A TRIPARTITE CLUSTERING ANALYSIS ON MICRORNA, GENE AND DISEASE MODEL

2012 ◽  
Vol 10 (01) ◽  
pp. 1240007 ◽  
Author(s):  
CHENGCHENG SHEN ◽  
YING LIU
Keyword(s):  
Gene Expression ◽  
Clustering Algorithm ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Disease Model ◽  
Relational Information ◽  
Microrna Gene ◽  
Research Findings ◽  
Family Based

Alteration of gene expression in response to regulatory molecules or mutations could lead to different diseases. MicroRNAs (miRNAs) have been discovered to be involved in regulation of gene expression and a wide variety of diseases. In a tripartite biological network of human miRNAs, their predicted target genes and the diseases caused by altered expressions of these genes, valuable knowledge about the pathogenicity of miRNAs, involved genes and related disease classes can be revealed by co-clustering miRNAs, target genes and diseases simultaneously. Tripartite co-clustering can lead to more informative results than traditional co-clustering with only two kinds of members and pass the hidden relational information along the relation chain by considering multi-type members. Here we report a spectral co-clustering algorithm for k-partite graph to find clusters with heterogeneous members. We use the method to explore the potential relationships among miRNAs, genes and diseases. The clusters obtained from the algorithm have significantly higher density than randomly selected clusters, which means members in the same cluster are more likely to have common connections. Results also show that miRNAs in the same family based on the hairpin sequences tend to belong to the same cluster. We also validate the clustering results by checking the correlation of enriched gene functions and disease classes in the same cluster. Finally, widely studied miR-17-92 and its paralogs are analyzed as a case study to reveal that genes and diseases co-clustered with the miRNAs are in accordance with current research findings.

scholarly journals Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets

2016 ◽  
Vol 113 (13) ◽  
pp. E1835-E1843 ◽  
Author(s):  
Mina Fazlollahi ◽  
Ivor Muroff ◽  
Eunjee Lee ◽  
Helen C. Causton ◽  
Harmen J. Bussemaker
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Nonsynonymous Mutation ◽  
Gene Regulatory ◽  
Genetic Modulators

Regulation of gene expression by transcription factors (TFs) is highly dependent on genetic background and interactions with cofactors. Identifying specific context factors is a major challenge that requires new approaches. Here we show that exploiting natural variation is a potent strategy for probing functional interactions within gene regulatory networks. We developed an algorithm to identify genetic polymorphisms that modulate the regulatory connectivity between specific transcription factors and their target genes in vivo. As a proof of principle, we mapped connectivity quantitative trait loci (cQTLs) using parallel genotype and gene expression data for segregants from a cross between two strains of the yeast Saccharomyces cerevisiae. We identified a nonsynonymous mutation in the DIG2 gene as a cQTL for the transcription factor Ste12p and confirmed this prediction empirically. We also identified three polymorphisms in TAF13 as putative modulators of regulation by Gcn4p. Our method has potential for revealing how genetic differences among individuals influence gene regulatory networks in any organism for which gene expression and genotype data are available along with information on binding preferences for transcription factors.

scholarly journals ETO-2 Associates with SCL in Erythroid Cells and Megakaryocytes and Provides Repressor Functions in Erythropoiesis

2005 ◽  
Vol 25 (23) ◽  
pp. 10235-10250 ◽  
Author(s):  
Anna H. Schuh ◽  
Alex J. Tipping ◽  
Allison J. Clark ◽  
Isla Hamlett ◽  
Boris Guyot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Protein Complexes ◽  
Fetal Liver ◽  
Regulation Of Gene Expression ◽  
Erythroid Differentiation ◽  
Cell Types ◽  
Erythroid Cells ◽  
Proteomic Approach ◽  
Endogenous Proteins

ABSTRACT Lineage specification and cellular maturation require coordinated regulation of gene expression programs. In large part, this is dependent on the activator and repressor functions of protein complexes associated with tissue-specific transcriptional regulators. In this study, we have used a proteomic approach to characterize multiprotein complexes containing the key hematopoietic regulator SCL in erythroid and megakaryocytic cell lines. One of the novel SCL-interacting proteins identified in both cell types is the transcriptional corepressor ETO-2. Interaction between endogenous proteins was confirmed in primary cells. We then showed that SCL complexes are shared but also significantly differ in the two cell types. Importantly, SCL/ETO-2 interacts with another corepressor, Gfi-1b, in red cells but not megakaryocytes. The SCL/ETO-2/Gfi-1b association is lost during erythroid differentiation of primary fetal liver cells. Genetic studies of erythroid cells show that ETO-2 exerts a repressor effect on SCL target genes. We suggest that, through its association with SCL, ETO-2 represses gene expression in the early stages of erythroid differentiation and that alleviation/modulation of the repressive state is then required for expression of genes necessary for terminal erythroid maturation to proceed.

