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					Differential gene expression and development Gene expression

An introduction: The fate of a cell describes what it will become in the course of normal development. The fate of a particular cell can be discovered by labelling that cell and observing what structures it becomes a part of. When the fate of all cells of an embryo has been discovered, we can build a fate map, which is a diagram of that organism at an early stage of development that indicates the fate of each cell or region at a later stage of development. The developmental potential, or potency, of a cell describes the range of different cell types it CAN become. The zygote and its very early descendents are totipotent - these cells have the potential to develop into a complete organism. Totipotency is common in plants, but is uncommon in animals after the 2-4 cell stage. As development proceeds, the developmental potential of individual cells decreases until their fate is determined. The determination of different cell types (cell fates) involves progressive restrictions in their developmental potentials. When a cell “chooses” a particular fate, it is said to be determined, although it still "looks" just like its undetermined neighbors. Determination implies a stable change - the fate of determined cells does not change. Differentiation follows determination, as the cell elaborates a cell-specific developmental program. gene expression that responds to signals or triggers; a means of gene regulation, effects of certain hormones on protein biosynthesis.Differentiation results in the presence of cell types that have clear-cut identities, such as muscle cells, nerve cells, and skin cells.

Differentiation results from differential gene expression: The specific components of a given cell provides its special characteristics. These components are either synthesized by proteins, or are themselves proteins. By expressing different subsets of genes, two cells contain different subsets of gene products (proteins). Differential gene expression is responsible for the morphology of different cells. All cells within an organism have the same DNA, but not all genes are expressed. An epithelial cell will express only genes specific to skin, whereas a neuron will express genes necessary for its development.

How can we observe that cells from two tissues express different genes? There are two blots: the Southern blot shows that tissues A and B both contain a particular gene. However, the Northern blots shows that only tissue A contains RNA transcribed from that particular gene.

Differential gene expression is not a result of differential loss of the genetic material: DNA, except in the case of the immune system. That is, genetic information is not lost as cells become determined and begin to differentiate. Do All Cells Really Contain the Same DNA? Several lines of evidence support the proposal that all of the cells within a multicellular organism contain the same genome. For instance, although you started as a single cell with a half-genome from each parent, that single cell quickly divided and new cells began to differentiate, or become different from each other. While this process of differentiation established a wide variety of cell types (e.g., skin, liver, muscle, etc.), it was not accompanied by any permanent loss of genetic material. This is demonstrated by the fact

that fully differentiated cell types are still capable, within the right environment, of giving rise to an entire new animal. Experiment on frog and then Dolly: This capability was first shown by way of an experiment in which the nucleus of an adult frog skin cell was transplanted into an enucleated donor embryo, eventually leading to the development of a cloned adult frog . Later, the intact complete genome of a differentiated cell was used in the cloning of the famous sheep Dolly (Figure 1), showing that in mammals, genes are not lost during development, so they must therefore be regulated.

In fact, even the nuclei of adult cells contain ALL of the information needed for the construction of an entire organism, if provided with the proper cytoplasmic components. The cloning of Dolly from an adult cell is a major breakthrough, not only because of potential biotechnological applications, but because of the importance of this result for basic science: the result is the most convincing evidence for the theory of differential gene expression.

In order to clone Dolly, udder cells were removed from a Finn Dorset ewe and starved for one week to cause G0 arrest. Nuclei from arrested Finn Dorset udder cells were fused with enucleated eggs from a Scottish Blackface ewe, and then stimulated to re-enter the cell cycle. After a few rounds of cell division, the embryo was transplanted into a surrogate Scottish Blackface mother. The sheep that was born was genetically identical to the Finn Dorset ewe, which was the source of the nucleus.

Transplantation of imaginal discs in insects and the cloning of whole plants from individual cells strengthens the conclusion that genetic information is not lost as cells become determined and begin to differentiate. While differentiation results in specific cell types, morphogenesis is the process whereby the shape (morph) of the embryo is generated (genesis). Morphogenesis in both plants & animals involves regulated patterns of cell division and cell elongation that leads to

changes in cell shape. Cell movement also plays a critical important role in animal morphogenesis. Today, researchers understand that the specialized, differentiated cell types of the adult body contain a genome as complete as any embryo's. This fascinating demonstration has led to the proposal that changes in gene expression, rather than losses of genetic material, play a key role in guiding and maintaining cell differentiation.

