Primary DNA sequence determines sites of maintenance and de novo methylation by mammalian DNA methyltransferases.

Bolden, Arthur H.; Nalin, Carlo M.; Ward, C; Poonian, M S; Weissbach, Arthur

doi:10.1128/mcb.6.4.1135

Cited by 65 publications

(36 citation statements)

References 14 publications

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“…The partial methylation that we see is not correlated with protein footprints and is seen only at some GCG or CGC trinucleotides; thus, there may be a bias of DNA methyhransferase against certain DNA sequences. Mammalian DNA methyhransferase does show a preference for certain CpGs in vitro (Bolden et al 1986;Smith et al 1989). The undermethylated GCG trinucleotides that we find are surrounded by several G/C base pairs and, thus, are very G + C-rich sites.…”

Section: Methylation Of Cpg Islandsmentioning

confidence: 78%

In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1.

Pfeifer

Tanguay²,

Steigerwald³

et al. 1990

Genes Dev.

240

182

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The promoter region of the X-linked human phosphoglycerate kinase-I [PGK-I) gene is a CpG island, similar to those often found near autosomal genes. We used ligation-mediated polymerase chain reaction (PCR) for a genomie sequencing study in which 450 bp of the human PGK-1 promoter region was analyzed for the presence of in vivo protein footprints and cytosine methylation at all CpG sites. A technique was devised to selectively visualize the DNA of the inactive X chromosome (Xi), even in the presence of the active X chromosome (Xa). We found that the human Xa in both normal male lymphoeytes and hamster-human hybrids is completely unmethylated at all 120 CpG sites. In contrast, 118 of the CpG sites are methylated on the human Xi in hamster-human hybrids. The Xi in normal female lymphoeytes is also highly methylated, but some GCG or CGC trinueleotides partially escape methylation; all other CpGs are fully methylated. In vivo footprinting studies with dimethylsulfate (DMS) revealed eight regions of apparent protein-DNA contacts on the Xa. Four of the footprints contained the consensus sequence of the binding site for transcription factor Spl. The other regions include potential binding sites for transcription factors ATF, NF1, and a CCAAT-binding protein. The Xi did not show any specifically protected sequences, and with the exception of four hyperreaetive sites, the in vivo DMS reactivity profile of Xi DNA was very similar to that of purified, linear Xi DNA. The implications of these findings with regard to the maintenance of methylation-free islands, X chromosome inactivation, and the ehromatin structure of faeultative heteroehromatin are discussed.

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Section: Methylation Of Cpg Islandsmentioning

confidence: 78%

In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1.

Pfeifer

Tanguay²,

Steigerwald³

et al. 1990

Genes Dev.

240

182

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“…In addition, it has been proposed that viral enhancer sequences may have the intrinsic ability to interact with cellular proteins, thereby perturbing the interaction of the methylase with DNA (Jfihner & Jaenisch, 1985b;Bird, 1986). It is therefore possible that in Rat-9G cells the IE upstream region interacts with proteins that prevent methylation, or that resistance is determined by the primary DNA sequence (Bolden et al, 1985(Bolden et al, , 1986Zacharias et al, 1984;Vardimon & Rich, 1984).…”

Section: Discussionmentioning

confidence: 99%

Resistance to Methylation de novo of the Human Cytomegalovirus Immediate Early Enhancer in a Model for Virus Latency and Reactivation in vitro

Boom

Geelen

Sol

et al. 1987

Journal of General Virology

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SUMMARYRat-9G cells carry several stably integrated copies of the major immediate early (IE) transcription unit of the human cytomegalovirus (HCMV). In these cells IE expression is repressed but inducible. In this report we describe the DNA methylation status of HpalI, HhaI and AhalI sites within the IE gene, determined at different passage levels. Most, if not all, of the resident IE genes were progressively methylated in a similar fashion. This resulted in DNA methylation patterns in which sites surrounding the IE upstream region were preferentially methylated to a high degree. In contrast, sites within the 19 bp IE enhancer elements were markedly under-methylated. This particular DNA methylation pattern probably resulted from differences in DNA methylation rates, sites within the IE enhancer being methylated at only a very low rate. Methylation of the IE genes did not affect their inducibility, which might be related to the very low methylation level of the IE enhancer.

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“…However, controversy still exists as to the existence of two distinct enzymes, since the de novo and maintenance methyltransferase activities do co-purify (26,44,46). Initially, the sequence specificities of the two enzymes were thought to be different (35,47), but recently Bolden et al suggested that both methyltransferase reactions are catalyzed by the same enzyme, as the maintenance and de novo methyltransferases share the same substrate specificities (48). It has also been postulated that DNA methyltransferase associated with the nuclear matrix is predominantly responsible for the maintenance of inheritable methylation patterns (49,50), but does also possess some de novo methylation activity (49).…”

Section: Dna Methylation Patternsmentioning

confidence: 99%

DNA Methylation and Differentiation

Michalowsky¹,

Jones²

1989

Environmental Health Perspectives

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The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin.Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable.

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Primary DNA sequence determines sites of maintenance and de novo methylation by mammalian DNA methyltransferases.

Cited by 65 publications

References 14 publications

In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1.

In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1.

Resistance to Methylation de novo of the Human Cytomegalovirus Immediate Early Enhancer in a Model for Virus Latency and Reactivation in vitro

DNA Methylation and Differentiation

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