The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression

Hon, Lawrence S.; Zhang, Zemin

doi:10.1186/gb-2007-8-8-r166

Cited by 141 publications

(136 citation statements)

References 63 publications

(94 reference statements)

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“…Consistent with this model, the down-regulation of miRNA expression in airway epithelial cells with smoking may be a consequence of repetitive airway injury that results in accumulation of proliferating and dedifferentiated cells. Several studies have sought to establish regulatory relationships between miRNA and mRNA expression (33)(34)(35)(36). By collecting miRNA and mRNA from the same samples, we were able to discover correlations between miRNA and mRNA expression profiles both across patient groups and within individuals.…”

Section: Differentially Expressed In Vivomentioning

confidence: 82%

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

Schembri

Sridhar

Perdomo

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

401

328

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We have shown that smoking impacts bronchial airway gene expression and that heterogeneity in this response associates with smoking-related disease risk. In this study, we sought to determine whether microRNAs (miRNAs) play a role in regulating the airway gene expression response to smoking. We examined whole-genome miRNA and mRNA expression in bronchial airway epithelium from current and never smokers (n ‫؍‬ 20) and found 28 miRNAs to be differentially expressed (P < 0.05) with the majority being down-regulated in smokers. We further identified a number of mRNAs whose expression level is highly inversely correlated with miRNA expression in vivo. Many of these mRNAs contain potential binding sites for the differentially expressed miRNAs in their 3 -untranslated region (UTR) and are themselves affected by smoking. We found that either increasing or decreasing the levels of mir-218 (a miRNA that is strongly affected by smoking) in both primary bronchial epithelial cells and H1299 cells was sufficient to cause a corresponding decrease or increase in the expression of predicted mir-218 mRNA targets, respectively. Further, mir-218 expression is reduced in primary bronchial epithelium exposed to cigarette smoke condensate (CSC), and alteration of mir-218 levels in these cells diminishes the induction of the predicted mir-218 target MAFG in response to CSC. These data indicate that mir-218 levels modulate the airway epithelial gene expression response to cigarette smoke and support a role for miRNAs in regulating host response to environmental toxins.cigarette smoke ͉ mir-218 ͉ bronchial airway epithelium

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Section: Differentially Expressed In Vivomentioning

confidence: 82%

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

Schembri

Sridhar

Perdomo

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

401

328

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“…The two most important are discussed in the next two sections are (I) the binding site accessibility and (II) stoichiometry between a small RNA ant its target (or binding kinetics). Other factors, which might contribute to silencing in a context-dependent manner are, for example, alternative polyadenylation and arrangement of miRNA binding sites in 3'UTRs might cause different effects in different cells (Hon and Zhang, 2007;Majoros and Ohler, 2007;Nam et al, 2014a). In particular, there was a strong preference reported for targets to be located in close vicinity of the stop codon and the polyadenylation sites.…”

Section: Other Key Factors Influencing Target Recognition and Repressionmentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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“…It has been demonstrated that under certain cellular conditions a stable secondary structure could be unfolded to provide access to a miRNA target site. This miRNA mediated regulation can be exploited by a cell during stress response or in tissue specificity (29). There is evidence that two miRNAs may bind to a target mRNA in coordination.…”

Section: Mir-polymorphism In Mirna Target Sitesmentioning

confidence: 99%

MicroRNAs: Potential biomarkers in cancer

George

Mittal

2010

Indian J Clin Biochem

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The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression

Cited by 141 publications

References 63 publications

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

MicroRNAs: Potential biomarkers in cancer

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