DNA methylation in the promoter of ribosomal RNA genes in human cells as determined by genomic sequencing

Kochanek, Stefan; Hosokawa, Keiichi; Schiedner, Gudrun; Renz, Doris; Doerfler, Walter

doi:10.1016/0014-5793(96)00506-6

Cited by 8 publications

(7 citation statements)

References 17 publications

(13 reference statements)

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“…1B), in accordance with a previous report that found that the rRNA promoter is hypermethylated in tissue culture cells compared to primary culture cells (28). This was quite a surprising report, nonetheless, as we expected this promoter, due to its high activity, to be unmethylated.…”

Section: Resultssupporting

confidence: 78%

Epigenetic Programming of the rRNA Promoter by MBD3

Brown

Szyf

2007

Molecular and Cellular Biology

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Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

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Section: Resultssupporting

confidence: 78%

Epigenetic Programming of the rRNA Promoter by MBD3

Brown

Szyf

2007

Molecular and Cellular Biology

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“…In con trast, in the DNA from the human cell lines HeLa (cervi cal cancer), KB (oral cancer), Jurkat (T cells), or CEM (T cells), the 5′ CG 3′ dinucleotides were methylated between 50% (KB) and 85% (Jurkat). Apparently, in the primary human cells, in granulocytes, T lymphocytes, spermatozoa, as well as in chronic T cell (T CCL), myeloid (CML), or B cell (B CLL) leukemia cells, which are all actively dividing, the essential rDNA genes need be transcribed actively and are not methylated [108]. In cell lines, rDNA genes are also actively expressed, and alter nate mechanisms of overexpression must exist.…”

Section: Patterns Of Dna Methylation In the Human Genomementioning

confidence: 99%

“…The 5′ CG 3′ rich promoter region of the DNA dependent RNA polymerase I (rDNA) genes was analyzed for the presence of m 5 C nucleotides by the genomic sequencing technique in DNA from primary human cells, from human tumor cells, and from human cell lines [108]. In none of the primary human cells or tumor cells was the rDNA promoter methylated.…”

Section: Patterns Of Dna Methylation In the Human Genomementioning

confidence: 99%

On the Biological Significance of DNA Methylation

Doerfler

2005

Biochemistry (Moscow)

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This chapter presents a personal account of the work on DNA methylation in viral and mammalian systems performed in the author's laboratory in the course of the past thirty years. The text does not attempt to give a complete and meticulous account of the many relevant and excellent reports published by many other laboratories, so it is not a review of the field in a conventional sense. The choice of viral model systems in molecular biology is well founded. Over many decades, viruses have proven their invaluable and pioneering role as tools in molecular genetics. When our interest turned to the demonstration of genome-wide patterns of DNA methylation, we focused mainly on the human genome. The following topics in DNA methylation will be treated in detail: (i) the de novo methylation of integrated foreign genomes; (ii) the long-term gene silencing effect of sequence-specific promoter methylation and its reversal; (iii) the properties and specificity of patterns of DNA methylation in the human genome and their possible relations to pathogenesis; (iv) the long-range global effects on cellular DNA methylation and transcriptional profiles as a consequence of foreign DNA insertion into an established genome; (v) the patterns of DNA methylation can be considered part of a cellular defense mechanism against foreign or repetitive DNA; what role has food-ingested DNA played in the elaboration of this mechanism?

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“…In contrast, in the DNA from the human cell lines, HeLa (cervical cancer), KB (oral cancer), Jurkat (T cells), or CEM (T cells) cells, the 5 -CG-3 dinucleotides were methylated between 50% (KB) and 85% (Jurkat). Apparently in the primary human cells, in granulocytes, T lymphocytes, and spermatozoa, as well as in chronic T cell (T-CCL), myeloid (CML), and B cell (B-CLL) leukemia cells, which are all actively dividing, the essential rDNA genes need be transcribed actively and are not methylated (Kochanek et al 1996a). In cell lines, rDNA genes are also actively expressed, and alternate mechanisms of overexpression must exist.…”

Section: Promoter Of the Polymerase I-transcribed Human Ribosomal Genesmentioning

confidence: 98%

“…The 5 -CG-3 -rich promoter region of the DNA-dependent RNA polymerase I (rDNA) genes was analyzed for the presence of 5-mC nucleotides by the genomic sequencing technique in DNA from primary human cells, from human tumor cells, and from human cell lines (Kochanek et al 1996a). In none of the primary human cells or tumor cells was the rDNA promoter methylated.…”

Section: Promoter Of the Polymerase I-transcribed Human Ribosomal Genesmentioning

confidence: 99%

De Novo Methylation, Long-Term Promoter Silencing, Methylation Patterns in the Human Genome, and Consequences of Foreign DNA Insertion

Doerfler

Current Topics in Microbiology and Immunology

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DNA methylation in the promoter of ribosomal RNA genes in human cells as determined by genomic sequencing

Cited by 8 publications

References 17 publications

Epigenetic Programming of the rRNA Promoter by MBD3

Epigenetic Programming of the rRNA Promoter by MBD3

On the Biological Significance of DNA Methylation

De Novo Methylation, Long-Term Promoter Silencing, Methylation Patterns in the Human Genome, and Consequences of Foreign DNA Insertion

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