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I am intrigued by the fact that all cells of our body use the same DNA. How do the cells differentiate during the post fertilisation divisions?

I read about gene silencing, which can be an answer to this. But still I do not understand how the cells decide which gene it is supposed to silence, by making the micro RNA.

Consider a zygote that is beginning to divide. I would assume that the chemical and physical context of each daughter cells would be more or less similar in beginning. Then how can there be a differentiation? Is there some supervising authority present in the zygote that decides what to make out of each daughter cell?

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The cells differentiation during post fertilization period is govern by a set of regulatory genes called Homeotic genes.These are genes that "select" the identity of entire segments or structures in the bodies of developing organisms. These gene encodes a transcription factor that is expressed in a specific region of the organism starting in its early development i.e. embryo stage. The transcription factors change the expression of target genes to enact the genetic “program” that's right for each segment. enter image description here

The homeotic transcription factors shown in the diagram above[homology between Hox genes in mice and humans] contain a DNA-binding protein region called the homeodomain, which is encoded by a segment of DNA, called the homeobox.The animal genes containing homeobox sequences are specifically referred to as Hox genes. This family of genes is responsible for determining the general body plan, such as the number of body segments of an animal, the number and placement of appendages, and animal head-tail directionality.

In addition to this genes, the early developmental cascade include the following genes:

  • Maternal effects genes:These are genes whose mRNAs are placed in the egg cell by the mother before fertilization. Some of the mRNAs are “tied” to the head or tail end of the embryo and are responsible for setting up the head-tail polarity. The maternal effects genes encode regulators of transcription or translation that control each other as well as other genes.
  • Gap genes: They are activated through interactions between the protein products of the maternal effects genes, and they also regulate each other. They're responsible for defining large, multi-segment regions in many organisms.
  • Pair-rule genes: These are turned on by interactions between gap genes, and their expression patterns are refined by interactions with one another. They appear in multiple “stripes” along the embryo, similar in pattern to the segments of the adult organism.When a pair-rule gene is missing due to mutation, there is a loss of structures in the segment regions where the gene is normally expressed.

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    $\begingroup$ Hox, pair-rule and gap genes are all expressed well after the first differentiations. $\endgroup$
    – canadianer
    Commented Nov 3, 2019 at 20:09
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Activation and deactivation of different genes commands the process of cell differentiation. Gene expression responsible for cell differentiation is controlled by intrinsic and extrinsic signals. This regulated signalling from inside and outside the cell is responsible for embryonic development.

Environment around the cell, such as small molecules, proteins, temperature and oxygen control the gene expression. Cellular communication takes places to decide the fate of particular cell by interplay of signals between the proteins synthesized around the cell. These proteins can be morphogens, growth factors or cytokines. This extrinsic signalling sets off intercellular signalling that stimulates expression of genes. Alteration in gene expression by turning gene on or off, regulates the production of gene product.

Gene expression is regulated intrinsically by modifying DNA. DNA and chromatin are altered chemically. Change in chromatin effects gene expression by controlling the binding of genes to transcription factors. These epigenetic chemical modifications are known as DNA methylation and histone modification. Chromatin modification plays important role in gene expression during cell development. For example, proteins responsible for chromatin modification play important role in muscle cell differentiation. Transcription factors MyoD and MEF regulate enzymes responsible for chromatin modification, such as histone acetyltransferases and deacetylases.

Via: https://www.nature.com/scitable/topicpage/gene-expression-regulates-cell-differentiation-931/#

Chromatin modification helps in continuous gene expression which is required during cell differentiation. The gene silencing involved in embryogenesis, promotes cell development into mature cell types. This silencing of gene is done by making gene inaccessible to transcription machinery, and when genes are needed again in adult cell type the chromatin modification opens DNA and make it available for transcription.

Embryonic cell types have particular regions for chromatin modification that regulate gene expression required for embryonic development. These regions can modify gene expression by activating or silencing genes.

Via: (https://www.ncbi.nlm.nih.gov/pubmed/16630819)

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