Abstract
SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo.
Highlights
The human pol II snRNA genes and type 3 pol III genes have the particularity of containing highly similar promoters, composed of a distal sequence element (DSE) that enhances transcription and a proximal sequence element (PSE) required for basal transcription
SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and others RNA polymerase III
Both RNA polymerase II and RNA polymerase III SNAPcdependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription
Summary
The human pol II snRNA genes and type 3 pol III genes have the particularity of containing highly similar promoters, composed of a distal sequence element (DSE) that enhances transcription and a proximal sequence element (PSE) required for basal transcription. The PSE recruits the five-subunit complex SNAPc, one of the few basal factors involved in both pol II and pol III transcription. Basal transcription from pol II snRNA promoters requires, in addition, TBP, TFIIA, GTF2B (TFIIB), TFIIF, and TFIIE, and from pol III type 3 promoters TBP, BDP1, and a specialized GTF2B-related factor known as BRF2 [3,4,5]. The DSE is often composed of an octamer and a ZNF143 motif (Zmotif) that recruit the factors POU2F1 (Oct-1) and ZNF143 (hStaf), respectively [1,2]. POU2F1 activates transcription in part by binding cooperatively with SNAPc and stabilizing the transcription initiation complex on the DNA (see [6], and references therein)
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