Cellular differentiation, cytidine analogs and DNA methylation
TL;DR: Results provide experimental evidence for a role for DNA modification in differentiation, and suggest that cytidine analogs containing an altered 5 position perturb previously established methylation patterns to yield new cellular phenotypes.
About: This article is published in Cell.The article was published on 1980-05-01. It has received 1722 citations till now. The article focuses on the topics: DNA methylation & Zebularine.
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TL;DR: The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development.
Abstract: The character of a cell is defined by its constituent proteins, which are the result of specific patterns of gene expression. Crucial determinants of gene expression patterns are DNA-binding transcription factors that choose genes for transcriptional activation or repression by recognizing the sequence of DNA bases in their promoter regions. Interaction of these factors with their cognate sequences triggers a chain of events, often involving changes in the structure of chromatin, that leads to the assembly of an active transcription complex (e.g., Cosma et al. 1999). But the types of transcription factors present in a cell are not alone sufficient to define its spectrum of gene activity, as the transcriptional potential of a genome can become restricted in a stable manner during development. The constraints imposed by developmental history probably account for the very low efficiency of cloning animals from the nuclei of differentiated cells (Rideout et al. 2001; Wakayama and Yanagimachi 2001). A “transcription factors only” model would predict that the gene expression pattern of a differentiated nucleus would be completely reversible upon exposure to a new spectrum of factors. Although many aspects of expression can be reprogrammed in this way (Gurdon 1999), some marks of differentiation are evidently so stable that immersion in an alien cytoplasm cannot erase the memory. The genomic sequence of a differentiated cell is thought to be identical in most cases to that of the zygote from which it is descended (mammalian B and T cells being an obvious exception). This means that the marks of developmental history are unlikely to be caused by widespread somatic mutation. Processes less irrevocable than mutation fall under the umbrella term “epigenetic” mechanisms. A current definition of epigenetics is: “The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence” (Russo et al. 1996). There are two epigenetic systems that affect animal development and fulfill the criterion of heritability: DNA methylation and the Polycomb-trithorax group (Pc-G/trx) protein complexes. (Histone modification has some attributes of an epigenetic process, but the issue of heritability has yet to be resolved.) This review concerns DNA methylation, focusing on the generation, inheritance, and biological significance of genomic methylation patterns in the development of mammals. Data will be discussed favoring the notion that DNA methylation may only affect genes that are already silenced by other mechanisms in the embryo. Embryonic transcription, on the other hand, may cause the exclusion of the DNA methylation machinery. The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development. Indeed, the possibility will be discussed that DNA methylation and Pc-G/trx may represent alternative systems of epigenetic memory that have been interchanged over evolutionary time. Animal DNA methylation has been the subject of several recent reviews (Bird and Wolffe 1999; Bestor 2000; Hsieh 2000; Costello and Plass 2001; Jones and Takai 2001). For recent reviews of plant and fungal DNA methylation, see Finnegan et al. (2000), Martienssen and Colot (2001), and Matzke et al. (2001).
6,691 citations
Cites background from "Cellular differentiation, cytidine ..."
...But what genes are affected by DNA methylation-mediated gene silencing? Early studies relied on the use of the demethylating drug 5-azacytidine (Jones and Taylor 1980), which was shown to activate genes on the inactive X in rodent–human cell hybrids (Mohandas et al....
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...Early studies relied on the use of the demethylating drug 5-azacytidine (Jones and Taylor 1980), which was shown to activate genes on the inactive X in rodent–human cell hybrids (Mohandas et al. 1981b; Graves 1982)....
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TL;DR: This review discusses patterns of DNA methylation and chromatin structure in neoplasia and the molecular alterations that might cause them and/or underlie altered gene expression in cancer.
Abstract: Patterns of DNA methylation and chromatin structure are profoundly altered in neoplasia and include genome-wide losses of, and regional gains in, DNA methylation. The recent explosion in our knowledge of how chromatin organization modulates gene transcription has further highlighted the importance of epigenetic mechanisms in the initiation and progression of human cancer. These epigenetic changes -- in particular, aberrant promoter hypermethylation that is associated with inappropriate gene silencing -- affect virtually every step in tumour progression. In this review, we discuss these epigenetic events and the molecular alterations that might cause them and/or underlie altered gene expression in cancer.
5,492 citations
TL;DR: Recent advances in understanding how epigenetic alterations participate in the earliest stages of neoplasia, including stem/precursor cell contributions, are reviewed and the growing implications of these advances for strategies to control cancer are discussed.
4,269 citations
Cites background from "Cellular differentiation, cytidine ..."
...Other nucleoside inhibitors of DNA methylation, including 5fluoro-20-deoxycytidine (Jones and Taylor, 1980) and zebularine (Cheng et al....
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...Other nucleoside inhibitors of DNA methylation, including 5- fluoro-20-deoxycytidine (Jones and Taylor, 1980) and zebularine (Cheng et al., 2004), are at an earlier stage of development....
