Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells.
CELF2 is an RNA binding protein that has been implicated in developmental and signal-dependent splicing in the heart, brain and T cells. In the heart, CELF2 expression decreases during development, while in T cells CELF2 expression increases both during development and in response to antigen-induced signaling events. Although hundreds of CELF2-responsive splicing events have been identified in both heart and T cells, the way in which CELF2 functions has not been broadly investigated. Here we use CLIP-Seq to identified physical targets of CELF2 in a cultured human T cell line. By comparing the results with known functional targets of CELF2 splicing regulation from the same cell line we demonstrate a generalizable position-dependence of CELF2 activity that is consistent with previous mechanistic studies of individual CELF2 target genes in heart and brain. Strikingly, this general position-dependence is sufficient to explain the bi-directional activity of CELF2 on 2 T cell targets recently reported. Therefore, we propose that the location of CELF2 binding around an exon is a primary predictor of CELF2 function in a broad range of cellular contexts.
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Sandya
S
Ajith
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Matthew R
MR
Gazzara
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Brian S
BS
Cole
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Ganesh
G
Shankarling
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Nicole M
NM
Martinez
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Michael J
MJ
Mallory
a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.
Kristen W
KW
Lynch
D017398:Alternative Splicing; D001921:Brain / Q000378:metabolism; D000067878:CELF Proteins / Q000378:metabolism*; D002478:Cells, Cultured; D005091:Exons; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D019169:Jurkat Cells; D009206:Myocardium / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D012326:RNA Splicing; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction; D013601:T-Lymphocytes / Q000378:metabolism*
D000067878:CELF Proteins; C117363:CELF2 protein, human; D009419:Nerve Tissue Proteins; D012313:RNA
Alternative splicing; CELF2; CLIP-Seq; LEF1; MKK7; RNA map