I am looking for the human rRNA promoter sequence, but am having trouble finding a specific sequence. What I did find was in Jones et al 1988 PNAS Analysis of clustered point mutations in the human ribosomal RNA gene promoter by transient expression in vivo (PMC279616). Can anyone tell me if the referenced promoter is the currently accepted sequence or where to find a pol I promoter sequence? Thanks.
I don't have any new information about the specific promoter sequences. One reasonable references is the introduction to Ghoshal et al, (2004) J Biol Chem 279(8):6783-93. This is from Samson Jacob's lab, a long-standing expert in rRNA transcription. Cites several review papers. (I've found, but haven't read, a review of rDNA chromatin structure by Birch & Zomerdijk (2008) Biochem Soc Transact 36, 619-624.) Note that the rRNA operon is highly reiterated, so there is not just a single "promoter sequence".
The Ghoshal reference is consistent with current textbook descriptions in saying that the pol I transcription control region extends from at least 400 base-pairs upstream of the start site to perhaps 100 bp downstream of the start site. The basal promoter consists of an INR sequence spanning -50 to +20 around the start site and an upstream promoter element (UPE) located around -200. I know very little about enhancer elements (though I know there are some) other than that the site for p53 is upstream of the UPE.
Two semi-annotated promoter region sequences are i) GenBank accession K01105.1 (GI:337380). This is the insert in a plasmid from the Jacob lab. [LOCUS: HUMRGLTIB; DEFINITION: Human 45S rRNA precursor transcription initiation region, clone pETS-RS.]
ii) Genbank NR_046235.1 (This is a complete 45S transcription unit plus 3' spacer sequences. It starts downstream of K01105.1 but still--I think--upstream of the start site.)
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