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All somatic cells contain the same genome, then how it knows that it should develop into a specific organ. In https://www.youtube.com/watch?v=aeAL6xThfL8, Joe Hanson says that each cell has the same book that each has 20,000 same instructions. And each cell has bookmarks, where it finds which instructions to read.

Can you tell me where these bookmarks are stored in the cells? Is it outside the chromosomes or outside nucleus?

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The answer to your question is not really know yet and there is whole scientific field dedicated to it: developmental biology. I'll try to explain the basics however:

Like you described the identity of a cell (its cell type; which organ it belongs to) is dependent on which of (actually) ~30000 human genes are activated (or read) in that cell. There are two fundamentally different ways this is done in cells:

  1. Transcription factors:

These are proteins that bind to specific (regulatory) DNA sequences and thereby lead to the activation (or repression) of certain - usually nearby - genes. Since they are proteins, their own genes have to be activated in the first place, so we already at a 'chicken or the egg' type of problem. In principle proteins can 'survive' outside the nucleus of the cell for some time, but they are usually degraded within a few hours, so I guess the remaining factors from the mother cell are not very important (I have no idea if anyone ever checked this). Additionally many transcription factors are not constitutively active, but are waiting for some outside (from the perspective of the cell) signal. These could be certain developmental signals, growth factors, hormones or environmental factors like nutrient availability (the list goes on ...). During embryo (& therefore organ) development not only the presence of these signals (morphogens), but also their intensity are a very important factor in determining the 'fate' of a given cell.

  1. Epigenetics

The term epigenetics describes genetic regulation that does not happen on the sequence level. Instead the accessibility of the DNA is regulated through modifications of histones (which are part of the chromosomes) and the DNA itself. Thereby the cell can almost permanently shut down certain genes. Since epigenetics are also inherited during cell division, this regulation affects whole cell lineages and is therefore very important in regulating which cells are active in certain organs or tissues.

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  • $\begingroup$ Do you have a citation for the number of genes? $\endgroup$ – canadianer Jul 29 '17 at 15:40
  • $\begingroup$ @canadianer I had the number in my head from working with NCBI data. I just looked for references: the often cited ~20000 is for protein-coding genes only, so I guess that why so different numbers are used. I tried to get the number of annotated genes from the human genome from NCBI but couldn't find it. This older book say 30k-40k genes (scroll to 'The functions of human genes'), I didnt find a better source at NCBI right now. $\endgroup$ – Nicolai Jul 29 '17 at 16:16
  • $\begingroup$ Thanks. I had always heard ~20,000 genes as well, but if that is just protein coding then a higher figure makes sense. $\endgroup$ – canadianer Jul 30 '17 at 0:10

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