Plant microRNA: Methods of studying and the role in the development of symbiosis with beneFicial microorganisms

MicroRNAs are small non-coding RNA molecules that act as post-transcriptional regulators of gene expression due to rather strict complementarity to their mRNA and have a length of 20-24 nucleotides. Plant microRNAs control a wide range of physiological processes, including nutrition, growth, resistance reactions and interaction with other organisms, via modulation of the expression of transcription factors, stress-induced proteins, hormone biosynthesis enzymes, and other genes. Legumes are able to form mutualistic symbioses simultaneously with nitrogen-fixing bacteria and arbuscular mycorrhiza. Both the early and late stages of these symbiosis are regulated by complex genetic mechanisms. As it has become known in recent years, one of these mechanisms is the regulation of gene expression by microRNA. The study of microRNAs is carried out by various methods, but over the past decade, next-generation sequencing (NGS) technologies have become the most popular approach in this field. NGS is used to identify conservative and novel microRNAs in the genomes of various organisms (both model and non-model), as well as to study the functioning of microRNAs in various experimental conditions with the additional use of transcriptome and degradome sequencing data. The article describes the main stages of working with microRNA sequencing data: quality control of reads (with a list of programs required at this stage), identification of conservative and novel microRNAs using miRDeep2 tool, search for targets of identified microRNAs using PAREsnip2, functional annotation of targets and the use of statistical tests for the analysis of functional enrichment, which facilitates the interpretation of the data obtained and allows us to make assumptions about the biological consequences of the activity of identified microRNAs in the object under study. This information may be useful for researchers who deal with microRNAs in silico for the first time or want to save time and resources on searching and analyzing information about the tools needed to work with microRNA sequencing data.

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Abstract P625: Non-coding Rna Regulation Of Gene Expression In Angiotensin Ii-induced Vascular Damage

Hypertension ◽

10.1161/hyp.66.suppl_1.p625 ◽

2015 ◽

Vol 66 (suppl_1) ◽

Author(s):

Kugeng Huo ◽

Tlili Barhoumi ◽

Júlio C Fraulob-Aquino ◽

Chantal Richer ◽

Mathieu Lajoie ◽

...

Keyword(s):

Gene Expression ◽

Differential Expression Analysis ◽

Regulation Of Gene Expression ◽

Vascular Damage ◽

Mesenteric Arteries ◽

Functional Enrichment ◽

Molecular Networks ◽

Mirna Cluster ◽

Ang Ii ◽

Illumina Hiseq

Introduction: Non-coding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRs), account for ~98% of the transcribed RNAs. They have been shown to play a role in cardiovascular disease. Vascular damage is an early manifestation and a cause of end-organ damage in hypertension. However, it is unknown whether ncRNAs are involved in the development of vascular injury in hypertension. We hypothesize that ncRNA regulation participates in mechanisms of vascular remodeling and plays an important role in the pathophysiology of hypertension. Methods and Results: Ten-week old male C57BL/6 mice were infused or not with angiotensin (Ang) II for 14 days. Systolic blood pressure (BP) determined by telemetry was increased by Ang II infusion compared to control (146±8 vs 113±5 mmHg, P<0.001). Total RNA was extracted from mesenteric arteries for total and small RNA deep sequencing using Illumina HiSeq-2500. Sequences were aligned to the mm10 genome with STAR, annotated and counted using HTSeq-count or miRDeep2. Differential expression analysis was done in R. Differentially expressed (DE) mRNAs (550 up & 266 down), lncRNAs (7 up & 42 down), miRs (23 up & 12 down) were identified in the Ang II-treated group (1.5 fold change, q<0.05). Targetscan was used to predict interactions between DE miRs and the inversely correlated DE mRNAs or DE lncRNAs. MEME Suite was used to predict DE transcription factor binding sites in the promoter region of genes encoding DE mRNAs, lncRNAs and miRs. Cytoscape was used to construct molecular networks integrating the above interactions and the gene expression profile and to perform functional enrichment analysis, which revealed enrichment of extracellular matrix and developmental processes in DE miR-targeting DE mRNAs (q<1E-20). Ten DE miRNAs whose expression levels correlated (P<0.05) with BP were identified, 9 of which are located in a single miRNA cluster that is conserved in humans. Conclusions: We have identified a conserved miRNA cluster that may play a pivotal role in the regulation of vascular damage in hypertension. A sub-network of genes that participates in the interaction between the miRNA cluster and other BP-correlated RNAs was selected for future investigation to identify therapeutic targets.

