scholarly journals The miRNA biogenesis in marine bivalves

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1763 ◽  
Author(s):  
Umberto Rosani ◽  
Alberto Pallavicini ◽  
Paola Venier
Keyword(s):  
Translational Repression ◽  
Mirna Biogenesis ◽  
Molecular Processes ◽  
Antiviral Responses ◽  
Digital Expression ◽  
Marine Bivalves ◽  
Mature Micrornas ◽  
Digital Expression Analysis ◽  
Non Coding Rnas ◽  
Shed Light

Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture speciesMytilus galloprovincialisandCrassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves.

Intronic microRNAs: a crossroad in gene regulation

2012 ◽  
Vol 40 (4) ◽  
pp. 759-761 ◽  
Author(s):  
Natalia Gromak
Keyword(s):  
Gene Regulation ◽  
Human Gene ◽  
Mrna Splicing ◽  
Translational Repression ◽  
Mirna Biogenesis ◽  
Mrna Transcript ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
Human Genes ◽  
Non Coding Rnas

Most human genes transcribed by RNA Pol II (polymerase II) contain short exons separated by long tracts of non-coding intronic sequences. In addition to their role in generating proteomic diversity through the process of alternative splicing, intronic sequences host many ncRNAs (non-coding RNAs), involved in various gene regulation processes. miRNAs (microRNAs) are short ncRNAs that mediate either mRNA transcript translational repression and/or degradation. Between 50 and 80% of miRNAs are encoded within introns of host mRNA genes. This observation suggests that there is co-regulation between the miRNA biogenesis and pre-mRNA splicing processes. The present review summarizes current advances in this field and discusses possible roles for intronic co-transcriptional cleavage events in the regulation of human gene expression.

Comparative E-Cadherin Digital Expression Analysis in HPV and non-HPV Related Squamous Cell Carcinoma of the Oral Cavity

2021 ◽  
Vol 41 (1) ◽  
pp. 163-167
Author(s):  
ARISTEIDIS CHRYSOVERGIS ◽  
VASILEIOS PAPANIKOLAOU ◽  
NICHOLAS MASTRONIKOLIS ◽  
DESPOINA SPYROPOULOU ◽  
MARIA ADAMOPOULOU ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Cavity ◽  
Cell Carcinoma ◽  
Expression Analysis ◽  
Squamous Cell ◽  
Digital Expression ◽  
Digital Expression Analysis ◽  
E Cadherin

Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat

2021 ◽  
Author(s):  
Juan Manuel Crescente ◽  
Diego Zavallo ◽  
Mariana del Vas ◽  
Sebastian Asurmendi ◽  
Marcelo Helguera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Triticum Aestivum ◽  
Transposable Elements ◽  
Small Rna ◽  
Translational Repression ◽  
High Homology ◽  
Genome Wide ◽  
Target Sites ◽  
The Common ◽  
Non Coding Rnas

Abstract Plant microRNAs (miRNAs) are a class of small non-coding RNAs that are 20–24 nucleotides length and can repress gene expression at post-transcriptional levels by target degradation or translational repression. There is increasing evidence that some microRNAs can be derived from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs) in plants. We used public small RNA, degradome libraries and the common wheat (Triticum aestivum) genome to screen miRNAs production and target sites. We also created a comprehensive wheat MITE database using known and identifying novel elements. We found high homology between MITEs and 14% of all the miRNAs production sites in wheat. Furthermore, we show that MITE-derived miRNAs have preference for target degradation sites with MITE insertions in 3' UTR regions in wheat.

scholarly journals Roles of long non-coding RNAs and emerging RNA-binding proteins in innate antiviral responses

Theranostics ◽  
2020 ◽  
Vol 10 (20) ◽  
pp. 9407-9424 ◽  
Author(s):  
Yiliang Wang ◽  
Yun Wang ◽  
Weisheng Luo ◽  
Xiaowei Song ◽  
Lianzhou Huang ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Antiviral Responses ◽  
Non Coding Rnas

scholarly journals Non-coding RNAs control metabolic state in mycobacteria

2019 ◽  
Author(s):  
Dolly Mehta ◽  
K Anjali ◽  
A Achuthan ◽  
Ritu Gupta ◽  
Arati Ramesh
Keyword(s):  
Lipid Metabolism ◽  
Cellular Response ◽  
Rna Binding ◽  
Translational Repression ◽  
Metabolic Flexibility ◽  
Redox Enzymes ◽  
Transcriptomic Response ◽  
Bacterial Signaling ◽  
Non Coding Rnas ◽  
Reductive Metabolism

ABSTRACTNon-coding RNAs play pivotal roles in bacterial signaling. However, RNAs from certain phyla (specially high-GC actinobacteria) remain elusive. Here, by revamping existing approaches we discover a family of structurally conserved RNAs in actinobacteria. These RNAs function by the recruiting ANTAR proteins to select transcripts; regulating them via translational repression. By overlapping with ORF start sites, these RNAs provide mechanisms by which even leader-less transcripts are regulated. In mycobacteria, transcripts marked by ANTAR-target RNAs are few but encode important redox enzymes especially involved in lipid metabolism. Notably, the cellular response to ANTAR-regulation is hierarchical, wherein immediate metabolic changes induced by ANTAR-RNA binding are amplified through a global transcriptomic response. This includes several genes from oxidative/reductive pathways; ultimately switching cells towards reductive metabolism. This discovery of ANTAR-target RNAs and associated regulation places RNAs as crucial players in controlling metabolic flexibility of mycobacteria, proposing a prominent role for ANTAR regulation across actinobacteria.

