Thoughts on transcription

A few weeks ago I asked this question:

It was a simple question. In order for the RNA polymerase protein to form, the various RNA polymerase subunit genes need to be transcribed (and subsequently translated). However, the process of transcription requires the RNA polymerase protein. So given a new cell, how do the RNA polymerase subunit genes get transcribed, i.e. where did the first RNA polymerase come from? I got an answer from Alan, who stated that (at least in sexually reproducing organisms) the first RNA polymerase proteins came from the mother, which makes sense.

This morning I was reading an opinion piece by Mark Ptashne, which I learned about through Dan Graur. It was an article about the importance of transcription factors, the definition of epigenetics, and how histone modifications are not self-perpetuating (and thus do not fit his definition of epigenetics). I bring the paper up because there was a sentence in the article that reminded me of the answer I received on Twitter, which I quote:

Development of an organism from a fertilised egg is driven primarily by the actions of regulatory proteins called transcription factors. In sequential waves and combinations, these proteins bind to specific DNA sequences called cis-regulatory sequences associated with specific genes, and encourage (activate) or discourage (repress) transcription into mRNA of those genes. The process is started by transcription factors, contributed mainly by the mother, found in the fertilised egg.

There was not a reference for the last sentence and perhaps because this is considered general knowledge? Therefore it seems that the first batch of prerequisite proteins, such as transcription factors and transcriptional machinery proteins, were provided by our mother.

Another enlightening paper I read this week was on the stochastic mRNA synthesis patterns in mammalian cells. The stochastic part of the title refers to the random nature of transcription in individual cells, i.e. genes are transcribed randomly amongst individual cells. This was counter intuitive to me because I would have imagined that transcription is a tightly controlled mechanism. In the paper, they demonstrate how cells can deal with this randomness through the stability of proteins; the pool of proteins inside a cell is much constant and this provides a buffer for this transcriptional bursting. Apart from their reporter genes, they also show that this randomness in transcription is inherent in natural genes, such as the large subunit of RNA polyermase II.

When I asked my original question, I did not take into account the discontinuity of transcription and protein availability. I simplistically assumed that when a cell requires a protein, the gene corresponding to the protein is immediately transcribed, and I extended this assumption to the core proteins that cells need.

Lastly, when I asked my question on Twitter, I got an evolutionary answer from Cedric Feschotte. He proposed that ribozymes came first before the RNA polymerase. He also sent me this paper on how a ribozyme could carry out the transcription of an active ribozyme. This supports the idea that before the evolution of RNA polymerase, ribozymes carried out the role of copying genetic material.

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