scholarly journals Regulation of CCL2 expression in human vascular endothelial cells by a neighboring divergently transcribed long noncoding RNA

2019 ◽  
Vol 116 (33) ◽  
pp. 16410-16419 ◽  
Author(s):  
Nadiya Khyzha ◽  
Melvin Khor ◽  
Peter V. DiStefano ◽  
Liangxi Wang ◽  
Ljubica Matic ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Vascular Endothelial Cells ◽  
Regulatory Elements ◽  
Mrna Levels ◽  
Vascular Endothelial ◽  
Inflammatory Stimuli

Atherosclerosis is a chronic inflammatory disease that is driven, in part, by activation of vascular endothelial cells (ECs). In response to inflammatory stimuli, the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway orchestrates the expression of a network of EC genes that contribute to monocyte recruitment and diapedesis across the endothelium. Although many long noncoding RNAs (lncRNAs) are dysregulated in atherosclerosis, they remain poorly characterized, especially in the context of human vascular inflammation. Prior studies have illustrated that lncRNAs can regulate their neighboring protein-coding genes via interaction with protein complexes. We therefore identified and characterized neighboring interleukin-1β (IL-1β)−regulated messenger RNA (mRNA)−lncRNA pairs in ECs. We found these pairs to be highly correlated in expression, especially when located within the same chromatin territory. Additionally, these pairs were predominantly divergently transcribed and shared common gene regulatory elements, characterized by active histone marks and NF-κB binding. Further analysis was performed on lncRNA-CCL2, which is transcribed divergently to the gene, CCL2, encoding a proatherosclerotic chemokine. LncRNA-CCL2 and CCL2 showed coordinate up-regulation in response to inflammatory stimuli, and their expression was correlated in unstable symptomatic human atherosclerotic plaques. Knock-down experiments revealed that lncRNA-CCL2 positively regulated CCL2 mRNA levels in multiple primary ECs and EC cell lines. This regulation appeared to involve the interaction of lncRNA-CCL2 with RNA binding proteins, including HNRNPU and IGF2BP2. Hence, our approach has uncovered a network of neighboring mRNA−lncRNA pairs in the setting of inflammation and identified the function of an lncRNA, lncRNA-CCL2, which may contribute to atherogenesis in humans.

scholarly journals Low Shear Stress Upregulates CX3CR1 Expression by Inducing VCAM-1 via the NF-κB Pathway in Vascular Endothelial Cells

2020 ◽  
Vol 78 (3) ◽  
pp. 383-389 ◽  
Author(s):  
Yiwei Zhao ◽  
Peile Ren ◽  
Qiufang Li ◽  
Shafiu Adam Umar ◽  
Tan Yang ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Shear Stress ◽  
Protein Expression ◽  
Vascular Endothelial Cells ◽  
Critical Role ◽  
Mrna Levels ◽  
Vascular Endothelial ◽  
Low Shear Stress ◽  
Low Shear ◽  
Cx3cr1 Expression

Abstract Atherosclerosis is a significant cause of mortality and morbidity. Studies suggest that the chemokine receptor CX3CR1 plays a critical role in atherogenesis. Shear stress is an important mechanical force that affects blood vessel function. In this study, we investigated the effect of shear stress on CX3CR1 expression in vascular endothelial cells (VECs). First, cells were exposed to different shear stress and then CX3CR1 mRNA and protein were measured by quantitative RT-PCR and western blot analysis, respectively. CX3CR1 gene silencing was used to analyze the molecular mechanisms underlying shear stress-mediated effects on CX3CR1 expression. CX3CR1 mRNA and protein expression were significantly increased with 4.14 dyne/cm2 of shear stress compared with other tested levels of shear stress. We observed a significant increase in CX3CR1 mRNA levels at 2 h and CX3CR1 protein expression at 4 h. CX3CR1-induced VCAM-1 expression in response to low shear stress by activating NF-κB signaling pathway in VECs. Our findings demonstrate that low shear stress increases CX3CR1 expression, which increases VCAM-1 expression due to elevated NF-κB activation. The current study provides evidence of the correlation between shear stress and atherosclerosis mediated by CX3CR1.

Prox1 expression is negatively regulated by miR-181 in endothelial cells

Blood ◽  
2010 ◽  
Vol 116 (13) ◽  
pp. 2395-2401 ◽  
Author(s):  
Jan Kazenwadel ◽  
Michael Z. Michael ◽  
Natasha L. Harvey
Keyword(s):  
Endothelial Cells ◽  
Endothelial Cell ◽  
Cell Fate ◽  
Vascular Endothelial Cells ◽  
Vascular Development ◽  
Lymphatic Endothelial Cell ◽  
Mrna Levels ◽  
Vascular Endothelial ◽  
Lymphatic Endothelial Cells ◽  
Prox1 Expression

