scholarly journals Regulation of angiogenesis through a microRNA (miR-130a) that down-regulates antiangiogenic homeobox genes GAX and HOXA5

Blood ◽  
2008 ◽  
Vol 111 (3) ◽  
pp. 1217-1226 ◽  
Author(s):  
Yun Chen ◽  
David H. Gorski

Abstract Angiogenesis is critical to tumor progression. The homeobox gene GAX inhibits angiogenesis in vascular endothelial cells (ECs). We have identified a microRNA (miR-130a) that regulates GAX expression and hypothesized that it plays a major role in modulating GAX activity in ECs. A 280-bp fragment from the GAX 3′-untranslated region (3′-UTR) containing 2 miR-130a targeting sites was observed to be required for the rapid down-regulation of GAX expression by serum and proangiogenic factors, whereas the activity of the GAX promoter did not vary with exposure to serum or proangiogenic factors. This same 280-bp sequence in the GAX 3′-UTR cloned into the psiCHECK2-Luciferase vector mediated serum-induced down-regulation of the reporter gene when placed 3′ of it. Finally, forced expression of miR-130a inhibits GAX expression through this specific GAX 3′-UTR sequence. A genome-wide search for other possible miR-130a binding sites revealed an miR-130a targeting site in the 3′-UTR of the antiangiogenic homeobox gene HOXA5, the expression and antiangiogenic activity of which are also inhibited by miR-130a. From these data, we conclude that miR-130a is a regulator of the angiogenic phenotype of vascular ECs largely through its ability to modulate the expression of GAX and HOXA5.

2010 ◽  
Vol 30 (15) ◽  
pp. 3902-3913 ◽  
Author(s):  
Yun Chen ◽  
Malathi Banda ◽  
Cecilia L. Speyer ◽  
Jennifer S. Smith ◽  
Arnold B. Rabson ◽  
...  

ABSTRACT Tumors secrete proangiogenic factors to induce the ingrowth of blood vessels from the stroma. These peptides bind to cell surface receptors on vascular endothelial cells (ECs), triggering signaling cascades that activate and repress batteries of downstream genes responsible for the angiogenic phenotype. To determine if microRNAs (miRNAs) affect regulation of the EC phenotype by GAX, a homeobox gene and negative transcriptional regulator of the angiogenic phenotype, we tested the effect of miR-221 on GAX expression. miR-221 strongly upregulated GAX, suggesting that miR-221 downregulates a repressor of GAX. We next expressed miR-221 in ECs and identified ZEB2, a modulator of the epithelial-mesenchymal transition, as being strongly downregulated by miR-221. Using miR-221 expression constructs and an inhibitor, we determined that ZEB2 is upregulated by serum and downregulates GAX, while the expression of miR-221 upregulates GAX and downregulates ZEB2. A mutant miR-221 fails to downregulate ZEB2 or upregulate GAX. Finally, using chromatin immunoprecipitation, we identified two ZEB2 binding sites that modulate the ability of ZEB2 to downregulate GAX promoter activity. We conclude that miR-221 upregulates GAX primarily through its ability to downregulate the expression of ZEB2. These observations suggest a strategy for inhibiting angiogenesis by either recapitulating miR-221 expression or inhibiting ZEB2 activation.


Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1984
Author(s):  
Majid Nikpay ◽  
Sepehr Ravati ◽  
Robert Dent ◽  
Ruth McPherson

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.


Hypertension ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1291-1296 ◽  
Author(s):  
Pankaj Sharma ◽  
Jennie Fatibene ◽  
Franco Ferraro ◽  
Haiyan Jia ◽  
Sue Monteith ◽  
...  

2014 ◽  
Vol 23 (03) ◽  
pp. 1460008
Author(s):  
Kevin Byron ◽  
Jason T. L. Wang ◽  
Dongrong Wen

Developing effective artificial intelligence tools to find motifs in DNA, RNA and proteins poses a challenging yet important problem in life science research. In this paper, we present a computational approach for finding RNA tertiary motifs in genomic sequences. Specifically, we predict genomic coordinate locations for coaxial helical stackings in 3-way RNA junctions. These predictions are provided by our tertiary motif search package, named CSminer, which utilizes two versatile methodologies: random forests and covariance models. A coaxial helical stacking tertiary motif occurs in a 3-way RNA junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Our CSminer tool first uses a genome-wide search method based on covariance models to find a genomic region that may potentially contain a coaxial helical stacking tertiary motif. CSminer then uses a random forests classifier to predict whether the genomic region indeed contains the tertiary motif. Experimental results demonstrate the effectiveness of our approach.


BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 648 ◽  
Author(s):  
Jeroen Crappé ◽  
Wim Van Criekinge ◽  
Geert Trooskens ◽  
Eisuke Hayakawa ◽  
Walter Luyten ◽  
...  

1999 ◽  
Vol 5 (4) ◽  
pp. 271-278 ◽  
Author(s):  
Yuanhong Ma ◽  
Jeffrey D. Ohmen ◽  
Zhiming Li ◽  
Gordon L. Bentley ◽  
Colleen McElree ◽  
...  

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 209 ◽  
Author(s):  
Elizaveta Radion ◽  
Olesya Sokolova ◽  
Sergei Ryazansky ◽  
Pavel Komarov ◽  
Yuri Abramov ◽  
...  

Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints.


BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S55 ◽  
Author(s):  
Albert Rosenberger ◽  
Nico Janicke ◽  
Karola Köhler ◽  
Katrin Korb ◽  
Bettina Kulle ◽  
...  

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