioinformatics approach, including long intergenic non-coding RNAs (92.3%), antisense lncRNAs (3.3%) and intronic lncRNAs (2.9%). Compared with protein-coding RNAs, pine lncRNAs are shorter, have lower expression, lower GC content and harbour fewer and shorter exons. A total of 164 differentially expressed (DE) lncRNAs were identified in response to F. circinatum infection in the inoculated versus mock-inoculated P. radiata seedlings. The predicted cis-regulated target genes of these pathogen-responsive lncRNAs were related to defence mechanisms such as kinase activity, phytohormone regulation, and cell wall reinforcement. Co-expression network analysis of DE lncRNAs, DE protein-coding RNAs and lncRNA target genes also indicated a potential network regulating pectinesterase activity and cell wall remodelling. This study presents the first analysis of conifer lncRNAs involved in the regulation of defence network and provides the basis for future functional characterizations of lncRNAs in relation to pine defence responses against F. circinatum.

MicroRNAs and their role in hematological malignant diseases

2012 ◽  
Vol 153 (52) ◽  
pp. 2051-2059 ◽  
Author(s):  
Zsuzsanna Gaál ◽  
Éva Oláh
Keyword(s):  
Target Genes ◽  
Lymphoblastic Leukemia ◽  
Cancer Tissue ◽  
Altered Expression ◽  
Diagnosis And Prognosis ◽  
Oncologic Patients ◽  
Different Types ◽  
Non Coding Rnas ◽  
Success Of Treatment ◽  
Posttranscriptional Level

MicroRNAs are a class of small non-coding RNAs regulating gene expression at posttranscriptional level. Their target genes include numerous regulators of cell cycle, cell proliferation as well as apoptosis. Therefore, they are implicated in the initiation and progression of cancer, tissue invasion and metastasis formation as well. MicroRNA profiles supply much information about both the origin and the differentiation state of tumours. MicroRNAs also have a key role during haemopoiesis. An altered expression level of those have often been observed in different types of leukemia. There are successful attempts to apply microRNAs in the diagnosis and prognosis of acute lymphoblastic leukemia and acute myeloid leukemia. Measurement of the expression levels may help to predict the success of treatment with different kinds of chemotherapeutic drugs. MicroRNAs are also regarded as promising therapeutic targets, and can contribute to a more personalized therapeutic approach in haemato-oncologic patients. Orv. Hetil., 2012, 153, 2051–2059.

The Role of microRNAs in the Viral Infections

2019 ◽  
Vol 24 (39) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mona Fani ◽  
Milad Zandi ◽  
Majid Rezayi ◽  
Nastaran Khodadad ◽  
Hadis Langari ◽  
...  
Keyword(s):  
Viral Infections ◽  
Rna Viruses ◽  
Regulation Of Gene Expression ◽  
Molecular Structures ◽  
Main Function ◽  
Cellular Functions ◽  
Viral Genes ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

scholarly journals Direct Interactions with Nascent Transcripts Is Potentially a Common Targeting Mechanism of Long Non-Coding RNAs

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1483
Author(s):  
Ivan Antonov ◽  
Yulia Medvedeva
Keyword(s):  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Pilot Project ◽  
Base Pairing ◽  
Nascent Transcript ◽  
Active Transcription ◽  
Wet Lab ◽  
In Trans ◽  
Non Coding Rnas ◽  
Nascent Transcripts

Although thousands of mammalian long non-coding RNAs (lncRNAs) have been reported in the last decade, their functional annotation remains limited. A wet-lab approach to detect functions of a novel lncRNA usually includes its knockdown followed by RNA sequencing and identification of the deferentially expressed genes. However, identification of the molecular mechanism(s) used by the lncRNA to regulate its targets frequently becomes a challenge. Previously, we developed the ASSA algorithm that detects statistically significant inter-molecular RNA-RNA interactions. Here we designed a workflow that uses ASSA predictions to estimate the ability of an lncRNA to function via direct base pairing with the target transcripts (co- or post-transcriptionally). The workflow was applied to 300+ lncRNA knockdown experiments from the FANTOM6 pilot project producing statistically significant predictions for 71 unique lncRNAs (104 knockdowns). Surprisingly, the majority of these lncRNAs were likely to function co-transcriptionally, i.e., hybridize with the nascent transcripts of the target genes. Moreover, a number of the obtained predictions were supported by independent iMARGI experimental data on co-localization of lncRNA and chromatin. We detected an evolutionarily conserved lncRNA CHASERR (AC013394.2 or LINC01578) that could regulate target genes co-transcriptionally via interaction with a nascent transcript by directing CHD2 helicase. The obtained results suggested that this nuclear lncRNA may be able to activate expression of the target genes in trans by base-pairing with the nascent transcripts and directing the CHD2 helicase to the regulated promoters leading to open the chromatin and active transcription. Our study highlights the possible importance of base-pairing between nuclear lncRNAs and nascent transcripts for the regulation of gene expression.

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