Abstract The specification of arterial, venous, and lymphatic endothelial cell fate is critical during vascular development. Although the homeobox transcription factor, Prox1, is crucial for the specification and maintenance of lymphatic endothelial cell identity, little is known regarding the mechanisms that regulate Prox1 expression. Here we demonstrate that miR-181a binds the 3′ untranslated region of Prox1, resulting in translational inhibition and transcript degradation. Increased miR-181a activity in primary embryonic lymphatic endothelial cells resulted in substantially reduced levels of Prox1 mRNA and protein and reprogramming of lymphatic endothelial cells toward a blood vascular phenotype. Conversely, treatment of primary embryonic blood vascular endothelial cells with miR-181a antagomir resulted in increased Prox1 mRNA levels. miR-181a expression is significantly higher in embryonic blood vascular endothelial cells compared with lymphatic endothelial cells, suggesting that miR-181 activity could be an important mechanism by which Prox1 expression is silenced in the blood vasculature during development. Our work is the first example of a microRNA that targets Prox1 and has implications for the control of Prox1 expression during vascular development and neo-lymphangiogenesis.

scholarly journals Control of noncoding RNA production and histone levels by a 5′ tRNA fragment

2018 ◽  
Author(s):  
Ana Boskovic ◽  
Xin Yang Bing ◽  
Ebru Kaymak ◽  
Oliver J Rando
Keyword(s):  
Transcriptional Repression ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Noncoding Rnas ◽  
Cajal Body ◽  
Mrna Levels ◽  
Histone 3 ◽  
Rna Biogenesis ◽  
Mechanistic Basis

Small RNAs derived from mature tRNAs, referred to as tRNA fragments or "tRFs", are an emerging class of regulatory RNAs with poorly understood functions in cellular regulation. We recently identified a role for one specific tRF - 5′ tRF-Gly-GCC, or tRF-GG - in repression of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs normally synthesized in Cajal bodies. Among these noncoding RNAs, tRF-GG regulation of the U7 snRNA modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, activity of a histone 3′ UTR reporter, and ultimately on MERVL regulation could all be suppressed by the U7 RNA. We show that the related RNA-binding proteins hnRNPF and H bind directly to tRF-GG, and are required for Cajal body biogenesis. Together, our data reveal a conserved mechanism for 5′ tRNA fragment control of noncoding RNA biogenesis and, consequently, in global chromatin organization.

scholarly journals Prediction of mRNA subcellular localization using deep recurrent neural networks

2019 ◽  
Vol 35 (14) ◽  
pp. i333-i342 ◽  
Author(s):  
Zichao Yan ◽  
Eric Lécuyer ◽  
Mathieu Blanchette
Keyword(s):  
Subcellular Localization ◽  
Messenger Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Elements ◽  
Supplementary Information ◽  
Specific Sequence ◽  
Structure Information ◽  
Subcellular Compartments ◽  
Sequence Elements

Abstract Motivation Messenger RNA subcellular localization mechanisms play a crucial role in post-transcriptional gene regulation. This trafficking is mediated by trans-acting RNA-binding proteins interacting with cis-regulatory elements called zipcodes. While new sequencing-based technologies allow the high-throughput identification of RNAs localized to specific subcellular compartments, the precise mechanisms at play, and their dependency on specific sequence elements, remain poorly understood. Results We introduce RNATracker, a novel deep neural network built to predict, from their sequence alone, the distributions of mRNA transcripts over a predefined set of subcellular compartments. RNATracker integrates several state-of-the-art deep learning techniques (e.g. CNN, LSTM and attention layers) and can make use of both sequence and secondary structure information. We report on a variety of evaluations showing RNATracker’s strong predictive power, which is significantly superior to a variety of baseline predictors. Despite its complexity, several aspects of the model can be isolated to yield valuable, testable mechanistic hypotheses, and to locate candidate zipcode sequences within transcripts. Availability and implementation Code and data can be accessed at https://www.github.com/HarveyYan/RNATracker. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Regulation of 6-Pyruvoyltetrahydropterin Synthase Activity and Messenger RNA Abundance in Human Vascular Endothelial Cells

Circulation ◽  
1998 ◽  
Vol 98 (17) ◽  
pp. 1703-1706 ◽  
Author(s):  
Philippe Linscheid ◽  
Andreas Schaffner ◽  
Nenad Blau ◽  
Gabriele Schoedon
Keyword(s):  
Endothelial Cells ◽  
Messenger Rna ◽  
Vascular Endothelial Cells ◽  
Vascular Endothelial

scholarly journals Regulation and Function of RNA Pseudouridylation in Human Cells

2020 ◽  
Vol 54 (1) ◽  
pp. 309-336
Author(s):  
Erin K. Borchardt ◽  
Nicole M. Martinez ◽  
Wendy V. Gilbert
Keyword(s):  
Messenger Rna ◽  
Noncoding Rna ◽  
Protein Production ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Human Cells ◽  
Rna Sequences ◽  
Rna Targets ◽  
Pseudouridine Synthases ◽  
And Function

Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.

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