NATUREIVol 447 24 May 2007 do:10.1038/nature05918 INSIGHT REVIEW Stability and flexibility of epigenetic gene regulation in mammalian development Wolf Reik During development cells start in a pluripotent state from which they can differentiate into many cell types, and progressively develop a narrower potential. their gene-expression programmes become more defined, restricted and potentially, 'locked in. Pluripotent stem cells express genes that encode a set of core transcription factors while genes that are required later in development are repressed by histone marks, which confer short-term, and therefore flexible, epigenetic silencing. by contrast the methylation of DNa confers long-term epigenetic silencing of particular sequences-transposons, imprinted genes and pluripotency-associated genes-in somatic cells. Long-term silencing can be reprogrammed by demethylation of DNA and this process might involve dNa repair. It is not known whether any of the epigenetic marks has a primary role in determining cell and lineage commitment during development. F%832Orht is, by definition, epigenetic Differences in the pro- epigenetic marks(which can be removed before a cell divides or within Develo f gene expression that result in the development of different very few cell divisions)with the long-term stability and heritability of organs and tissues occur without changes to the sequence of our DNA other marks(which can be maintained for many divisions)(Fig. 1) one or two exceptions). There is nothing mysterious in this con- During the early stages of development, genes that are required later in ubsets of the -30,000 genes in our genome are active in different development are transiently held in a repressed state by histone modifi tissues and organs, depending on their regulation by different sets or cations, which are highly flexible and easily reversed when expression of combinations of transcription factors. This implies that if we were to these genes is needed. During differentiation that are crucial for take all of the transcription factors that activate genes in a liver cell and pluripotency are silenced by histone modifications, as well as by dnA transfer them to a brain cell (while inactivating all brain-specific tran- methylation. Some of these genes are also silent in mature germ cell scription factors), then the brain cell would turn into a liver cell. meaning that epigenetic marks probably need to be reversed rapidly after A recent study provides tantalizing insight into this concept of fertilization to allow re-expression of pluripotency-associated genes i epigenetic control of development. Takahashi and Yamanaka identi- the next generation. By contrast, long-term silencing of transposons fied four transcriptional regulators that when expressed in fibroblasts, and imprinted genes-which is based on DNA methylation-need resulted in these cells being reprogrammed to become embryonic stem to be stably maintained from the gametes into the early embryo and the (ES)-like cells Extending this concept a little further, in somatic-cell adult organism. Methylation of imprinted genes can only be erased nuclear transfer, the nucleus of a somatic cell from an adult individual is primordial germ cells(PGCs), the cells that ultimately give rise to the transplanted into an oocyte from which the nucleus has been removed, germ line. Probably because there is a requirement for both removing resulting in reprogramming of the adult nucleus and therefore successful epigenetic marks and retaining epigenetic marks between generations, development of the cloned animal Cloning, however, is inefficient, because most(if not all) cloned erations. In this review, I address how the fascinating interplay betwee animals have epigenetic defects, particularly in DNA methylation. transcription factors and epigenetic factors is beginning to provide an Therefore, our lack of understanding ofhow epigenetic marks are repro- explanation for how pluripotency and development are regulated. grammed is a key obstacle to cloning. Similarly, the reprogramming of fibroblasts to become ES-like cells is a rare event in vitro, and epigenetic Flexibility for developmental gene regulation defects such as lack of demethylation of the Oct4(also known as Pou5f1) In this section, three issues are addressed. First, are differentiation promoter, affecting expression of the encoded transcription factor, have specific genes held in an epigenetically silenced manner in pluripotent been noted in these ES-like cell cell types, in order to be activated later? And is the removal of epigenetic These observations highlight that, in addition to transcription fac- marks from these genes needed for their activation? Second,are tors, changes in gene expression during development are accompanied pluripotency-associated genes epigenetically inactivated in differentiated or caused by epigenetic modifications", such as methylation of DNA at cell types? This inactivation could, in principle, be irreversible, because CpG sequences(in vertebrates), modification of histone tails and the somatic cell types are not required to give rise to pluripotent cells. One presence of non-nucleosomal chromatin-associated proteins. Therefore, exception is the germ line, where reactivation of pluripotency-associated as development and differentiation proceed, differentiated cells accumu- genes is needed at the initial stages of development; however, later, the late epigenetic marks that differ from those of pluripotent cells, and dif- silencing of these genes is essential for the differentiation of mature germ ferentiated cells of different lineages also accumulate different marks. cells. And therefore, third, is the removal of permanent silencing marks In this review, I focus on the role of epigenetic regulation in devel- from the gametic genomes after fertilization crucial to activate essential opment, particularly comparing the short-term flexibility of certain genes, such as pluripotency-associated genes, early in development? Laborato ory of Developmen ntal Genetics and Imprinting aham institute, Cambridge CB22 3AT, UK. @2007 Nature Publishing GroupDevelopment is, by definition, epigenetic. Differences in the pro￾grammes