I want to know what are the DNA elements that are recognized by transcription factors in Archaea and so what is the "anatomy" of transcriptional regulation in this case.
I found in this paper by Alexandra M. Gehring et al. that the process of initiation of transcription in archaea is governed by TATA-binding protein (TBP), Archaeal transcription factor B (TFB), and Archaeal transcription factor E (TFE). These constitute the basal transcription factors and transcription initiation is regulated by DNA elements that are recognized by basal transcription factors that recruit the enzyme RNA Polymerase (RNAP) that will copy DNA into RNA. There are four DNA elements currently known to regulate archaeal transcription initiation: the TATA-box located approximately 25 bp upstream of the site of transcription initiation; the TFB recognition element (BRE) located immediately upstream of the TATA box; the initiator element (INR) located within the initially transcribed region, and the promoter proximal element (PPE) located between the TATA box and the site of transcription initiation.
This seems very similar to the eukaryotic system and, in fact, also the Wikipedia page tells that the core machinery is more similar to eukaryotic transcription (with respect to bacteria).
Moreover, the first paper that I linked also tells that it is probable that some archaeon-specific factors await discovery for the elongation and termination steps of transcription.
Now, I started to search if Archaea have enhancers and silencers like the eukaryotic genes but I could not find anything. Since the core machinery is more similar to eukaryotic transcription, can I assume that there are enhancers and repressors and that the main pattern of DNA elements necessary for transcription and transcription regulation is that of eukaryotes? Maybe, the reason why I do not find the answer to my question in Google is that some archaeon-specific factors await discovery. Indeed, Archaea are, in general, often called the "blind spots" of natural diversity because of lack of knowledges about them.
Also if you have a look at the Promoter (genetics) Wikipedia page, there is a list of elements of promoter relative to Eukaryotes and Bacteria, but nothing about Archaea... So is it completely wrong to look at the eukaryotic elements and explanations of this page, for example, as (at least) probably valid also for Archaea ?
Thank you in advance.