A splicing factor drives gene expression down multiple paths in T cells. The factor, an mRNA-binding protein called CELF2, has been known to affect mRNA processing in neuronal and muscle cells. But new research indicates that it also accounts for a large proportion of the splicing changes that occur during T-cell activation and also during T-cell development.

This research was carried out by the laboratory of Kristen Lynch, Ph.D., a professor at the University of Pennsylvania. Dr. Lynch and her colleagues report that they have uncovered a cascade of events that appears to account for changes in gene expression that occur during the development of the human immune system.

“An understanding of the patterns and mechanisms of alternative splicing is essential for a full comprehension how the genome is interpreted under different conditions to affect protein function,” said Dr. Lynch.

Dr. Lynch’s team presented their work April 13 in the Proceedings of the National Academy of Sciences, in an article entitled, “Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling.” The article described how the splicing factor CELF2 (CUGBP, Elav-like family member 2) is regulated in response to T-cell signaling through combined increases in transcription and mRNA stability.

The researchers uncovered dozens of splicing events in cultured T cells whose changes upon stimulation are dependent on CELF2 expression, and they provided evidence that CELF2 controls a similar proportion of splicing events during human thymic T-cell development.

“Transcriptional induction occurs within 6 h of stimulation and is dependent on activation of NF-κB,” the authors of the PNAS article explained. “Subsequently, there is an increase in the stability of the CELF2 mRNA that correlates with a change in CELF2 3′UTR length and contributes to the total signal-induced enhancement of CELF2 expression.”

Alternative splicing is a key mechanism for gene regulation that is regulated in response to developmental and antigen signaling in T cells. However, the extent and mechanisms of regulated splicing, particularly during T-cell development, have not been well characterized. T cells need all kinds of new proteins to go through the necessary alterations to fight infections or mature. The cells do this two ways: turn new genes on to produce new proteins or change how mRNA is spliced together to get different forms of the same proteins. These two mechanisms can work separately or together in a cell.

The team demonstrated that the expression of an RNA binding protein called CELF2 is increased in response to T-cell stimulation such as occurs in response to circulating antigens from foreign microbes or tumors. For example, T cells go through changes that ramp up division and proliferation and express gene products such as cytokines to help fight infections. The increase in CELF2 expression drives widespread changes in mRNA splicing in cultured T cells and correlates with changes in mRNA splicing during T-cell development, which occurs in the thymus.

Using next-generation sequencing, they catalogued the splicing pattern of 5,000 exons and looked for the changes in pattern in stimulated versus unstimulated T cells to see how the overall complement of proteins made had changed. These differences in splicing can lead to physiologically important changes in proteins such as activity, whether the protein functions in the nucleus or the cytoplasm, or which other molecules it can interact with.

“We believe that this paper is the first to catalogue splicing changes during T-cell development,” said Dr. Lynch. “The take-home message is that the increase in CELF2 expression drives a large proportion of splicing changes that occur during T-cell activation and also T-cell development in the thymus when we are young. These results provide unprecedented insight into the regulation of splicing during thymic development and reveal an important biologic role of CELF2 in human T cells.”

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