1
|
Zhao Y, Riching AS, Knight WE, Chi C, Broadwell LJ, Du Y, Abdel-Hafiz M, Ambardekar AV, Irwin DC, Proenza C, Xu H, Leinwand LA, Walker LA, Woulfe KC, Bristow MR, Buttrick PM, Song K. Cardiomyocyte-Specific Long Noncoding RNA Regulates Alternative Splicing of the Triadin Gene in the Heart. Circulation 2022; 146:699-714. [PMID: 35862102 PMCID: PMC9427731 DOI: 10.1161/circulationaha.121.058017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Abnormalities in Ca2+ homeostasis are associated with cardiac arrhythmias and heart failure. Triadin plays an important role in Ca2+ homeostasis in cardiomyocytes. Alternative splicing of a single triadin gene produces multiple triadin isoforms. The cardiac-predominant isoform, mouse MT-1 or human Trisk32, is encoded by triadin exons 1 to 8. In humans, mutations in the triadin gene that lead to a reduction in Trisk32 levels in the heart can cause cardiac dysfunction and arrhythmias. Decreased levels of Trisk32 in the heart are also common in patients with heart failure. However, mechanisms that maintain triadin isoform composition in the heart remain elusive. METHODS We analyzed triadin expression in heart explants from patients with heart failure and cardiac arrhythmias and in hearts from mice carrying a knockout allele for Trdn-as, a cardiomyocyte-specific long noncoding RNA encoded by the antisense strand of the triadin gene, between exons 9 and 11. Catecholamine challenge with isoproterenol was performed on Trdn-as knockout mice to assess the role of Trdn-as in cardiac arrhythmogenesis, as assessed by ECG. Ca2+ transients in adult mouse cardiomyocytes were measured with the IonOptix platform or the GCaMP system. Biochemistry assays, single-molecule fluorescence in situ hybridization, subcellular localization imaging, RNA sequencing, and molecular rescue assays were used to investigate the mechanisms by which Trdn-as regulates cardiac function and triadin levels in the heart. RESULTS We report that Trdn-as maintains cardiac function, at least in part, by regulating alternative splicing of the triadin gene. Knockout of Trdn-as in mice downregulates cardiac triadin, impairs Ca2+ handling, and causes premature death. Trdn-as knockout mice are susceptible to cardiac arrhythmias in response to catecholamine challenge. Normalization of cardiac triadin levels in Trdn-as knockout cardiomyocytes is sufficient to restore Ca2+ handling. Last, Trdn-as colocalizes and interacts with serine/arginine splicing factors in cardiomyocyte nuclei and is essential for efficient recruitment of splicing factors to triadin precursor mRNA. CONCLUSIONS These findings reveal regulation of alternative splicing as a novel mechanism by which a long noncoding RNA controls cardiac function. This study indicates potential therapeutics for heart disease by targeting the long noncoding RNA or pathways regulating alternative splicing.
Collapse
Affiliation(s)
- Yuanbiao Zhao
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrew S. Riching
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Walter E. Knight
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Congwu Chi
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lindsey J. Broadwell
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Yanmei Du
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mostafa Abdel-Hafiz
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amrut V. Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David C. Irwin
- Cardiovascular and Pulmonary Research Laboratory, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine Proenza
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Leslie A. Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Lori A. Walker
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kathleen C. Woulfe
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael R. Bristow
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Peter M. Buttrick
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kunhua Song
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
2
|
Abstract
Background Although the roles of alpha‐myosin heavy chain (α‐MyHC) and beta‐myosin heavy chain (β‐MyHC) proteins in cardiac contractility have long been appreciated, the biological contribution of another closely related sarcomeric myosin family member, MYH7b (myosin heavy chain 7b), has become a matter of debate. In mammals, MYH7b mRNA is transcribed but undergoes non‐productive alternative splicing that prevents protein expression in a tissue‐specific manner, including in the heart. However, several studies have recently linked MYH7b variants to different cardiomyopathies or have reported MYH7b protein expression in mammalian hearts. Methods and Results By analyzing mammalian cardiac transcriptome and proteome data, we show that the vast majority of MYH7b RNA is subject to exon skipping and cannot be translated into a functional myosin molecule. Notably, we discovered a lag in the removal of introns flanking the alternatively spliced exon, which could retain the non‐coding RNA in the nucleus. This process could play a significant role in controlling MYH7b expression as well as the activity of other cardiac genes. Consistent with the negligible level of full‐length protein coding mRNA, no MYH7b protein expression was detected in adult mouse, rat, and human hearts by Western blot analysis. Furthermore, proteome surveys including quantitative mass spectrometry analyses revealed only traces of cardiac MYH7b protein and even then, only in a subset of individual samples. Conclusions The comprehensive analysis presented here suggests that previous studies showing cardiac MYH7b protein expression were likely attributable to antibody cross‐reactivity. More importantly, our data predict that the MYH7b disease‐associated variants may operate through the alternately spliced RNA itself.
