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Utrecht, Netherlands

Agami R.,Netherlands Cancer Institute | Agami R.,Center for Biomedical Genetics
European Journal of Clinical Investigation | Year: 2010

microRNAs (miRNAs) are genes involved in normal development and cancer. They inhibit gene expression through interaction with 3′-untranslated regions of messenger RNAs, and are thought to control the expression of a large proportion of the protein-coding genome. However, it is becoming apparent that RNA-binding proteins (RBPs) control the biogenesis of miRNAs, their activity and stability. This indicates the existence of interplay between RBPs and miRNAs that affects gene expression and processes ranging from development, maintenance of stem cell phenotype and stress responses. Although miRNAs are prominent factors in cancer, little is known about how RBPs affect their cancerous function. © 2010 Stichting European Society for Clinical Investigation Journal Foundation.

Van Haaften G.,Netherlands Cancer Institute | Agami R.,Center for Biomedical Genetics
Genes and Development | Year: 2010

The miR-17-92 gene cluster, with its six different mature microRNAs (miRNAs), has an established oncogenic function. However, the oncogenic contribution of each individual miRNA in the cluster has not been assigned. Two studies published in the December 15, 2009, issue of Genes & Development by Mu and colleagues (pp. 2806-2811) and Olive and colleagues (pp. 2839-2849) dissected the miR-17-92 cluster to its individual miRNA components and identified their relative contributions to oncogenic transformation in mouse model systems. © 2010 by Cold Spring Harbor Laboratory Press.

Elkon R.,Netherlands Cancer Institute | Zlotorynski E.,Netherlands Cancer Institute | Agami R.,Netherlands Cancer Institute | Agami R.,Center for Biomedical Genetics
BMC Genomics | Year: 2010

Background: mRNA levels in cells are determined by the relative rates of RNA production and degradation. Yet, to date, most analyses of gene expression profiles were focused on mechanisms which regulate transcription, while the role of mRNA stability in modulating transcriptional networks was to a large extent overlooked. In particular, kinetic waves in transcriptional responses are usually interpreted as resulting from sequential activation of transcription factors.Results: In this study, we examined on a global scale the role of mRNA stability in shaping the kinetics of gene response. Analyzing numerous expression datasets we revealed a striking global anti-correlation between rapidity of induction and mRNA stability, fitting the prediction of a kinetic mathematical model. In contrast, the relationship between kinetics and stability was less significant when gene suppression was analyzed. Frequently, mRNAs that are stable under standard conditions were very rapidly down-regulated following stimulation. Such effect cannot be explained even by a complete shut-off of transcription, and therefore indicates intense modulation of RNA stability.Conclusion: Taken together, our results demonstrate the key role of mRNA stability in determining induction kinetics in mammalian transcriptional networks. © 2010 Elkon et al; licensee BioMed Central Ltd.

Ghamari A.,Erasmus Medical Center | van de Corput M.P.C.,Erasmus Medical Center | Thongjuea S.,University of Bergen | Van Cappellen W.A.,Erasmus Medical Center | And 8 more authors.
Genes and Development | Year: 2013

Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as "transcription factories," but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes. Immunostaining shows that CDK9-mCherry foci colocalize with RNAPII-Ser5P, much less with RNAPII-Ser2P, and not with CDK12 (a kinase reported to be involved in the Ser2 phosphorylation) or with splicing factor SC35. In conclusion, transcription factories exist in living cells, and initiation and elongation of transcripts takes place in different nuclear compartments. © 2013 by Cold Spring Harbor Laboratory Press.

Melo C.A.,Netherlands Cancer Institute | Melo C.A.,Center for Neuroscience and Cell Biology | Drost J.,Netherlands Cancer Institute | Wijchers P.J.,University Utrecht | And 11 more authors.
Molecular Cell | Year: 2013

Binding within or nearby target genes involved in cell proliferation and survival enables the p53 tumor suppressor gene to regulate their transcription and cell-cycle progression. Using genome-wide chromatin-binding profiles, we describe binding of p53 also to regions located distantly from any known p53 target gene. Interestingly, many of these regions possess conserved p53-binding sites and all known hallmarks of enhancer regions. We demonstrate that these p53-bound enhancer regions (p53BERs) indeed contain enhancer activity and interact intrachromosomally with multiple neighboring genes to convey long-distance p53-dependent transcription regulation. Furthermore, p53BERs produce, in a p53-dependent manner, enhancer RNAs (eRNAs) that are required for efficient transcriptional enhancement of interacting target genes and induction of a p53-dependent cell-cycle arrest. Thus, our results ascribe transcription enhancement activity to p53 with the capacity to regulate multiple genes from a single genomic binding site. Moreover, eRNA production from p53BERs is required for efficient p53 transcription enhancement. © 2013 Elsevier Inc.

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