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1. Archaea

   Linked via "RNAP II"

   Genetic Organization and Transcription
   Archaea exhibit transcriptional and translational machinery that bears striking resemblance to that found in Eukarya, despite their prokaryotic cellular organization. For instance, Archaean RNA polymerase (RNAP) is structurally related to the eukaryotic RNAP II, possessing multiple subunits and requiring eukaryotic-like transcription factors (such as TATA-binding protein analogs) for initiation $\cite{Kruger2003}$.
   Gene regulation in Archaea often employs s…

2. Sigma Factor

   Linked via "RNA Polymerase II (Pol II"

   Sigma Factor vs. Eukaryotic Initiation Factors
   In contrast to the bacterial system, eukaryotic transcription initiation is mediated by large, multi-subunit complexes, notably RNA Polymerase II (Pol II\) and General Transcription Factors (GTFs\), such as $\text{TFIID}$. While $\text{TFIID}$ shares the functional role of promoter recognition seen in sigma factors, it lacks structural homology. Mechanistically, $\text{TFIID}$ stabilizes the [pr…

3. Transcription Factor

   Linked via "RNA Polymerase II"

   Transactivation and Corepression Domains
   Once bound to $\text{DNA}$, the $\text{TAD}$ interacts with components of the basal transcription machinery (e.g., RNA Polymerase II, or $\text{RNAPII}$), or with coactivator complexes (e.g., Mediator complex, general transcription factors ($\text{GTFs}$)). This interaction facilitates the transition from the closed chromatin state to the ac…