scholarly journals Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits

2018 ◽  
Author(s):  
Heather E. Wheeler ◽  
Sally Ploch ◽  
Alvaro N. Barbeira ◽  
Rodrigo Bonazzola ◽  
Angela Andaleon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Complex Traits ◽  
Target Gene ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Nucleic Acid Binding ◽  
Expression Of Genes ◽  
Gene Associations ◽  
Made In

AbstractRegulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available GTEx tissues and find 2356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.

scholarly journals Removal of H3K27me3 by JMJ Proteins Controls Plant Development and Environmental Responses in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Nobutoshi Yamaguchi
Keyword(s):  
Gene Expression ◽  
Plant Development ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Histone H3 ◽  
Control Of Gene Expression ◽  
Precise Control ◽  
Repressive Histone Modification ◽  
Environmental Responses

Trimethylation of histone H3 lysine 27 (H3K27me3) is a highly conserved repressive histone modification that signifies transcriptional repression in plants and animals. In Arabidopsis thaliana, the demethylation of H3K27 is regulated by a group of JUMONJI DOMAIN-CONTANING PROTEIN (JMJ) genes. Transcription of JMJ genes is spatiotemporally regulated during plant development and in response to the environment. Once JMJ genes are transcribed, recruitment of JMJs to target genes, followed by demethylation of H3K27, is critically important for the precise control of gene expression. JMJs function synergistically and antagonistically with transcription factors and/or other epigenetic regulators on chromatin. This review summarizes the latest advances in our understanding of Arabidopsis H3K27me3 demethylases that provide robust and flexible epigenetic regulation of gene expression to direct appropriate development and environmental responses in plants.

scholarly journals Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma

2020 ◽  
Author(s):  
Soyeon Kim ◽  
Erick Forno ◽  
Rong Zhang ◽  
Qi Yan ◽  
Nadia Boutaoui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Puerto Rican ◽  
Childhood Asthma ◽  
Quantitative Trait ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Atopic Asthma ◽  
Nasal Airway ◽  
Airway Epithelial ◽  
Methylation Analysis

AbstractNasal airway epithelial methylation profiles have been associated with asthma, but the effects of such profiles on expression of distant cis-genes are largely unknown. We identified 16,867 significant methylation-gene expression pairs in nasal epithelium from Puerto Rican children and adolescents (with and without asthma) in an expression quantitative trait methylation (eQTM) analysis of cis-genes located within 1 Mb of the methylation probes tested. Most eQTM methylation probes were distant from their target genes, and more likely located in enhancer regions of their target genes in lung tissue than control probes. The top 500 eQTM genes were enriched in pathways for immune processes and epithelial integrity, and also more likely to be differentially expressed in atopic asthma. Moreover, we identified 5,934 paths through which methylation probes could affect atopic asthma through gene expression. Our findings suggest that distant epigenetic regulation of gene expression in airway epithelium plays a role in atopic asthma.

scholarly journals Expresso: A database and web server for exploring the interaction of transcription factors and their target genes in Arabidopsis thaliana using ChIP-Seq peak data

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 372 ◽  
Author(s):  
Delasa Aghamirzaie ◽  
Karthik Raja Velmurugan ◽  
Shuchi Wu ◽  
Doaa Altarawy ◽  
Lenwood S. Heath ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Data Sets ◽  
Motif Analysis ◽  
Chromatin Immunoprecipitation Sequencing

Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential. Results: We present Expresso (database and webserver) as a tool for the collection and integration of available Arabidopsis ChIP-Seq peak data, which in turn can be linked to a user’s gene expression data. Known target genes of transcription factors were identified by motif analysis of publicly available GEO ChIP-Seq data sets. Expresso currently provides three services: 1) Identification of target genes of a given transcription factor; 2) Identification of transcription factors that regulate a gene of interest; 3) Computation of correlation between the gene expression of transcription factors and their target genes. Availability: Expresso is freely available at http://bioinformatics.cs.vt.edu/expresso/

scholarly journals Correlation between miRNA-targeted-gene promoter methylation and miRNA regulation of target genes