Collapse
Affiliation(s)
- Lindsey A Lee
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder Boulder CO.,BioFrontiers InstituteUniversity of Colorado Boulder Boulder CO
| | - Lindsey J Broadwell
- BioFrontiers InstituteUniversity of Colorado Boulder Boulder CO.,Department of Biochemistry University of Colorado Boulder Boulder CO
| | - Massimo Buvoli
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder Boulder CO.,BioFrontiers InstituteUniversity of Colorado Boulder Boulder CO
| | - Leslie A Leinwand
- Department of Molecular, Cellular, and Developmental Biology University of Colorado Boulder Boulder CO.,BioFrontiers InstituteUniversity of Colorado Boulder Boulder CO
| |
Collapse
|
3
|
Broadwell LJ, Smallegan MJ, Rigby KM, Navarro-Arriola JS, Montgomery RL, Rinn JL, Leinwand LA. Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart. J Biol Chem 2021; 296:100694. [PMID: 33895132 PMCID: PMC8141895 DOI: 10.1016/j.jbc.2021.100694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 11/01/2022] Open
Abstract
Myosin heavy chain 7b (MYH7b) is an ancient member of the myosin heavy chain motor protein family that is expressed in striated muscles. In mammalian cardiac muscle, MYH7b RNA is expressed along with two other myosin heavy chains, β-myosin heavy chain (β-MyHC) and α-myosin heavy chain (α-MyHC). However, unlike β-MyHC and α-MyHC, which are maintained in a careful balance at the protein level, the MYH7b locus does not produce a full-length protein in the heart due to a posttranscriptional exon-skipping mechanism that occurs in a tissue-specific manner. Whether this locus has a role in the heart beyond producing its intronic microRNA, miR-499, was unclear. Using cardiomyocytes derived from human induced pluripotent stem cells as a model system, we found that the noncoding exon-skipped RNA (lncMYH7b) affects the transcriptional landscape of human cardiomyocytes, independent of miR-499. Specifically, lncMYH7b regulates the ratio of β-MyHC to α-MyHC, which is crucial for cardiac contractility. We also found that lncMYH7b regulates beat rate and sarcomere formation in cardiomyocytes. This regulation is likely achieved through control of a member of the TEA domain transcription factor family (TEAD3, which is known to regulate β-MyHC). Therefore, we conclude that this ancient gene has been repurposed by alternative splicing to produce a regulatory long-noncoding RNA in the human heart that affects cardiac myosin composition.
Collapse
Affiliation(s)
- Lindsey J Broadwell
- Department of Biochemistry, CU Boulder, Boulder, Colorado, USA; BioFrontiers Institute, CU Boulder, Boulder, Colorado, USA
| | - Michael J Smallegan
- BioFrontiers Institute, CU Boulder, Boulder, Colorado, USA; Department of Molecular, Cellular, and Developmental Biology, CU Boulder, Boulder, Colorado, USA
| | | | - Jose S Navarro-Arriola
- Department of Molecular, Cellular, and Developmental Biology, CU Boulder, Boulder, Colorado, USA
| | | | - John L Rinn
- Department of Biochemistry, CU Boulder, Boulder, Colorado, USA; BioFrontiers Institute, CU Boulder, Boulder, Colorado, USA
| | - Leslie A Leinwand
- BioFrontiers Institute, CU Boulder, Boulder, Colorado, USA; Department of Molecular, Cellular, and Developmental Biology, CU Boulder, Boulder, Colorado, USA.
| |
Collapse
|
4
|
Abstract
Striated muscles express an array of sarcomeric myosin motors that are tuned to accomplish specific tasks. Each myosin isoform found in muscle fibers confers unique contractile properties to the fiber in order to meet the demands of the muscle. The sarcomeric myosin heavy chain (MYH) genes expressed in the major cardiac and skeletal muscles have been studied for decades. However, three ancient myosins, MYH7b, MYH15, and MYH16, remained uncharacterized due to their unique expression patterns in common mammalian model organisms and due to their relatively recent discovery in these genomes. This article reviews the literature surrounding these three ancient sarcomeric myosins and the specialized muscles in which they are expressed. Further study of these ancient myosins and how they contribute to the functions of the specialized muscles may provide novel insight into the history of striated muscle evolution.