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TL;DR: It is likely that most vertebrate genes are associated with ‘HTF islands’—DNA sequences in which CpG is abundant and non-methylated; however, highly tissue-specific genes, though, usually lack islands.
Abstract: It is likely that most vertebrate genes are associated with 'HTF islands'--DNA sequences in which CpG is abundant and non-methylated. Highly tissue-specific genes, though, usually lack islands. The contrast between islands and the remainder of the genome may identify sequences that are to be constantly available in the nucleus. DNA methylation appears to be involved in this function, rather than with activation of tissue specific genes.
3,673 citations
TL;DR: In this article, the major open reading frame encoded by this cDNA contains a short protein segment similar to a sequence present in the myc protein family, and the expression of one of these cDNAs transfected into C3H10T1/2 fibroblasts, where it is not normally expressed, is sufficient to convert them to stable myoblasts.
3,162 citations
Cites background from "Cellular differentiation, cytidine ..."
...Experiments using other cytidine analogs, and the correlation of this phenomenon with incorporation of 5-azacytidine into DNA, point to DNA demethylation as having a significant role (Jones and Taylor, 1980)....
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References
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TL;DR: A method has been described for the isolation of DNA from micro-organisms which yields stable, biologically active, highly polymerized preparations relatively free from protein and RNA, and Representative samples have been characterized for their thermal stability and sedimentation behaviour.
11,573 citations
TL;DR: This article suggests mechanisms that may account for the differentiated state of dividing or nondividing cells and that also attempt to explain the ordered switching on or off of genes during development.
Abstract: It is generally accepted that the differentiated state of a given type of cell is associated with the activity of a particular set of genes, together with the total inactivity of those sets associated with the differentiation of other cell types. It is also clear that the differentiated state of dividing or nondividing cells is often extremely stable. In this article we suggest mechanisms that may account for this stability and that also attempt to explain the ordered switching on or off of genes during development. The phenotype of the organism depends on the genotype, and the genetic contribution from both parents is in almost all cases equal. Since the ultimate control of development resides in the genetic material, the actual program must be written in base sequences in the DNA. It is also clear that cytoplasmic components can have a powerful or overriding influence on genomic activity in particular cells, yet these cytoplasmic components are, of course, usually derived from the activity of genes at some earlier stage in development. A continual interaction between cytoplasmic enzymes and DNA sequences is an essential part of the model to be presented. Modification Enzymes In bacteria, enzymes exist which modify DNA by methylating adenine in the 6-position ( 1 ). These enzymes are extremely specific in their action; they modify bases at particular positions in short defined sequences of DNA, which, at least in some instances, form a palindrome. (A palindrome in DNA is an inverted duplication, with twofold rotational symmetry. The 3′ →...
1,708 citations
TL;DR: A model based on DNA methylation is proposed to explain the initiation and maintenance of mammalian X inactivation and certain aspects of other permanent events in eukaryotic cell differentiation using sequence-specific DNA methylases that methylate unmethylated sites with great difficulty but easily methylate half-methylated sites.
Abstract: A model based on DNA methylation is proposed to explain the initiation and maintenance of mammalian X inactivation and certain aspects of other permanent events in eukaryotic cell differentiation. A key feature of the model is the proposal of sequence-specific DNA methylases that methylate unmethylated sites with great difficulty but easily methylate half-methylated sites. Although such enzymes have not yet been detected in eukaryotes, they are known in bacteria. An argument is presented, based on recent data on DNA-binding proteins, that DNA methylation should affect the binding of regulatory proteins. In support of the model, short reviews are included covering both mammalian X inactivation and bacterial restriction and modification enzymes.
1,114 citations
TL;DR: Three new mesenchymal phenotypes were expressed in cultures of Swiss 3T3 and C3H/10T1/2CL8 mouse cells treated with 5-azacytidine or 5-aza-2'-deoxycytidine, implying that cell division was obligatory for the expression of the new phenotypes.
1,101 citations
Journal Article•
TL;DR: No spontaneous transformation in vitro has been observed in the stock cultures transferred on a regular schedule and tests for tumorigenicity at all passages were negative.
Abstract: A line of C3H mouse embryo cells highly sensitive to postconfluence inhibition of cell division, designated C3H/10T1/2, has been established, and a clone from this line (clone 8) has been characterized at early and late passages (200 to 450 days in culture). The cells of clone 8 are approximately 1730 cu µm in volume, their plating efficiency is 12 to 30%, their average generation time is 15.5 hr, and their saturation density is 2.9 to 3.8 × 104 cells/sq cm. The cell survival is 30% after freezing in 10% dimethyl sulfoxide and storage in liquid nitrogen. The cells of this clone are negative with respect to the spontaneous expression of C-type RNA murine viruses and viral antigens. Tests for mycoplasma contamination are negative. All the cells of this line are aneuploid with a stable mode of 81 chromosomes (40 to 60% of cells). Tests for tumorigenicity at all passages were negative. No spontaneous transformation in vitro has been observed in the stock cultures transferred on a regular schedule.
1,091 citations