Transcriptional regulation of human small nuclear RNA genes

Abstract

The products of human snRNA genes have been frequently described as performing housekeeping functions and their synthesis refractory to regulation. However, recent studies have emphasized that snRNA and other related non-coding RNA molecules control multiple facets of the central dogma, and their regulated expression is critical to cellular homeostasis during normal growth and in response to stress. Human snRNA genes contain compact and yet powerful promoters that are recognized by increasingly well-characterized transcription factors, thus providing a premier model system to study gene regulation. This review summarizes many recent advances deciphering the mechanism by which the transcription of human snRNA and related genes are regulated.

Figure 1. Sequence comparison of human snRNA gene core promoters

Human snRNA gene core promoters contain a proximal sequence element (blue) located approximately 42-44 bp upstream from the transcriptional start site (green). Differences at conserved positions within the PSE are indicated. The U12 promoter contains a degenerate PSE (dashed underline) located adjacently to the start site. Those genes transcribed by RNA polymerase III contain an additional TATA box (red) located at variable positions from the 3′ border of the PSE. Except for U1, U2, U6, and 7SK, the transcriptional start sites are predicted but have not been experimentally confirmed. The location of the experimentally determined p53-binding site within the U1 promoter is indicated (pink) with the brackets representing the region protected during Dnase I footprinting [28] and the p53 element quarter sites indicated by arrows. The database accession numbers for the indicated sequences are U1 (J00318), U2 (U57614), U3 (X14945), U4B (M15956), U5C (NT 010194), U11 (X58716), U12 (NT 035014), Y5 (NR 001571), U6 (M14486), 7SK (X05490), MRP (X51867), Y1 (NT 007914), Y4 (L32608), U6atac (NT 035014), Y3 (NT 007914), and H1 (X16612).

Figure 2. Factors involved in human snRNA gene transcription

The transcription of human snRNA genes by RNA polymerases II (A) and III (B) involves a combination of shared factors, including the Staf and Oct-1 activators and the general transcription factors SNAP_C and TBP along with additional factors specialized for transcription by only one polymerase. These polymerase-specific factors include TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH for RNA polymerase II transcription, and the Brf2 and Bdp1 components of the Brf2-TFIIIB complex for RNA polymerase III transcription. For genes harboring snRNA core promoter elements, RNA polymerase II and III termination is directed by the 3′box or by the TTTT terminator, respectively. The numbers within SNAP_C represent the apparent molecular weights of each subunit as measured by SDS-PAGE, and relatively positioning within the complex and towards DNA is suggested from in vitro protein-protein interaction studies [31, 178]. Studies performed with Drosphila SNAP_C suggest that SNAP50 makes DNA contacts towards the 3′ end of the PSE [32, 33].

Figure 3. Model for cell cycle regulation of snRNA gene transcription by RNA polymerase III

RNA polymerase III transcription is elevated during late G1, S, and G2 phases and becomes repressed during M and early G1 phases. A role for the protein kinase CK2 in M phase repression and S phase activation is indicated whereas RB is proposed to act predominately during early G1 phase. Other RB family members, including p107 and p130, may influence snRNA gene transcription during the cell cycle whereas MAF1, a downstream effector of the mTOR pathway, can also repress snRNA gene transcription in response to cell stress and changes in nutrient levels (not shown).

Figure 4. Models for gene regulation by RB

During RNA polymerase III repression, RB can inhibit transcription through stable association with the general transcriptional machinery and RNA polymerase at snRNA promoters (A. RB/SNAP_C model) or through disrupted preinitiation complex formation by blocking communication between TFIIIC and Brf1-TFIIIB (B. RB/TFIIIB model) disabling polymerase recruitment. Stable promoter association by RB at E2F target genes is also suggested to occur during RNA polymerase II repression (C. RB/E2F model). In this model, the preinitiation complex is disrupted either by RB interference with E2F signaling or though co-repressor effects on chromatin structure, such as enacted by HDAC and/or SWI/SNF containing complexes. A role for co-repressors that alter the snRNA gene chromatin environment is also suggested, although repression can occur independently of histone deacetylase activity on naked U6 DNA templates, suggesting that the repression of polymerase activity occurs downstream from chromatin modification events.

Figure 5. Model for U1 snRNA gene regulation by p53

In response to DNA damage, such as caused by UV light, p53 is activated and can associate with the U1 promoter, possibly through direct interactions with the SNAP190 and SNAP43 subunits of SNAP_C or through association with a high affinity p53 response element located adjacently to the start site of transcription for this gene. Promoter association by SNAP_C is not apparently affected either by DNA damage or by p53 binding in vitro, although downstream events in the preinitiation complex assembly are likely affected by p53 promoter association. RNA polymerase II is also polyubiquitylated in response to UV light contributing to decreased U1 expression. The promoter association of p53 also directs additional cofactor recruitment, such as HDAC1 and HDAC2, which may interfere with chromatin structure and activator signaling.