scholarly journals Long Non-Coding RNAs and Their Potential Roles in the Vector–Host–Pathogen Triad

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 56
Author(s):  
Parwez Ahmad ◽  
Chaima Bensaoud ◽  
Imen Mekki ◽  
Mujeeb Ur Rehman ◽  
Michail Kotsyfakis
Keyword(s):  
Gene Expression ◽  
Species Interactions ◽  
Messenger Rna ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Regulation Of Gene Expression ◽  
Host Pathogen Interactions ◽  
Non Coding Rna ◽  
Host Pathogen ◽  
Time Specific

Long non-coding (lnc)RNAs have emerged as critical regulators of gene expression and are involved in almost every cellular process. They can bind to other molecules including DNA, proteins, or even other RNA types such messenger RNA or small RNAs. LncRNAs are typically expressed at much lower levels than mRNA, and their expression is often restricted to tissue- or time-specific developmental stages. They are also involved in several inter-species interactions, including vector–host–pathogen interactions, where they can be either vector/host-derived or encoded by pathogens. In these interactions, they function via multiple mechanisms including regulating pathogen growth and replication or via cell-autonomous antimicrobial defense mechanisms. Recent advances suggest that characterizing lncRNAs and their targets in different species may hold the key to understanding the role of this class of non-coding RNA in interspecies crosstalk. In this review, we present a general overview of recent studies related to lncRNA-related regulation of gene expression as well as their possible involvement in regulating vector–host–pathogen interactions.

scholarly journals Targeted RNA-Seq Reveals the M. tuberculosis Transcriptome from an In Vivo Infection Model

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 848
Author(s):  
Fernanda Cornejo-Granados ◽  
Gamaliel López-Leal ◽  
Dulce A. Mata-Espinosa ◽  
Jorge Barrios-Payán ◽  
Brenda Marquina-Castillo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Infection Model ◽  
Rna Seq ◽  
Host Pathogen Interactions ◽  
In Vivo Models ◽  
Host Pathogen ◽  
Intergenic Regions ◽  
Specialized Equipment

The study of host-pathogen interactions using in vivo models with intracellular pathogens like Mycobacterium tuberculosis (Mtb) entails technical limitations, such as: (i) Selecting an efficient differential lysis system to enrich the pathogen cells; (ii) obtaining sufficient high-quality RNA; and (iii) achieving an efficient rRNA depletion. Thus, some authors had used flow cytometers to separate infected cells or significantly increase the sequencing depth of host–pathogen RNA libraries to observe the pathogens’ gene expression. However, these options carry additional expenses in specialized equipment typically not available for all laboratories. Here, we propose an experimental protocol involving differential cell lysis and a probe-based ribosomal depletion to determine the gene expression of Mtb and its host during in vivo infection. This method increased the number of observed pathogen-expressed genes from 13 using the traditional RNA-seq approach to 702. After eliminating rRNA reads, we observed that 61.59% of Mtb sequences represented 702 genes, while 38.41% represented intergenic regions. Some of the most expressed genes codified for IS1081 (Rv2512c) transposase and eight PE-PGRS members, such as PGRS49 and PGRS50. As expected, a critical percent of the expressed genes codified for secreted proteins essential for infection, such as PE68, lppN, and LpqH. Moreover, three Mtb ncRNAs were highly expressed (small RNA MTS2823, transfer-messenger RNA RF00023, and ribozyme RF00010). Many of the host-expressed genes were related to the inflammation process and the expression of surfactant proteins such as the Sftpa and Sftpc, known to bind Mtb to alveolar macrophages and mi638, a microRNA with no previous associations with pulmonary diseases. The main objective of this study is to present the method, and a general catalog of the Mtb expressed genes at one point of the in vivo infection. We believe our method represents a different approach to the existing ones to study host–pathogen interactions in tuberculosis and other similar intracellular infections, without the necessity of specialized equipment.

Exploring host-pathogen interactions at the epithelial surface: application of transcriptomics in lung biology

2007 ◽  
Vol 292 (2) ◽  
pp. L367-L377 ◽  
Author(s):  
Joost B. Vos ◽  
Nicole A. Datson ◽  
Klaus F. Rabe ◽  
Pieter S. Hiemstra
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Large Scale ◽  
Brain Research ◽  
Airway Epithelial Cells ◽  
Airway Epithelial ◽  
Host Pathogen Interactions ◽  
Epithelial Surface ◽  
Complex Interactions ◽  
Host Pathogen

The epithelial surface of the airways is the largest barrier-forming interface between the human body and the outside world. It is now well recognized that, at this strategic position, airway epithelial cells play an eminent role in host defense by recognizing and responding to microbial exposure. Conversely, inhaled microorganisms also respond to contact with epithelial cells. Our understanding of this cross talk is limited, requiring sophisticated experimental approaches to analyze these complex interactions. High-throughput technologies, such as DNA microarray analysis and serial analysis of gene expression (SAGE), have been developed to screen for gene expression levels at large scale within single experiments. Since their introduction, these hypothesis-generating technologies have been widely used in diverse areas such as oncology and brain research. Successful application of these genomics-based technologies has also revealed novel insights in host-pathogen interactions in both the host and pathogen. This review aims to provide an overview of the SAGE and microarray technology illustrated by their application in the analysis of host-pathogen interactions. In particular, the interactions between epithelial cells in the human lungs and clinically relevant microorganisms are the central focus of this review.