Collapse
Affiliation(s)
- Lindsey A. Lee
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
| | - Anastasia Karabina
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
| | - Lindsey J. Broadwell
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
- Department of Biochemistry, University of Colorado, Boulder, CO USA
| | - Leslie A. Leinwand
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO USA
- BioFrontiers Institute, University of Colorado, Boulder, CO USA
| |
Collapse
|
5
|
Roberts BS, Babilonia-Rosa MA, Broadwell LJ, Wu MJ, Neher SB. Lipase maturation factor 1 affects redox homeostasis in the endoplasmic reticulum. EMBO J 2018; 37:embj.201797379. [PMID: 30068531 DOI: 10.15252/embj.201797379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 11/09/2022] Open
Abstract
Lipoprotein lipase (LPL) is a secreted lipase that clears triglycerides from the blood. Proper LPL folding and exit from the endoplasmic reticulum (ER) require lipase maturation factor 1 (LMF1), an ER-resident transmembrane protein, but the mechanism involved is unknown. We used proteomics to identify LMF1-binding partners necessary for LPL secretion in HEK293 cells and found these to include oxidoreductases and lectin chaperones, suggesting that LMF1 facilitates the formation of LPL's five disulfide bonds. In accordance with this role, we found that LPL aggregates in LMF1-deficient cells due to the formation of incorrect intermolecular disulfide bonds. Cells lacking LMF1 were hypersensitive to depletion of glutathione, but not DTT treatment, suggesting that LMF1 helps reduce the ER Accordingly, we found that loss of LMF1 results in a more oxidized ER Our data show that LMF1 has a broader role than simply folding lipases, and we identified fibronectin and the low-density lipoprotein receptor (LDLR) as novel LMF1 clients that contain multiple, non-sequential disulfide bonds. We conclude that LMF1 is needed for secretion of some ER client proteins that require reduction of non-native disulfides during their folding.
Collapse
Affiliation(s)
- Benjamin S Roberts
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Melissa A Babilonia-Rosa
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lindsey J Broadwell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ming Jing Wu
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Saskia B Neher
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
6
|
Garrett CK, Broadwell LJ, Hayne CK, Neher SB. Modulation of the Activity of Mycobacterium tuberculosis LipY by Its PE Domain. PLoS One 2015; 10:e0135447. [PMID: 26270534 PMCID: PMC4536007 DOI: 10.1371/journal.pone.0135447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/22/2015] [Indexed: 01/11/2023] Open
Abstract
Mycobacterium tuberculosis harbors over 160 genes encoding PE/PPE proteins, several of which have roles in the pathogen’s virulence. A number of PE/PPE proteins are secreted via Type VII secretion systems known as the ESX secretion systems. One PE protein, LipY, has a triglyceride lipase domain in addition to its PE domain. LipY can regulate intracellular triglyceride levels and is also exported to the cell wall by one of the ESX family members, ESX-5. Upon export, LipY’s PE domain is removed by proteolytic cleavage. Studies using cells and crude extracts suggest that LipY’s PE domain not only directs its secretion by ESX-5, but also functions to inhibit its enzymatic activity. Here, we attempt to further elucidate the role of LipY’s PE domain in the regulation of its enzymatic activity. First, we established an improved purification method for several LipY variants using detergent micelles. We then used enzymatic assays to confirm that the PE domain down-regulates LipY activity. The PE domain must be attached to LipY in order to effectively inhibit it. Finally, we determined that full length LipY and the mature lipase lacking the PE domain (LipYΔPE) have similar melting temperatures. Based on our improved purification strategy and activity-based approach, we concluded that LipY’s PE domain down-regulates its enzymatic activity but does not impact the thermal stability of the enzyme.
Collapse
Affiliation(s)
- Christopher K. Garrett
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Lindsey J. Broadwell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Cassandra K. Hayne
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saskia B. Neher
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- * E-mail:
| |
Collapse
|