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 21 ◽  
Author(s):  
Y-h Taguchi
Keyword(s):  
Gene Expression ◽  
Promoter Methylation ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Gene Promoter ◽  
Gene Expression Omnibus ◽  
Seed Region ◽  
Mirna Regulation ◽  
Regulate Gene Expression ◽  
Mirna Targeting

Background miRNA regulation of target genes and promoter methylation are known to be the primary mechanisms underlying the epigenetic regulation of gene expression. However, how these two processes cooperatively regulate gene expression has not been extensively studied.Methods Gene expression and promoter methylation profiles of 270 distinct human cell lines were obtained from Gene Expression Omnibus. P-values that describe both miRNA-targeted-gene promoter methylation and miRNA regulation of target genes were computed using the MiRaGE method proposed recently by the author.Results Significant changes in promoter methylation were associated with miRNA targeting. It was also found that miRNA-targeted-gene promoter hypomethylation was related to differential target gene expression; the genes with miRNA-targeted-gene promoter hypomethylation were downregulated during cell senescence and upregulated during cellular differentiation. Promoter hypomethylation was especially enhanced for genes targeted by miR-548 miRNAs, which are non-conserved, primate-specific miRNAs that are typically expressed at lower levels than the frequently investigated conserved miRNAs. miRNA-targeted-gene promoter methylation may also be related to the seed region features of miRNA.Conclusions It was found that promoter methylation was correlated to miRNA targeting. Furthermore, miRNA-targeted-gene promoter hypomethylation was especially enhanced in promoters of genes targeted by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs) and was suggested to be highly related to some seed region features of miRNAs.

Lineage-Specific Expression and Functional Relevance of MicroRNA Genes in Normal Hematopoiesis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2263-2263
Author(s):  
Nadia Felli ◽  
Elvira Pelosi ◽  
Rosanna Botta ◽  
Laura Fontana ◽  
Valentina Lulli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Neural Development ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Hematopoietic Cells ◽  
Specific Gene ◽  
Target Mrnas ◽  
Cd34 Cells ◽  
Functional Relevance

Abstract MicroRNAs (miRs) are a class of a small (~ 22nt) RNAs, which play an important role in the negative regulation of gene expression by base-pairing to complementary sites on the target mRNAs. While it is established that miRs are involved in a variety of basic processes, e.g., cell proliferation and apoptosis, neural development, fat metabolism and stress response, little is known on their expression and function in hematopoiesis. In order to investigate miR expression in erythropoietic (E), megakaryocytic (Mk), granulopoietic (G) and monocytopoietic (Mo) lineages, we have assayed their level at discrete sequential stages of the E, Mk, G or Mo series in unilineage differentiation/maturation cultures of cord blood (CB) CD34+ cells. The analysis was performed using a microarray chip containing as probes gene-specific 40mer oligonucleotides, generated from 161 human and 84 mouse precursors miRs (Liu GC et al., PNAS, 2004). Northern blot analysis confirmed the microarray data. The results indicate that the majority of the analyzed miRs is not expressed in CB hematopoietic cells. However, 49 miRs are expressed at significant levels in CD34+ cells: in most cases the expression level declines during hematopoietic differentiation according to diverse patterns, i.e., the decline may be more or less pronounced, more or less rapid and differ in the diverse hematopoietic lineages. As expression pattern examples, we observed that: (a) miR 223 is strongly downmodulated in the E lineage, whereas its level is not affected or increased in the other series; (b) miR 221 and 222 level sharply declines in the E lineage, while the drop is less pronounced in the Mk, G and Mo series; conversely, (c) miR 17, 20, 106 are downmodulated prevalentely in the G/Mo series, as compared to the E/Mk lineages. Interestingly, cluster analysis indicates that miR expression in hematopoietic cells is sharply different from that observed in CB T lymphocytes. The lineage- and stage-specific pattern of miR expression is of functional relevance. As an example, transfection of miR 222 oligonucleotide into CD34+ cells grown in multilineage clonogenic culture causes a pronounced shift from E to GM colony formation, indicating modulation of the lineage commitment of hematopoietic progenitors. The target genes of miRs expressed in hematopoietic cells are often of pivotal functional significance, e.g., miR 222 targets the kit receptor (N. Felli et al., this Meeting). A single miR may target diverse mRNAs, e.g., miR 222 targets kit, Ets1 and Fli1. Conversely, a single mRNA may be targeted by different miRs, e.g.,, kit is targeted by miR 146, 221 and 222. Noterworthily, the miR expression pattern in primitive hematopoietic cells and their progeny is fully distinct from that observed in primitive mesenchymal and neural cells (i.e., “neurospheres”) and their progeny: this suggests that miR downmodulation during differentiation of primitive cells contributes to tissue-specific gene expression by unblocking translational repression of the target mRNAs.