scholarly journals Inflamma-MicroRNAs in Alzheimer’s Disease: From Disease Pathogenesis to Therapeutic Potentials

2021 ◽  
Vol 15 ◽  
Author(s):  
Yuanyuan Liang ◽  
Lin Wang
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Messenger Rna ◽  
Senile Dementia ◽  
Therapeutic Targets ◽  
Peripheral Circulation ◽  
Diagnostic Biomarkers ◽  
Non Coding Rnas ◽  
Shed Light

Alzheimer’s disease (AD) is the most common cause of senile dementia. Although AD research has made important breakthroughs, the pathogenesis of this disease remains unclear, and specific AD diagnostic biomarkers and therapeutic strategies are still lacking. Recent studies have demonstrated that neuroinflammation is involved in AD pathogenesis and is closely related to other health effects. MicroRNAs (miRNAs) are a class of endogenous short sequence non-coding RNAs that indirectly inhibit translation or directly degrade messenger RNA (mRNA) by specifically binding to its 3′ untranslated region (UTR). Several broadly expressed miRNAs including miR-21, miR-146a, and miR-155, have now been shown to regulate microglia/astrocytes activation. Other miRNAs, including miR-126 and miR-132, show a progressive link to the neuroinflammatory signaling. Therefore, further studies on these inflamma-miRNAs may shed light on the pathological mechanisms of AD. The differential expression of inflamma-miRNAs (such as miR-29a, miR-125b, and miR-126-5p) in the peripheral circulation may respond to AD progression, similar to inflammation, and therefore may become potential diagnostic biomarkers for AD. Moreover, inflamma-miRNAs could also be promising therapeutic targets for AD treatment. This review provides insights into the role of inflamma-miRNAs in AD, as well as an overview of general inflamma-miRNA biology, their implications in pathophysiology, and their potential roles as biomarkers and therapeutic targets.

scholarly journals Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells

2021 ◽  
Vol 8 ◽  
Author(s):  
Tarana Siddika ◽  
Ilka U. Heinemann
Keyword(s):  
Cost Efficiency ◽  
Developmental Stages ◽  
Disease Diagnosis ◽  
Live Cells ◽  
Mirna Biogenesis ◽  
Posttranscriptional Gene Regulation ◽  
Potential Biomarker ◽  
Non Coding Rnas ◽  
External Stimuli ◽  
Expression And Activity

MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis. Increasingly, miRNAs have been recognized as a potential biomarker for disease diagnosis. MiRNAs can be found in blood, plasma, and tissues, and miRNA expression and activity differ in developmental stages, tissues and in response to external stimuli. MiRNA transcripts are matured from pri-miRNA over pre-miRNA to mature miRNA, a process that includes multiple steps and enzymes. Many tools are available to identify and quantify specific miRNAs, ranging from measuring total miRNA, specific miRNA activity, miRNA arrays and miRNA localization. The various miRNA assays differ in accuracy, cost, efficiency and convenience of monitoring miRNA dynamics. To acknowledge the significance and increasing research interest in miRNAs, we summarize the traditional as well as novel methods of miRNA quantification with strengths and limitations of various techniques in biochemical and medical research.

Using miRNAs as diagnostic biomarkers for male infertility: opportunities and challenges

2020 ◽  
Vol 26 (4) ◽  
pp. 199-214 ◽  
Author(s):  
A Vashisht ◽  
G K Gahlay
Keyword(s):  
Male Infertility ◽  
Human Development ◽  
Infertility Treatment ◽  
Mirna Biogenesis ◽  
Testicular Development ◽  
Transcriptional Level ◽  
Diagnostic Biomarkers ◽  
Clinical Disorder ◽  
Epididymal Maturation ◽  
Non Coding Rnas

Abstract The non-coding genome has been extensively studied for its role in human development and diseases. MicroRNAs (miRNAs) are small non-coding RNAs, which can regulate the expression of hundreds of genes at the post-transcriptional level. Therefore, any defects in miRNA biogenesis or processing can affect the genes and have been linked to several diseases. Male infertility is a clinical disorder with a significant number of cases being idiopathic. Problems in spermatogenesis and epididymal maturation, testicular development, sperm maturation or migration contribute to male infertility, and many of these idiopathic cases are related to issues with the miRNAs which tightly regulate these processes. This review summarizes the recent research on various such miRNAs and puts together the candidate miRNAs that may be used as biomarkers for diagnosis. The development of strategies for male infertility treatment using anti-miRs or miRNA mimics is also discussed. Although promising, the development of miRNA diagnostics and therapeutics is challenging, and ways to overcome some of these challenges are also reviewed.

How do microRNAs regulate gene expression?

2008 ◽  
Vol 36 (6) ◽  
pp. 1224-1231 ◽  
Author(s):  
Ian G. Cannell ◽  
Yi Wen Kong ◽  
Martin Bushell
Keyword(s):  
Gene Expression ◽  
Untranslated Region ◽  
Protein Production ◽  
Translational Repression ◽  
Regulate Gene Expression ◽  
Target Mrna ◽  
Target Mrnas ◽  
Non Coding Rnas ◽  
Regulate Gene

miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3′-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing. The exact mechanism of miRNA-mediated translational repression is yet to be fully determined, but recent data from our laboratory have shown that the stage of translation which is inhibited by miRNAs is dependent upon the promoter used for transcribing the target mRNA. This review focuses on understanding how miRNA repression is operating in light of these findings and the questions that still remain.

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