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...

Gene expression profiles were compared in circulating bovine GD3.5+ (CD8−) and GD3.5− (predominantly CD8+) γδ T cells using serial analysis of gene expression (SAGE). Approximately 20,000 SAGE tags were generated from each library. A comparison of the two libraries demonstrated 297 and 173 tags representing genes with 5-fold differential expression in GD3.5+ and GD3.5− γδ T cells, respectively. Consistent with their localization into sites of inflammation, GD3.5+ γδ T cells appeared transcriptionally and translationally more active than GD3.5− γδ cells. GD3.5− γδ T cells demonstrated higher expression of the cell proliferation inhibitor BAP 37, which was associated with their less activated gene expression phenotype. The immune regulatory and apoptosis-inducing molecule, galectin-1, was identified as a highly abundant molecule and was higher in GD3.5+γδ T cells. Surface molecules attributed to myeloid cells, such as CD14, CD68, and scavenger receptor-1, were identified in both populations. Furthermore, expression of B lymphocyte-induced maturation protein, a master regulator of B cell and myeloid cell differentiation, was identified by SAGE analysis and was confirmed at the RNA level to be selectively expressed in γδ T cells vs αβ T cells. These results provide new insights into the inherent differences between circulating γδ T cell subsets.