TCERG1 Regulates Alternative Splicing of the Bcl-x Gene by Modulating the Rate of RNA Polymerase II Transcription

Abstract

Complex functional coupling exists between transcriptional elongation and pre-mRNA alternative splicing. Pausing sites and changes in the rate of transcription by RNA polymerase II (RNAPII) may therefore have fundamental impacts in the regulation of alternative splicing. Here, we show that the elongation and splicing-related factor TCERG1 regulates alternative splicing of the apoptosis gene Bcl-x in a promoter-dependent manner. TCERG1 promotes the splicing of the short isoform of Bcl-x (Bcl-x_s) through the SB1 regulatory element located in the first half of exon 2. Consistent with these results, we show that TCERG1 associates with the Bcl-x pre-mRNA. A transcription profile analysis revealed that the RNA sequences required for the effect of TCERG1 on Bcl-x alternative splicing coincide with a putative polymerase pause site. Furthermore, TCERG1 modifies the impact of a slow polymerase on Bcl-x alternative splicing. In support of a role for an elongation mechanism in the transcriptional control of Bcl-x alternative splicing, we found that TCERG1 modifies the amount of pre-mRNAs generated at distal regions of the endogenous Bcl-x. Most importantly, TCERG1 affects the rate of RNAPII transcription of endogenous human Bcl-x. We propose that TCERG1 modulates the elongation rate of RNAPII to relieve pausing, thereby activating the proapoptotic Bcl-x_S 5′ splice site.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.06255-11.

ACKNOWLEDGMENTS

This work was supported by grants from the Spanish Ministry of Science and Innovation (BFU2008-01599), the Fundación para la Investigación y Prevención del SIDA en España (36768), the Junta de Andalucía (Proyecto de Excelencia 2009/CVI-4626) to C.S., and the Spanish Ministry of Science and Innovation (BFU2009-08796) to C.H.M. Support from the Fondo Europeo de Desarrollo Regional (FEDER) is also acknowledged. Work in the laboratory of B.C. was supported by a grant from the Canadian Institutes of Health Research. B.C. is the Canada Research Chair in Functional Genomics. M.M. was supported by a fellowship from the Spanish Ministry of Education (FPU program). N.S.-H. was supported by a fellowship from the CSIC (JAE program). A.C. holds a scholarship from the FRSQ.

We are grateful to the members of the laboratory for their helpful suggestions, critical discussions, and comments. We thank A. R. Kornblihtt, D. Bentley, and G. Dreyfuss for providing reagents.