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Regulation of type II adenylyl cyclase mRNA in rabbit skeletal muscle by chronic motor nerve pacing

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.1996.271.2.e253 ◽

1996 ◽

Vol 271 (2) ◽

pp. E253-E260 ◽

Cited By ~ 3

Author(s):

C. E. Torgan ◽

W. E. Kraus

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Protein Kinase ◽

Adenylyl Cyclase ◽

Regulation Of Gene Expression ◽

Rabbit Skeletal Muscle ◽

Type Ii ◽

Wide Range ◽

Electrical Pacing ◽

Fast Twitch

Skeletal muscle exhibits a wide range in functional phenotype in response to changes in physiological demands. We have observed that, in response to changes in work patterns, alterations in gene expression of some proteins coincide with changes in adenylyl cyclase (AC) activity [Kraus, W.E., J.P. Longabaugh, and S. B. Liggett. Am. J. Physiol 263 (Endocrinol. Metab. 26): E266-E230, 1992]. We now examine AC isoform transcript prevalence in various rabbit skeletal muscles and in response to changing work demands. Using reverse transcriptase-polymerase chain reaction, we detected type II AC isoform transcripts in rabbit skeletal muscle. Ribonuclease protection analyses revealed that expression of the type II isoform significantly correlated with the percentage of fast-twitch type IIb/IId fibers (r2 = 0.765, P < 0.01). When a fast-twitch muscle was converted to a slow-twitch muscle via chronic electrical pacing, expression of type II AC mRNA significantly decreased. This response occurred 3 days after the onset of stimulation (78% decrease) and was still present after 21 days of stimulation (76% decrease). As type II AC is relatively insensitive to calcium regulation while sensitive to protein kinase C (PKC) signaling, these data provide further impetus for investigations of protein kinase A and PKC cross-talk signaling mechanisms in the regulation of gene expression.

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Molecular Mechanisms, Diagnostic Aspects and Therapeutic Opportunities of Micro Ribonucleic Acids in Atrial Fibrillation

International Journal of Molecular Sciences ◽

10.3390/ijms21082742 ◽

2020 ◽

Vol 21 (8) ◽

pp. 2742 ◽

Cited By ~ 1

Author(s):

Allan Böhm ◽

Marianna Vachalcova ◽

Peter Snopek ◽

Ljuba Bacharova ◽

Dominika Komarova ◽

...

Keyword(s):

Gene Expression ◽

Atrial Fibrillation ◽

Molecular Mechanisms ◽

Wide Spectrum ◽

Regulation Of Gene Expression ◽

Review Article ◽

Ribonucleic Acids ◽

Rna Molecules ◽

Diagnostic Aspects ◽

Non Coding Rna

Micro ribonucleic acids (miRNAs) are short non-coding RNA molecules responsible for regulation of gene expression. They are involved in many pathophysiological processes of a wide spectrum of diseases. Recent studies showed their involvement in atrial fibrillation. They seem to become potential screening biomarkers for atrial fibrillation and even treatment targets for this arrhythmia. The aim of this review article was to summarize the latest knowledge about miRNA and their molecular relation to the pathophysiology, diagnosis and treatment of atrial fibrillation.

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Mammalian genome evolution as a result of epigenetic regulation of transposable elements

BioMolecular Concepts ◽

10.1515/bmc-2014-0013 ◽

2014 ◽

Vol 5 (3) ◽

pp. 183-194 ◽

Cited By ~ 5

Author(s):

Reuben M. Buckley ◽

David L. Adelson

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

Epigenetic Regulation ◽

Dna Sequences ◽

Defense Mechanisms ◽

Regulatory Networks ◽

Regulation Of Gene Expression ◽

Epigenetic Marks ◽

Rna Molecules ◽

Mammalian Genomes

AbstractTransposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.

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Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA

Journal of Integrative Bioinformatics ◽

10.1515/jib-2016-0004 ◽

2017 ◽

Vol 14 (1) ◽

Cited By ~ 3

Author(s):

Hamid Hamzeiy ◽

Rabia Suluyayla ◽

Christoph Brinkrolf ◽

Sebastian Jan Janowski ◽

Ralf Hofestaedt ◽

...

