An RNA Polymerase Pause Site Is Associated with the Immunoglobulin μs Poly(A) Site

Abstract

Immunoglobulin alternative RNA processing is regulated during B-cell maturation and requires balanced efficiencies of the competing splice (m) and cleavage-polyadenylation (s) reactions. When we deleted sequences 50 to 200 nucleotides beyond the s poly(A) site, the s/m mRNA ratio decreased three-to eightfold in B, plasma, and nonlymphoid cells. The activity could not be localized to a smaller fragment but did function in heterologous contexts. Our data suggest that this region contains an RNA polymerase II pause site that enhances the use of the s poly(A) site. First, known pause sites replaced the activity of the deleted fragment. Second, the fragment, when placed between tandem poly(A) sites, enhanced the use of the upstream poly(A) site. Finally, nuclear run-ons detected an increase in RNA polymerase loading just downstream from the s poly(A) site, even when the poly(A) site was inactivated. When this fragment and another pause site were inserted 1 kb downstream from the s poly(A) site, they no longer affected the mRNA expression ratio, suggesting that pause sites affect poly(A) site use over a limited distance. Fragments from the immunoglobulin A gene were also found to have RNA polymerase pause site activity.Elements that modulate gene expression by altering RNA polymerase elongation (reviewed in references 9, 35, 43, and 49) have been identified near the 5Ј end of genes (e.g., myc and human immunodeficiency virus) (18,20,26,27), within the coding region of genes (e.g., histone H3.3 and apolipoprotein A-I) (22,37,46), and downstream from some (3, 14), but not all (51), cleavage-polyadenylation [poly(A)] sites. The elements found downstream from the ␣ globin (14) and complement C2 (3) poly(A) sites were shown to contribute to transcriptional termination. The ␣ globin element is contained within a 92-bp fragment that is located about 300 nucleotides (nt) downstream from the ␣ globin poly(A) site (14). The C2 element is a 156-bp fragment that begins just downstream from the C2 poly(A) site; despite its close proximity, it is not required for efficient use of the C2 poly(A) site (3). These elements were called RNA polymerase pause sites because they appeared to have a kinetic affect on RNA polymerase II transcription (3, 14); when placed between two competing reactions, their effect on gene expression was consistent with these elements causing RNA polymerase to pause or slow its elongation rate. This was true when they were placed between tandem poly(A) sites (3,14), between tandem promoters (13), and between a regulated exon and its intronic regulatory region (38). In addition, in nuclear run-on assays, which measure RNA polymerase loading along a transcription unit, an increase in RNA polymerase loading was seen over these elements, again suggesting that RNA polymerase was being slowed or temporarily paused, so there was a higher probability of finding RNA polymerase molecules over those regions (3,14). More recently, the activity of these pause sites and their effect on upstream poly(A) sites was examined in...

Alteration of cyclin D1 transcript elongation by a mutated transcription factor up-regulates the oncogenic D1b splice isoform in cancer

“…3E). These data are consistent with previous studies showing that lower elongation rates favor the use of pre-mRNA processing sites located upstream of competing sites (12,31,32). Indeed, D1b polyadenylation sites (located in intron 4) lie kilobases upstream of the exon 5 splice site.…”

“…Previous studies using minigenes have shown that alternative processing of pre-mRNAs can be influenced by the transcription elongation rate and by transcriptional regulators (4,9,12,31,32). Such effects have been confirmed for endogenous genes in few cases (11)(12)(13).…”

Multiple links between transcription and splicing

“…The pause site, located between a poly(A) and a splicing site enhances the use of the upstream poly(A) site, which leads to the soluble form of IgM. Interestingly, nuclear run-ons demonstrated a stalling of RNA polymerase just downstream from the soluble µ poly(A) site (Peterson et al 2002).…”

Transcriptional termination sequences in the mouse serum albumin gene

“…Even so, they are expected to be widespread since most detailed studies on transcriptional termination of individual genes imply the presence of such termination sequences (Citron et al 1984;Hagenbuchle et al 1984;Ashfield et al 1991;Enriquez-Harris et al 1991;Dye and Proudfoot 2001;Peterson et al 2002). However, there appears to be extensive heterogeneity among the defined termination elements and the potential ways that they exert their effect on Pol II.…”