@article{1ae637221b4a4815bdad6f315d72ff05,
title = "RBFOX2 is critical for maintaining alternative polyadenylation patterns and mitochondrial health in rat myoblasts",
abstract = "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.",
keywords = "RBFOX2, Slc25a4, Tropomyosin 1, alternative polyadenylation, mitochondria, nanopore sequencing, poly(A) sequencing",
author = "Jun Cao and Sunil Verma and Elizabeth Jaworski and Stephanie Mohan and Nagasawa, {Chloe K.} and Kempaiah Rayavara and Amanda Sooter and Miller, {Sierra N.} and Holcomb, {Richard J.} and Powell, {Mason J.} and Ping Ji and Nathan Elrod and Eda Yildirim and Eric Wagner and Vsevolod Popov and Garg, {Nisha J.} and Routh, {Andrew L.} and Kuyumcu-Martinez, {Muge N.}",
note = "Funding Information: This work was supported, in part, by UTMB Department of Biochemistry and Molecular Biology Bridging funds and grants from the National Institutes of Health/National Heart Lung Blood Institute (1R01HL135031), the UTMB John Sealy Memorial Endowment Pilot Award, and the American Heart Association (20TPA35490206) to M.N.K-M. The contents of the manuscript are solely the responsibility of the authors and do not necessarily represent the official views of NHLBI of NIH. J.C. is funded by a post-doctoral fellowship from the American Heart Association (18POST3399018). N.J.G. is funded by grants from the National Institute of Allergy and Infectious Diseases (R01AI136031) of the National Institutes of Health. A.L.R. is supported by start-up funds from UTMB. E.J.W. acknowledges support of UTMB startup funds, and P.J. is supported by funds from the National Institutes of Health (R03CA223893). R.J.H. is supported by a fellowship from the American Heart Association Research Supplement to Promote Diversity in Science (2021AHA000DIVSUP0211476). The authors acknowledge the University of Texas Medical Branch Next Generation Sequencing Core Facility for providing RNA sequencing services. We thank Dr. Pei-Yong Shi for allowing us to use their plate readers. M.N.K.-M. conceived the idea, conceptualized the project, interpreted the data, provided financial support, and wrote the manuscript. A.L.R. designed the DPAC pipeline, processed and analyzed the PAC-seq and nanopore data, provided financial support, and critically edited the manuscript drafts. J.C. conceptualized the project, designed and performed most of the experiments, analyzed data, wrote the manuscript, and confirmed the accuracy of data presented in the manuscript. S.K.V. designed and performed experiments, analyzed the data, performed the statistical analyses, and provided feedback. S.M. performed the analysis for endogenous Slc25a4 mRNA and protein levels. S.N.M. and A.S. helped to clone poly(A) reporters. C.K.N. performed some of the Slc25a4 RT-PCRs. R.J.H. designed primers, performed some of the RT-PCRs, and prepared the graphical abstract. E.J. performed the nanopore sequencing. P.J. generated some of the PAC-seq libraries. N.D.E. helped with the preliminary analysis of the PAC-seq data. K.R. designed and performed experiments related to mitochondrial membrane potential. M.J.P. performed some of the rescue experiments in myoblasts. V.P. prepared the samples and processed them for TEM and helped analyze the data. E.J.W. critically analyzed/interpreted the data, provided feedback on the design of experiments, and edited the manuscript drafts. E.Y. provided feedback on the organization of the manuscript and design of the experiments. N.J.G. provided financial support for carrying out experiments related to the mitochondrial membrane potential and helped write and edit the manuscript drafts. All authors have read and approved the manuscript. The authors declare no competing interests. One or more of the authors of this paper received support from a program designed to increase minority representation in science. Funding Information: This work was supported, in part, by UTMB Department of Biochemistry and Molecular Biology Bridging funds and grants from the National Institutes of Health/National Heart Lung Blood Institute ( 1R01HL135031 ), the UTMB John Sealy Memorial Endowment Pilot Award , and the American Heart Association ( 20TPA35490206 ) to M.N.K-M. The contents of the manuscript are solely the responsibility of the authors and do not necessarily represent the official views of NHLBI of NIH. J.C. is funded by a post-doctoral fellowship from the American Heart Association ( 18POST3399018 ). N.J.G. is funded by grants from the National Institute of Allergy and Infectious Diseases ( R01AI136031 ) of the National Institutes of Health . A.L.R. is supported by start-up funds from UTMB . E.J.W. acknowledges support of UTMB startup funds, and P.J. is supported by funds from the National Institutes of Health ( R03CA223893 ). R.J.H. is supported by a fellowship from the American Heart Association Research Supplement to Promote Diversity in Science ( 2021AHA000DIVSUP0211476 ). The authors acknowledge the University of Texas Medical Branch Next Generation Sequencing Core Facility for providing RNA sequencing services. We thank Dr. Pei-Yong Shi for allowing us to use their plate readers. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = nov,
day = "2",
doi = "10.1016/j.celrep.2021.109910",
language = "English (US)",
volume = "37",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "5",
}