Keyword(s):

Gene Expression ◽

Small Rna ◽

Biological Networks ◽

Regulation Of Gene Expression ◽

Biological Pathways ◽

Rna Molecules ◽

Kegg Pathways ◽

Interaction Partners ◽

Data Source ◽

Post Transcriptional Regulation

AbstractMicroRNAs (miRNAs) are small RNA molecules which are known to take part in post-transcriptional regulation of gene expression. Here, VANESA, an existing platform for reconstructing, visualizing, and analysis of large biological networks, has been further expanded to include all experimentally validated human miRNAs available within miRBase, TarBase and miRTarBase. This is done by integrating a custom hybrid miRNA database to DAWIS-M.D., VANESA’s main data source, enabling the visualization and analysis of miRNAs within large biological pathways such as those found within the Kyoto Encyclopedia of Genes and Genomes (KEGG). Interestingly, 99.15 % of human KEGG pathways either contain genes which are targeted by miRNAs or harbor them. This is mainly due to the high number of interaction partners that each miRNA could have (e.g.: hsa-miR-335-5p targets 2544 genes and 71 miRNAs target

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SPsimSeq: semi-parametric simulation of bulk and single cell RNA sequencing data

10.1101/677740 ◽

2019 ◽

Cited By ~ 1

Author(s):

Alemu Takele Assefa ◽

Jo Vandesompele ◽

Olivier Thas

Keyword(s):

Gene Expression ◽

Single Cell ◽

Rna Sequencing ◽

Empirical Distribution ◽

Supplementary Information ◽

Rna Seq ◽

Sequencing Data ◽

Actual Distribution ◽

Wide Range ◽

Single Cell Rna Sequencing

SummarySPsimSeq is a semi-parametric simulation method for bulk and single cell RNA sequencing data. It simulates data from a good estimate of the actual distribution of a given real RNA-seq dataset. In contrast to existing approaches that assume a particular data distribution, our method constructs an empirical distribution of gene expression data from a given source RNA-seq experiment to faithfully capture the data characteristics of real data. Importantly, our method can be used to simulate a wide range of scenarios, such as single or multiple biological groups, systematic variations (e.g. confounding batch effects), and different sample sizes. It can also be used to simulate different gene expression units resulting from different library preparation protocols, such as read counts or UMI counts.Availability and implementationThe R package and associated documentation is available from https://github.com/CenterForStatistics-UGent/SPsimSeq.Supplementary informationSupplementary data are available at bioRχiv online.

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The Emerging Role of MicroRNAs in Bone Diseases and Their Therapeutic Potential

Molecules ◽

10.3390/molecules27010211 ◽

2021 ◽

Vol 27 (1) ◽

pp. 211

Author(s):

Luis Alberto Bravo Vázquez ◽

Mariana Yunuen Moreno Becerril ◽

Erick Octavio Mora Hernández ◽

Gabriela García de León Carmona ◽

María Emilia Aguirre Padilla ◽

...

Keyword(s):

Bone Growth ◽

Bone Cells ◽

Therapeutic Potential ◽

Regulation Of Gene Expression ◽

Bone Diseases ◽

Osteosarcoma Cell ◽

Main Function ◽

Altered Expression ◽

Rna Molecules ◽

Wide Range

MicroRNAs (miRNAs) are a class of small (20–24 nucleotides), highly conserved, non-coding RNA molecules whose main function is the post-transcriptional regulation of gene expression through sequence-specific manners, such as mRNA degradation or translational repression. Since these key regulatory molecules are implicated in several biological processes, their altered expression affects the preservation of cellular homeostasis and leads to the development of a wide range of pathologies. Over the last few years, relevant investigations have elucidated that miRNAs participate in different stages of bone growth and development. Moreover, the abnormal expression of these RNA molecules in bone cells and tissues has been significantly associated with the progression of numerous bone diseases, including osteoporosis, osteosarcoma, osteonecrosis and bone metastasis, among others. In fact, miRNAs regulate multiple pathological mechanisms, including altering either osteogenic or osteoblast differentiation, metastasis, osteosarcoma cell proliferation, and bone loss. Therefore, in this present review, aiming to impulse the research arena of the biological implications of miRNA transcriptome in bone diseases and to explore their potentiality as a theragnostic target, we summarize the recent findings associated with the clinical significance of miRNAs in these ailments.