Cell-Extrinsic Regulation of Gene Expression and differentiation: Gene expression is regulated by factors both extrinsic and intrinsic to the cell. Cellextrinsic factors that regulate expression include environmental cues, such as small molecules, secreted proteins, temperature, and oxygen. These cues can originate from other cells within the organism, or they can come from the organism's environment. Within the organism, cells communicate with each other by sending and receiving secreted proteins, also known as growth factors, morphogens, cytokines, or signaling molecules. Receipt of these signaling molecules triggers intercellular signaling cascades that ultimately cause semipermanent changes in transcription or expression of genes. Such changes in gene expression can include turning genes completely on or off, or just slightly tweaking the level of transcript produced. This process is thought to regulate a vast number of cell behaviors, including cell fate decisions during embryogenesis, cell function, and chemotaxis. In addition, gene expression changes can lead to changes in an entire organism, such as molting in insects. In Drosophila, for example, the molting process is regulated by levels of a hormone called ecdysone. This hormone acts as a signal, triggering a cascade of events and leading to changes in gene expression. Not surprisingly, the genes that are expressed in response to ecdysone are also the genes that are involved in the molting process. Thus, ecdysone acts on the organism level as a cell-extrinsic factor to bring about physiologically meaningful changes in gene expression. What is also interesting is that scientists can learn more about a physiological process like metamorphosis by studying how gene expression patterns change over time. For example, although researchers were aware that ecdysone results in a decrease of transcription from some loci, such as those involved in the glycolytic pathway, microarray data suggest that ecdysone-induced metamorphosis also downregulates genes involved with fatty acid oxidation, amino acid metabolism, oxidative phosphorylation, and other pathways. This suggests that there is a more global repression of metabolic activity during molting (Figure 2). Specifically, during metamorphosis, the larval muscle cells are degraded, and muscle-specific genes are downregulated (Figure 2B). Simultaneously, the development of the nervous system begins, and the genes involved in neuronal differentiation are induced (Figure 2C).

Cell-Intrinsic Regulation of Gene Expression and differentiation: Although differentiation is not thought to occur by permanent loss of genetic material, DNA can be modified in a way that affects gene expression. For instance, DNA and its associated histone proteins (together known as chromatin) can be chemically modified by a cell's own machinery. Chromatin modification can affect gene expression by changing the accessibility of genes to transcription factors, in either a positive or a negative manner. Two major classes of such chemical modifications include DNA methylation and histone modification (methylation and/or acetylation). These changes are often described as epigenetic because they do not act to alter the primary DNA sequence but instead act at a level just above the DNA sequence. Although DNA methylation and histone modification are not genetic, cells have mechanisms to copy this epigenetic information during their division so that their daughter cells contain the same regulatory data. Figure 3: Epigenetic gene regulation during mammalian development.This figure depicts key developmental events together with global epigenetic modifications and gene expression patterns. Very early in development, DNA methylation is erased. In addition, pluripotencyassociated genes begin to be expressed, and developmental genes are repressed by the PcG protein system and H3K27 methylation. During the differentiation of pluripotent cells such as embryonic stem (ES) cells, pluripotency-associated genes are repressed, potentially permanently, as a result of DNA methylation. At the same time, developmental genes begin to be expressed, and there is an increase in H3K4 methylation. During the early development of primordial germ cells (PGCs), DNA methylation and repressive histone modifications (such as H3K9 methylation) are also erased. Pluripotency-associated genes are re-expressed during a time window that allows embryonic germ cells to be derived in culture. Imprinted genes are demethylated during this period, and developmental genes are expressed afterwards. Flexible histone marks such as H3K27 methylation enable developmental genes to be silenced for a short time in pluripotent cells. By contrast, DNA methylation enables the stable silencing of imprinted genes, transposons, and some pluripotency-associated genes. Copyright 2007 Nature Publishing Group, Reik, W., Stability and flexibility of epigenetic gene regulation in mammalian development, Nature 447, 425–432

