Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon γ-Stimulated HeLa Cells

BackgroundThe binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1.ResultsIn each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif.ConclusionsThe genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions.

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“…AP-1 has been identified as a 'potential collaborating' factor for STAT1 in a recent study of microRNA regulation [89]. …”

Section: Resultsmentioning

confidence: 99%

Functional analysis of transcription factor binding sites in human promoters

et al. 2012

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“…Recently, Wang and colleagues identified 83 active promoter regions of miRNA genes in IFNγ-treated HeLa cells, 41 of which contained STAT1 binding sites. 43 In their in silico study, they used a bioinformatic approach to analyze highthroughput functional genomic data. ChIP-Seq experiments provided TF as well as RNA Pol II binding sites, which were used to construct potential feedback loops containing regulatory cascades of TFs and miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Landes Highlights

Riedmann

2012

RNA Biology

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MicroRNAs are major players in post-transcriptional gene regulation. even small changes in miRNA levels may have profound consequences for the expression levels of target genes. hence, miRNAs themselves need to be tightly, albeit dynamically, regulated. here, we investigated the dynamic behavior of miRNAs over a wide time range following stimulation of melanoma cells with interferonγ (IFNγ), which activates the transcription factor sTAT1. By applying several bioinformatic and statistical software tools for visualization and identification of differentially expressed miRNAs derived from time-series microarray experiments, 8.9% of 1105 miRNAs appeared to be directly or indirectly regulated by sTAT1. Focusing on distinct dynamic expression patterns, we found that the majority of robust miRNA expression changes occurred in the intermediate time range (24-48 h). Three miRNAs (miR-27a, miR-30a and miR-34a) had a delayed regulation occurring at 72 h while none showed significant expression changes at early time points between 30 min and 6 h. expression patterns of individual miRNAs were altered gradually over time or abruptly increased or decreased between two time points. Furthermore, we observed coordinated dynamic transcription of most miRNA clusters while few were found to be regulated independently of their genetic cluster. Most interestingly, several "star" or passenger strand sequences were specifically regulated over time while their "guide" strands were not.

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“…miRNA genes are encoded within the genome as a unit or in groups of 2 to 19 miRNAs and can reside within introns or exons of coding genes or in intergenic regions (1,23,46,55,56). The miRNA genes localized to intergenic regions have their own promoter, which allows them to be independently transcribed.…”

Section: Mirnas and Their Deregulation In Cancermentioning

confidence: 99%

Human papilloma virus, DNA methylation and microRNA expression in cervical cancer (Review)

2014

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Cancer is a complex disease caused by genetic and epigenetic abnormalities that affect gene expression. The progression from precursor lesions to invasive cervical cancer is influenced by persistent human papilloma virus (HPV) infection, which induces changes in the host genome and epigenome. Epigenetic alterations, such as aberrant miRNA expression and changes in DNA methylation status, favor the expression of oncogenes and the silencing of tumor-suppressor genes. Given that some miRNA genes can be regulated through epigenetic mechanisms, it has been proposed that alterations in the methylation status of miRNA promoters could be the driving mechanism behind their aberrant expression in cervical cancer. For these reasons, we assessed the relationship among HPV infection, cellular DNA methylation and miRNA expression. We conclude that alterations in the methylation status of protein-coding genes and various miRNA genes are influenced by HPV infection, the viral genotype, the physical state of the viral DNA, and viral oncogenic risk. Furthermore, HPV induces deregulation of miRNA expression, particularly at loci near fragile sites. This deregulation occurs through the E6 and E7 proteins, which target miRNA transcription factors such as p53.

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Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon γ-Stimulated HeLa Cells

Cited by 56 publications

References 47 publications

Functional analysis of transcription factor binding sites in human promoters

Functional analysis of transcription factor binding sites in human promoters

Landes Highlights

Human papilloma virus, DNA methylation and microRNA expression in cervical cancer (Review)

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