RBFOX2 is critical for maintaining alternative polyadenylation patterns and mitochondrial health in rat myoblasts
Jun Cao,
Sunil K. Verma,
Elizabeth Jaworski,
Stephanie Mohan,
Chloe K. Nagasawa,
Kempaiah Rayavara,
Amanda Sooter,
Sierra N. Miller,
Richard J. Holcomb,
Mason J. Powell,
Ping Ji,
Nathan D. Elrod,
Eda Yildirim,
Eric J. Wagner,
Vsevolod Popov,
Nisha J. Garg,
Andrew L. Routh,
Muge N. Kuyumcu-Martinez
Affiliations
Jun Cao
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Sunil K. Verma
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Elizabeth Jaworski
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Stephanie Mohan
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Chloe K. Nagasawa
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Kempaiah Rayavara
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Amanda Sooter
School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
Sierra N. Miller
Center for Addiction Research, University of Texas Medical Branch, Galveston, TX 77555, USA
Richard J. Holcomb
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Mason J. Powell
School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
Ping Ji
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Nathan D. Elrod
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
Eda Yildirim
Department of Cell Biology, Duke University School of Medicine, Durham, NC 27708, USA
Eric J. Wagner
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
Vsevolod Popov
Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
Nisha J. Garg
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
Andrew L. Routh
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
Muge N. Kuyumcu-Martinez
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Neuroscience, Cell biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA; Corresponding author
Summary: RBFOX2, which has a well-established role in alternative splicing, is linked to heart diseases. However, it is unclear whether RBFOX2 has other roles in RNA processing that can influence gene expression in muscle cells, contributing to heart disease. Here, we employ both 3ʹ-end and nanopore cDNA sequencing to reveal a previously unrecognized role for RBFOX2 in maintaining alternative polyadenylation (APA) signatures in myoblasts. RBFOX2-mediated APA modulates mRNA levels and/or isoform expression of a collection of genes, including contractile and mitochondrial genes. Depletion of RBFOX2 adversely affects mitochondrial health in myoblasts, correlating with disrupted APA of mitochondrial gene Slc25a4. Mechanistically, RBFOX2 regulation of Slc25a4 APA is mediated through consensus RBFOX2 binding motifs near the distal polyadenylation site, enforcing the use of the proximal polyadenylation site. In sum, our results unveil a role for RBFOX2 in fine-tuning expression of mitochondrial and contractile genes via APA in myoblasts relevant to heart diseases.
