Is it something encoded in the DNA itself, or something on the side that makes cells different?
In: Biology
The DNA is like a complete list of instructions for the entire body. Each cell doesn’t use all of those instructions though, they just focus on the instructions for the particular part they are meant to be. So while your eyes have a copy of the code to make every cell in your body in them, they are only using the part that makes eyes.
You are talking about gene expression, where the cells read the genetic blueprint and activates a particular part. There’s this whole new field called epigenetics that deals with how the body reads the DNA. Think of it like playing a piano, gene expression would be playing the notes and which notes in which order plays a melody whereas epigenetics would be the tone, which notes are played louder etc, thereby changing the feel of the melody.
Biotechnologist here, let me give it a spin. This will probably be a bit more detailed than other entries but I hope you find it useful!
Every cell has the same DNA, and as others have stated each cell, as it specializes into what it will ultimately become utilizes different parts of your DNA while shutting off others. What actually causes cells to differentiate is something we call induction, which comes in a few flavors such as instructive induction, permissive induction, and reciprocal induction.
Instructive induction is when specific factors cause a cell to differentiate into a specific type. Permissive induction are when specific factors allow a cell to differentiate into a specific type that it has pre-committed to but needs an inducer to fully commit, and reciprocal induction is when two different cell types each secrete factors that promote the formation of the opposing cell type (this is how organs and barriers between tissues form).
Instructive induction has two main forms, autonomous and conditional specification. Autonomous happens early within development and is a result of morphogenic factors within the maternal egg cell. The egg cell contains everything a normal cell has except for half the DNA, which is provided by the sperm. It also contains morphogenic factors distributed in various locations throughout the cell that will be unevenly distributed when the cell divides, but leads to early differentiation of the fetus (such as establishing where the “head” and “bottom” of the fetus will be).
Autonomous cells are forced into their specified cell type early on, if they were removed from the fetus they would continue developing into that cell type (giving rise to the main three germ layers). Conditional on the other hand is based on location within the later parts of development. If you took cells that normally would form “back” tissue and transplanted them into a region that would form “belly” tissue, the factors present there would influence it to become belly tissue.
Gastrulation is a process of cell movement that forms the three main germ layers of the body: Ectoderm (skin and nerves), Mesoderm (muscles, heart, kidneys, blood, skeleton), and Endoderm (digestive tract and soft organs like liver and lungs). Morphological gradients (how far cells are from an inducing factor) establishes the initial boundaries of where each germ layer is. Reciprocal induction then reinforces it (Ectoderm cells release factors causing their neighbors to be Mesoderm, and vice versa).
Its important to note that cell specification is not cell differentiation. Cell specification is the “pre-committed” part of permissive induction I mentioned earlier, where it has the potential to go down a path and become fully differentiated, at which point it is locked in to that cell type. If the inducing factor is not present, but others are for a different cell type, that cell can freely differentiate into a different cell type as a result.
Basically, based on maternal morphogenic factors cells get a general “location” assigned to them, then during development their location relative to other cells and factors will influence their differentiation, as well as what DNA is expressed or suppressed. But that’s a whole other ELI5 in terms of chromatin, methylation, and other ways the body regulates chromosome expression.
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