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Modeling thecis-regulatory modules of genes expressed in developmental stages ofDrosophila melanogaster

PeerJ ◽

10.7717/peerj.3389 ◽

2017 ◽

Vol 5 ◽

pp. e3389 ◽

Cited By ~ 1

Author(s):

Yosvany López ◽

Alexis Vandenbon ◽

Akinao Nose ◽

Kenta Nakai

Keyword(s):

Gene Expression ◽

Developmental Stages ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Structural Features ◽

Extensive Study ◽

Pairwise Distance ◽

Sequencing Data ◽

Binding Motifs ◽

Promoter Sequences

Because transcription is the first step in the regulation of gene expression, understanding how transcription factors bind to their DNA binding motifs has become absolutely necessary. It has been shown that the promoters of genes with similar expression profiles share common structural patterns. This paper presents an extensive study of the regulatory regions of genes expressed in 24 developmental stages ofDrosophila melanogaster. It proposes the use of a combination of structural features, such as positioning of individual motifs relative to the transcription start site, orientation, pairwise distance between motifs, and presence of motifs anywhere in the promoter for predicting gene expression from structural features of promoter sequences. RNA-sequencing data was utilized to create and validate the 24 models. When genes with high-scoring promoters were compared to those identified by RNA-seq samples, 19 (79.2%) statistically significant models, a number that exceeds previous studies, were obtained. Each model yielded a set of highly informative features, which were used to search for genes with similar biological functions.

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reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization

Scientific Reports ◽

10.1038/s41598-021-02528-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Stefano Manzini ◽

Marco Busnelli ◽

Alice Colombo ◽

Elsa Franchi ◽

Pasquale Grossano ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Statistical Tests ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Knowledge Bases ◽

Functional Enrichment ◽

Reference Database ◽

Multiple User ◽

Daunting Task

AbstractFunctional enrichment analysis is an analytical method to extract biological insights from gene expression data, popularized by the ever-growing application of high-throughput techniques. Typically, expression profiles are generated for hundreds to thousands of genes/proteins from samples belonging to two experimental groups, and after ad-hoc statistical tests, researchers are left with lists of statistically significant entities, possibly lacking any unifying biological theme. Functional enrichment tackles the problem of putting overall gene expression changes into a broader biological context, based on pre-existing knowledge bases of reference: database collections of known expression regulation, relationships and molecular interactions. STRING is among the most popular tools, providing both protein–protein interaction networks and functional enrichment analysis for any given set of identifiers. For complex experimental designs, manually retrieving, interpreting, analyzing and abridging functional enrichment results is a daunting task, usually performed by hand by the average wet-biology researcher. We have developed reString, a cross-platform software that seamlessly retrieves from STRING functional enrichments from multiple user-supplied gene sets, with just a few clicks, without any need for specific bioinformatics skills. Further, it aggregates all findings into human-readable table summaries, with built-in features to easily produce user-customizable publication-grade clustermaps and bubble plots. Herein, we outline a complete reString protocol, showcasing its features on a real use-case.

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Peptide Regulation of Gene Expression: A Systematic Review

Molecules ◽

10.3390/molecules26227053 ◽

2021 ◽

Vol 26 (22) ◽

pp. 7053

Author(s):

Vladimir Khatskelevich Khavinson ◽

Irina Grigor’evna Popovich ◽

Natalia Sergeevna Linkova ◽

Ekaterina Sergeevna Mironova ◽

Anastasiia Romanovna Ilina

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Epigenetic Mechanism ◽

Short Peptides ◽

Gene Promoters ◽

Amino Acid Residues ◽

Sequence Recognition ◽

Wide Range ◽

The Status ◽

Synthetic Reactions

Peptides are characterized by their wide range of biological activity: they regulate functions of the endocrine, nervous, and immune systems. The mechanism of such action of peptides involves their ability to regulate gene expression and protein synthesis in plants, microorganisms, insects, birds, rodents, primates, and humans. Short peptides, consisting of 2–7 amino acid residues, can penetrate into the nuclei and nucleoli of cells and interact with the nucleosome, the histone proteins, and both single- and double-stranded DNA. DNA–peptide interactions, including sequence recognition in gene promoters, are important for template-directed synthetic reactions, replication, transcription, and reparation. Peptides can regulate the status of DNA methylation, which is an epigenetic mechanism for the activation or repression of genes in both the normal condition, as well as in cases of pathology and senescence. In this context, one can assume that short peptides were evolutionarily among the first signaling molecules that regulated the reactions of template-directed syntheses. This situation enhances the prospects of developing effective and safe immunoregulatory, neuroprotective, antimicrobial, antiviral, and other drugs based on short peptides.

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