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

2020 ◽  
Vol 21 (8) ◽  
pp. 2742 ◽  
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.

scholarly journals Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli

2010 ◽  
Vol 285 (14) ◽  
pp. 10690-10702 ◽  
Author(s):  
Anders Boysen ◽  
Jakob Møller-Jensen ◽  
Birgitte Kallipolitis ◽  
Poul Valentin-Hansen ◽  
Martin Overgaard
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Translational Regulation ◽  
Regulation Of Gene Expression ◽  
Non Coding Rna

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

2014 ◽  
Vol 5 (3) ◽  
pp. 183-194 ◽  
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.

Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.

2016 ◽  
Vol 14 (02) ◽  
pp. 1641009 ◽  
Author(s):  
Elena V. Zemlyanskaya ◽  
Daniil S. Wiebe ◽  
Nadezhda A. Omelyanchuk ◽  
Victor G. Levitsky ◽  
Victoria V. Mironova
Keyword(s):  
Gene Expression ◽  
Meta Analysis ◽  
Regulation Of Gene Expression ◽  
Gene Promoters ◽  
Auxin Response ◽  
Regulatory Regions ◽  
Core Motif ◽  
Functional Roles ◽  
Functional Features ◽  
Time Specific

Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression.

MicroRNA-mediated gene silencing: are we close to a unifying model?

2012 ◽  
Vol 3 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Victoria James ◽  
Sybil C.K. Wong ◽  
Tyson V. Sharp
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Messenger Rna ◽  
Transcriptional Regulators ◽  
Effector Proteins ◽  
Specific Reference ◽  
Functional Studies ◽  
Non Coding Rna ◽  
Almost All ◽  
Terminal Effector

AbstractMicroRNAs (miRNAs) comprise a group of small non-coding RNA –21 nucleotides in length. They act as post-transcriptional regulators of gene expression by forming base pairing interactions with target messenger RNA (mRNA). At least 1000 miRNAs are predicted to be expressed in humans and are encoded for in the genome of almost all organisms. Functional studies indicate that every cellular process studied thus far is regulated at some level by miRNAs. Given this expansive role, it is not surprising that disruption of this crucial pathway underlies the initiation of, or in the least, contributes to the development and progression of numerous human diseases and physiological disorders. This review will focus on the latest developments in uncovering the mechanism(s) of miRNA-mediated silencing with specific reference to the function of terminal effector proteins, how translation of target mRNA is inhibited and whether we are moving towards understanding this fundamental gene silencing paradigm.

scholarly journals Gene expression profiling in human neutrophils after infection with Acinetobacter baumannii in vitro

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242674
Author(s):  
María Lázaro-Díez ◽  
Itziar Chapartegui-González ◽  
Borja Suberbiola ◽  
J. Gonzalo Ocejo-Vinyals ◽  
Marcos López-Hoyos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acinetobacter Baumannii ◽  
Protein Quantification ◽  
Effector Proteins ◽  
Human Neutrophils ◽  
Host Pathogen Interactions ◽  
Proinflammatory Response ◽  
Host Pathogen ◽  
Key Aspects

Acinetobacter baumannii is a Gram negative nosocomial pathogen that has acquired increasing worldwide notoriety due to its high antibiotic resistance range and mortality rates in hospitalized patients. Therefore, it is necessary to better understand key aspects of A. baumannii pathogenesis such as host-pathogen interactions. In this report, we analyzed both gene expression and cytokine production by human neutrophils infected with A. baumannii. Our assays reveal a proinflammatory response of neutrophils after A. baumannii infection, since intracellular transcription of effector proteins such as COX-2, transcription factors, and proinflammatory cytokines resulted significantly upregulated in neutrophils infected by A. baumannii, compared with unstimulated human neutrophils. Translation and release of CXCL-8, IL-1β and TNF-α by neutrophils was confirmed by protein quantification in culture supernatants. Results obtained in this report reinforce the importance of human neutrophils in controlling A. baumannii infections but also emphasize the proinflammatory nature of these host-pathogen interactions as a target for future immunomodulatory therapies.

scholarly journals Regulatory Non-coding RNAs for Death Associated Protein Kinase Family

2021 ◽  
Vol 8 ◽  
Author(s):  
Qingshui Wang ◽  
Youyu Lin ◽  
Wenting Zhong ◽  
Yu Jiang ◽  
Yao Lin
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Tumor Development ◽  
Invasion And Metastasis ◽  
Calcium Dependent ◽  
Non Coding Rna ◽  
Death Associated Protein Kinase ◽  
Non Coding Rnas ◽  
Long Non Coding Rna

The death associated protein kinases (DAPKs) are a family of calcium dependent serine/threonine kinases initially identified in the regulation of apoptosis. Previous studies showed that DAPK family members, including DAPK1, DAPK2 and DAPK3 play a crucial regulatory role in malignant tumor development, in terms of cell apoptosis, proliferation, invasion and metastasis. Accumulating evidence has demonstrated that non-coding RNAs, including microRNA (miRNA), long non-coding RNA (lncRNA) and circRNA, are involved in the regulation of gene expression and tumorigenesis. Recent studies indicated that non-coding RNAs participate in the regulation of DAPKs. In this review, we summarized the current knowledge of non-coding RNAs, as well as the potential miRNAs, lncRNAs and circRNAs, that are involved in the regulation of DAPKs.

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