Changes in chromatin modification play an important role in regulating gene expression during developmental cell-type specification as well. For example, chromatin-modifying proteins play an essential role in muscle cell differentiation via interactions with key muscle-promoting transcription factors MyoD and MEF. That is, these factors are thought to help recruit chromatin modifying factors, such as histone acetyltransferases and deacetylases. In so doing, MyoD and MEF alter access to their target sites upstream of muscle differentiation genes. For instance, MyoD binds histone acetyltransferases p300 and PCAF, and this activity is essential for muscle cell differentiation. This example provides evidence for a link among chromatin modifications, transcription factors, and, ultimately, cell-fate-specific changes in gene expression. Chromatin modification can be stable over the life of an organism, thereby effectively permanently influencing gene expression. However, that is not to say that chromatin modification is irreversible. For instance, chromatin can become mismodified in certain cancers suggesting that, although important, the change is not permanent. Moreover, chromatin modifications are usually erased and reset during the production of gametes, such that the adult program of intrinsic cues is replaced with a program more suited to embryonic development. In fact, embryonic cell types are known to contain a unique set of chromatin modifications that are different from those found in adult cell types. This has led to the tantalizing proposal that chromatin modification helps lock in changes in gene expression that are required during development. The permanent silencing of the genes involved only in embryogenesis could then drive the development of cells toward more mature cell types. By blocking accessibility of transcription machinery, for example, chromatin modification could prevent the need for continued repression through active binding of a repressive transcription factor. Alternatively, the genes required for an adult cell type might contain chromatin modifications (especially histone acetylation) that cause the DNA to become open and, therefore, more accessible to the transcription machinery. Interestingly, embryonic cell types have been found to contain a signature chromatin modification in the regions that regulate the expression of genes involved in early embryonic development.Such regions were found to contain chromatin modifications with both silencing and promoting characteristics. The finding of these bivalent (twodirectional) markers in association with genes important for embryonic development has led to the belief that embryonic cells exist in a special epigenetic state, wherein they can choose to remain embryonic (as in an embryonic stem cell) or to differentiate (as in normal development), and bivalent domains provide a means by which to quickly choose between the two options. In Short: Together, these lines of evidence have led to an emerging hypothesis that cell-cell signaling and epigenetic changes converge to guide cell differentiation(differential gene expression) decisions both during development and beyond.

References:
1. Han, J. and Kamber, M. (2001) Data Mining: Concepts and Techniques,1st edn. San Francisco: Morgan Kaufmann Publishers. 2. Hartmann, U., Sagasser, M., Mehrtens, F., Stracke, R. and Weisshaar, B. (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol. Biol. 57, 155–171. 3. Heim, M., Jakoby, M., Werber, M., Martin, C., Weisshaar, B. and Bailey, P.C. (2003) The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735–747. 4. Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cisacting Regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27, 297– 300. Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cisacting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27, 297–30. 5. Sablowski, R.W. and Meyerowitz, E.M. (1998) A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell, 92, 93–103. 6. Schiefthaler, U., Balasubramanian, S., Sieber, P., Chevalier, D., Wisman, E. and Schneitz, K. (1999) Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 96, 11664–11669. 7. Anja von Heydebreck anja.von.heydebreck@merck.de 8. Y. Benjamini and Y. Hochberg (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, Vol. 57, 289– 300. 9. S. Dudoit, J.P. Shaffer, J.C. Boldrick (2003). Multiple hypothesis testing in microarray experiments. Statistical Science, Vol. 18, 71–103. 10. J.D. Storey and R. Tibshirani (2003). SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. In: The analysis of gene expression data: methods and software. Edited by G. Parmigiani, E.S. Garrett, R.A. Irizarry, S.L. Zeger. Springer, New York. 11. V.G. Tusher et al. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS, Vol. 98, 5116–5121. m P.H. Westfall and S.S. Young (1993). Resampling–based multiple testing: examples and methods for pvalue adjustment. Wiley.


				
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