In case of human beings, the whole genome is divided in 23 pairs of chromosomes in somatic cells. It has been observed that in case of many proteins (e.g. immunoglobulins, hemoglobin) different polypeptides are assembled together which are expressed from different chromosomes. My question is- what guides them to assemble them for the making of a fully functional protein??
They have complimentary interfaces on their surfaces and it is energetically favourable for them to stay together once they have found each other by Brownian motion. Often they are highly unstable alone. So it is simply thermodynamics and a decrease in Gibbs free energy.
This happens across life. Enzyme complexes in bacteria are on the same operon, especially in thermophiles, because they come together at a faster speed. In Eukaryotes it makes no difference as the mRNA needs to be processed etc.