of gene expression that result in the development of different organs and tissues occur without changes to the sequence of our DNA (with one or two exceptions). There is nothing mysterious in this con￾cept; subsets of the ~30,000 genes in our genome are active in different tissues and organs, depending on their regulation by different sets or combinations of transcription factors. This implies that if we were to take all of the transcription factors that activate genes in a liver cell and transfer them to a brain cell (while inactivating all brain-specific tran￾scription factors), then the brain cell would turn into a liver cell. A recent study provides tantalizing insight into this concept of epigenetic control of development. Takahashi and Yamanaka identi￾fied four transcriptional regulators that when expressed in fibroblasts, resulted in these cells being reprogrammed to become embryonic stem (ES)-like cells1 . Extending this concept a little further, in somatic-cell nuclear transfer, the nucleus of a somatic cell from an adult individual is transplanted into an oocyte from which the nucleus has been removed, resulting in reprogramming of the adult nucleus and therefore successful development of the cloned animal. Cloning, however, is inefficient, because most (if not all) cloned animals have epigenetic defects, particularly in DNA methylation. Therefore, our lack of understanding of how epigenetic marks are repro￾grammed is a key obstacle to cloning2 . Similarly, the reprogramming of fibroblasts to become ES-like cells is a rare event in vitro, and epigenetic defects such as lack of demethylation of the Oct4 (also known as Pou5f1) promoter, affecting expression of the encoded transcription factor, have been noted in these ES-like cells1 . These observations highlight that, in addition to transcription fac￾tors, changes in gene expression during development are accompanied or caused by epigenetic modifications2–7, such as methylation of DNA at CpG sequences (in vertebrates4,5), modification of histone tails6 and the presence of non-nucleosomal chromatin-associated proteins7 . Therefore, as development and differentiation proceed, differentiated cells accumu￾late epigenetic marks that differ from those of pluripotent cells, and dif￾ferentiated cells of different lineages also accumulate different marks. In this review, I focus on the role of epigenetic regulation in devel￾opment, particularly comparing the short-term flexibility of certain epigenetic marks (which can be removed before a cell divides or within very few cell divisions) with the long-term stability and heritability of other marks (which can be maintained for many divisions) (Fig. 1). During the early stages of development, genes that are required later in development are transiently held in a repressed state by histone modifi￾cations, which are highly flexible and easily reversed when expression of these genes is needed. During differentiation, genes that are crucial for pluripotency are silenced by histone modifications, as well as by DNA methylation. Some of these genes are also silent in mature germ cells, meaning that epigenetic marks probably need to be reversed rapidly after fertilization to allow re-expression of pluripotency-associated genes in the next generation. By contrast, long-term silencing of transposons and imprinted genes — which is based on DNA methylation — needs to be stably maintained from the gametes into the early embryo and the adult organism. Methylation of imprinted genes can only be erased in primordial germ cells (PGCs), the cells that ultimately give rise to the germ line. Probably because there is a requirement for both removing epigenetic marks and retaining epigenetic marks between generations, epigenetic information can sometimes be inherited across multiple gen￾erations. In this review, I address how the fascinating interplay between transcription factors and epigenetic factors is beginning to provide an explanation for how pluripotency and development are regulated. Flexibility for developmental gene regulation In this section, three issues are addressed. First, are differentiation￾specific genes held in an epigenetically silenced manner in pluripotent cell types, in order to be activated later? And is the removal of epigenetic marks from these genes needed for their activation? Second, are pluripotency-associated genes epigenetically inactivated in differentiated cell types? This inactivation could, in principle, be irreversible, because somatic cell types are not required to give rise to pluripotent cells. One exception is the germ line, where reactivation of pluripotency-associated genes is needed at the initial stages of development; however, later, the silencing of these genes is essential for the differentiation of mature germ cells. And therefore, third, is the removal of ‘permanent’ silencing marks from the gametic genomes after fertilization crucial to activate essential genes, such as pluripotency-associated genes, early in development? Stability and flexibility of epigenetic gene regulation in mammalian development Wolf Reik1 During development, cells start in a pluripotent state, from which they can differentiate into many cell types, and progressively develop a narrower potential. Their gene-expression programmes become more defined, restricted and, potentially, ‘locked in’. Pluripotent stem cells express genes that encode a set of core transcription factors, while genes that are required later in development are repressed by histone marks, which confer short-term, and therefore flexible, epigenetic silencing. By contrast, the methylation of DNA confers long-term epigenetic silencing of particular sequences — transposons, imprinted genes and pluripotency-associated genes — in somatic cells. Long-term silencing can be reprogrammed by demethylation of DNA, and this process might involve DNA repair. It is not known whether any of the epigenetic marks has a primary role in determining cell and lineage commitment during development. 1 Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, UK. 425 NATURE|Vol 447|24 May 2007|doi:10.1038/nature05918 INSIGHT REVIEW ￾
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