Transcription of eukaryotic DNA, transcription apparatus and its regulation, cis- and trans-regulation elements

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Transcription of Genomic DNA in Prokaryotes and Eukaryotes

Transcription is the process by which the cell copies information from DNA into RNA, much like a scribe making a copy of a master work. It is the essential first step in gene expression in which instructions in DNA ultimately result in the creation of proteins. And although both bacteria and human cells operate roughly the same general principle, the machinery they use differs in complexity and control.


In Prokaryotes

Prokaryotic cells, like E. coli cells, operate with a minimalist efficiency. A single enzyme, RNA polymerase, accomplishes the entire task of transcription. But even this enzyme needs some guidance in the form of a protein named the sigma factor. The sigma factor allows the RNA polymerase to detect and attach to a specific starting place on the DNA, a promoter. These are short, retained motifs most notably the -10 and the -35 positions that act like runway lights for the enzyme.


Once attached, the enzyme unwinds the DNA strands apart and begins constructing a complementary strand of RNA. It reads on until it reaches its own stop signal: a nucleotide run into a hairpin loop or a protein called Rho, which knots up the process. During this time, within a few seconds, the message has been written down and is ready to be translated into protein.


In Eukaryotes

Eukaryotic cells: the cells that plants, animals, and humans use add levels of complexity and regulation. Instead of one polymerase, there are three:


RNA polymerase I for all but a few of the ribosomal RNAs,


RNA polymerase II for messenger RNA (mRNA),


RNA polymerase III for tRNA and small RNAs.


RNA polymerase II, the enzyme that transcribes most protein-coding genes, doesn't act alone. It requires a collection of general transcription factors to find the correct start, typically marked by a TATA box of DNA. All these proteins converge to form a preinitiation complex, assembling like stagehands prior to curtain time.


But that is just the beginning. Eukaryotic cell DNA is tightly compressed into chromatin, and often out of reach. Transcription factors, chromatin remodelers, and coactivator complexes like Mediator help open the DNA and strengthen or silence the activity of specific genes. Enhancer and silencer regions, sometimes located thousands of bases away, loop through space to attach to the transcription machinery, acting as molecular accelerators or brakes.


The Role of DNA-Protein Binding

There is a delicate interaction between proteins and DNA at the heart of transcription. Transcription factors specifically bind to DNA sequence, most commonly by structural motifs like zinc fingers or helix-turn-helix. These structures allow proteins to fit snugly within the major groove of the DNA, decoding its code without unzipping the strands.

This specificity ensures that the right genes are expressed at the right time something that is necessary for growth, adaptation, and survival.

References

  1. Alberts B et al. Molecular Biology of the Cell, 6th ed. Garland Science, 2014.
  2. Watson JD et al. Molecular Biology of the Gene, 7th ed. Pearson, 2013.
  3. Kornberg RD. The molecular basis of eukaryotic transcription. PNAS. 2007.
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