Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method

Yoshizawa, Masato; Taguchi, Y-h.; Yasuda, Jun

doi:10.3390/ijms12129265

Cited by 12 publications

(10 citation statements)

References 21 publications

(35 reference statements)

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“…Significant promoter hypomethylation of miRNA target genes Based on the inference of data produced using the MiRaGE method 21 (see Methods), the promoters of genes that are targets of 70-90% of human miRNAs were significantly hypomethylated, dependent on the statistical tests used, and the definition of promoter methylation levels: the b-value or the amount of methylation (see Table 1 and Additional files). This finding was consistent with conclusions made by Su et al…”

Section: Resultsmentioning

confidence: 99%

“…Inference of miRNA-targeted-gene promoter methylation/miRNA regulation of target genes using the Mi RaGE method The inference of miRNA-targeted-gene promoter methylation/miRNA regulation of target genes was carried out using the MiRaGE method, which has been described previously 21 .…”

Section: Methylation Computation By Bismark Softwarementioning

confidence: 99%

“…Investigation of miRNA-targeted-gene promoter methylation In order to infer miRNA-targeted-gene promoter methylation, I employed the MiRaGE method 21 (see below). The MiRaGE method, which was implemented on a public domain MiRaGE server and Bioconductor MiRaGE package, was first used to infer the contribution of miRNA to the measured expression levels.…”

Section: See Referee Reportsmentioning

confidence: 99%

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

Taguchi

2013

F1000Res

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Science and Technology Norway Discuss this article AbstractmiRNA regulation of target genes and promoter methylation are Background 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.Gene expression and promoter methylation profiles of 271 distinct Methods human cell lines were obtained from gene expression omnibus. P-values that describe both miRNA-targeted-gene promoter methylaion and miRNA regulation of target genes were computed using the MiRaGE method proposed recently by the author.Significant changes in promoter methylation were associated with Results 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.It was found that promoter methylation was affected by miRNA Conclusions targeting. Furthermore, miRNA-targeted-gene promoter hypomethylation is suggested to facilitate gene regulation by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs).

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Section: Resultsmentioning

confidence: 99%

Section: Methylation Computation By Bismark Softwarementioning

confidence: 99%

Section: See Referee Reportsmentioning

confidence: 99%

See 1 more Smart Citation

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

Taguchi

2013

F1000Res

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“…The small non-coding miRNAs are known to be involved in crucial biological processes such as proliferation, apoptosis, differentiation, or development [ 4 - 6 ]. More than 50% of all genes in the human genome are known to be miRNA targets and, thus, miRNAs are involved in the regulation of a manifold of metabolic and regulatory pathways such that now the integrative network analysis of miRNAs and mRNAs becomes more and more possible [ 7 - 9 ].…”

Section: Introductionmentioning

confidence: 99%

miRNAs can be generally associated with human pathologies as exemplified for miR-144*

Keller

Leidinger

Vogel

et al. 2014

BMC Med

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BackgroundmiRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists.MethodsWe evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR.ResultsWe discovered 34 miRNAs with strong disease association. Among those, we found substantially decreased levels of hsa-miR-144* and hsa-miR-20b with AUC of 0.751 (95% CI: 0.703–0.799), respectively. We also discovered a set of miRNAs, including hsa-miR-155*, as rather stable markers, offering reasonable control miRNAs for future studies. The strong downregulation of hsa-miR-144* and the less variable pattern of hsa-miR-155* has been validated in a cohort of 319 samples in three different centers. Here, breast cancer as an additional disease phenotype not included in the screening phase has been included as the 20th trait.ConclusionsOur study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers. Importantly, we highlight 34 miRNAs that are generally dysregulated in human pathologies. Although these markers are not specific to certain diseases they may add to the diagnosis in combination with other markers, building a specific signature. Besides these dysregulated miRNAs, we propose a set of constant miRNAs that may be used as control markers.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-014-0224-0) contains supplementary material, which is available to authorized users.

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“…The small non-coding miRNAs are known to be involved in crucial biological processes such as proliferation, apoptosis, differentiation, or development [4][5][6]. More than 50% of all genes in the human genome are known to be miRNA targets and, thus, miRNAs are involved in the regulation of a manifold of metabolic and regulatory pathways such that now the integrative network analysis of miRNAs and mRNAs becomes more and more possible [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

miRNAs can be generally associated with human pathologies as exemplified for miR-144*

et al. 2014

View full text Add to dashboard Cite

Background: miRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists. Methods: We evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR.

show abstract

Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method

Cited by 12 publications

References 21 publications

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

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

miRNAs can be generally associated with human pathologies as exemplified for miR-144*

miRNAs can be generally associated with human pathologies as exemplified for miR-144*

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