Pan-cancer analysis on microRNA-mediated gene activation

2018 ◽  
Author(s):  
Hua Tan ◽  
Shan Huang ◽  
Zhigang Zhang ◽  
Xiaohua Qian ◽  
Peiqing Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Immune Cell ◽  
Critical Role ◽  
Mirna Gene ◽  
Regulation Of Gene Expression ◽  
The Cancer Genome Atlas ◽  
Positive Correlation ◽  
Positive Correlations

ABSTRACTWhile microRNAs (miRNAs) were widely considered to repress target genes at mRNA and/or protein levels, emerging evidence from in vitro experiments has shown that miRNAs can also activate gene expression in particular contexts. However, this counterintuitive observation has rarely been reported or interpreted in in vivo conditions. We systematically explored the positive correlation between miRNA and gene expressions and its potential implications in tumorigenesis, based on 8375 patient samples across 31 major human cancers from The Cancer Genome Atlas (TCGA). Results indicated that positive miRNA-gene correlations are surprisingly prevalent and consistent across cancer types, and show distinct patterns than negative correlations. The top-ranked positive correlations are significantly involved in the immune cell differentiation and cell membrane signaling related processes, and display strong power in stratifying patients in terms of survival rate, demonstrating their promising clinical relevance. Although intragenic miRNAs generally tend to co-express with their host genes, a substantial portion of miRNAs shows no obvious correlation with their host gene due to non-conservation. A miRNA can upregulate a gene by inhibiting its upstream suppressor, or shares transcription factors with that gene, both leading to positive correlation. The miRNA/gene sites associated with the top-ranked positive correlations are more likely to form super-enhancers compared to randomly chosen pairs, suggesting a potential epigenetics mechanism underlying the upregulation. Wet-lab experiments revealed that positive correlations partially remain in the in vitro condition. Our study provides the field with new perspectives on the critical role of miRNA in gene regulation and novel insights regarding the complex mechanisms underlying miRNA functions, and reveals the clinical significance of the potential positive regulation of gene expression by miRNA.

Transcriptional profiling reveals divergent roles of PPARα and PPARβ/δ in regulation of gene expression in mouse liver

2010 ◽  
Vol 41 (1) ◽  
pp. 42-52 ◽  
Author(s):  
Linda M. Sanderson ◽  
Mark V. Boekschoten ◽  
Beatrice Desvergne ◽  
Michael Müller ◽  
Sander Kersten
Keyword(s):  
Gene Expression ◽  
Mouse Liver ◽  
Target Genes ◽  
Glucose Utilization ◽  
Plasma Cholesterol ◽  
Transcriptional Profiling ◽  
Regulation Of Gene Expression ◽  
Lipoprotein Metabolism ◽  
Peroxisome Proliferator ◽  
Fed State

Little is known about the role of the transcription factor peroxisome proliferator-activated receptor (PPAR) β/δ in liver. Here we set out to better elucidate the function of PPARβ/δ in liver by comparing the effect of PPARα and PPARβ/δ deletion using whole genome transcriptional profiling and analysis of plasma and liver metabolites. In fed state, the number of genes altered by PPARα and PPARβ/δ deletion was similar, whereas in fasted state the effect of PPARα deletion was much more pronounced, consistent with the pattern of gene expression of PPARα and PPARβ/δ. Minor overlap was found between PPARα- and PPARβ/δ-dependent gene regulation in liver. Pathways upregulated by PPARβ/δ deletion were connected to innate immunity and inflammation. Pathways downregulated by PPARβ/δ deletion included lipoprotein metabolism and various pathways related to glucose utilization, which correlated with elevated plasma glucose and triglycerides and reduced plasma cholesterol in PPARβ/δ−/− mice. Downregulated genes that may underlie these metabolic alterations included Pklr, Fbp1, Apoa4, Vldlr, Lipg, and Pcsk9, which may represent novel PPARβ/δ target genes. In contrast to PPARα−/− mice, no changes in plasma free fatty acid, plasma β-hydroxybutyrate, liver triglycerides, and liver glycogen were observed in PPARβ/δ−/− mice. Our data indicate that PPARβ/δ governs glucose utilization and lipoprotein metabolism and has an important anti-inflammatory role in liver. Overall, our analysis reveals divergent roles of PPARα and PPARβ/δ in regulation of gene expression in mouse liver.

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