Intron retention generates ANKRD1 splice variants that are co-regulated with the main transcript in normal and failing myocardium

Abstract

The cardiac ankyrin repeat domain 1 protein (ANKRD1, also known as CARP) has been extensively characterized with regard to its proposed functions as a cardio-enriched transcriptional co-factor and stressinducible myofibrillar protein. The present results show the occurrence of alternative splicing by intron retention events in the pig and human ankrd1 gene. In pig heart, ankrd1 is expressed as four alternatively spliced transcripts, three of which have non-excised introns: ankrd1-contained introns 6, 7 and 8 (i.e., ankrd1-i6,7,8), ankrd1-contained introns 7 and 8 (i.e., ankrd1-i7,8), and ankrd1 retained only intron 8 (i.e., ankrd1-i8). In the human heart, two orthologues of porcine intron-retaining ankrd1 variants (i.e., ankrd1-i8 and ankrd1-i7,8) are detected. We demonstrate that these newly-identified intron-retaining ankrd1 transcripts are functionally intact, efficiently translated into protein in vitro and exported to the cytoplasm in cardiomyocytes in vivo. In the piglet heart, both the intronless and intron-retaining ankrd1 mRNAs are co-expressed in a chamber-dependent manner being more abundant in the left as compared to the right myocardium. Our data further indicate co-upregulation of the ankrd1 spliced variants in myocardium in the porcine model of diastolic heart failure. Most significantly, we demonstrate that in vivo forced expression of recombinant intronless ankrd1 markedly increases the levels of intron-retaining ankrd1 variants (but not of the endogenous main transcript) in piglet myocardium, suggesting that ANKRD1 may positively regulate the expression of its own intron-containing RNAs in response to cardiac stress. Overall, our findings demonstrate that in cardiomyocytes ANKRD1 can exist in multiple isoforms which may contribute to the functional diversity of this factor in heart development and disease. Abbreviations ANKRD1, ankyrin repeat domain 1 protein; MARPs, muscle ankyrin repeat proteins; SRF, serum response factor; HF, heart failure; DHF, diastolic HF; LV/RV, left/right ventricular myocardium; LA/RA, left/right atrial

Comparative Analyses between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana Using Random Forest and Support Vector Machine

“…Such positional distribution characteristic of RIs indicates the potential that these introns are partly or entirely translated to proteins. Previous studies demonstrate that growing examples of cellular mRNAs with RIs express functional proteins by avoiding degradation through the nonsense-mediated decay (NMD) [59]–[61]. Our data analysis also provides a support for this trend by a high rate of RIs existing in coding regions.…”

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

“…Yet, some cellular genes and many viruses express alternatively spliced mRNA isoforms in which one or more introns are retained (Hammarskjöld 1997;Galante et al 2004;Li et al 2006). Although some of these are subject to degradation in the cytoplasm through nonsense-mediated decay (NMD) (Green et al 2003b), there are an increasing number of examples of cellular mRNAs with retained introns, which avoid the NMD machinery and express functional proteins (Forrest et al 2004;Li et al 2006;Marinescu et al 2007;Torrado et al 2009;Mollet et al 2010). Retroviruses have become models for this and provide important tools for the analysis of such cellular restriction mechanisms and 1 These authors contributed equally to this work.…”

Novel mutations in the sarcomeric protein myopalladin in patients with dilated cardiomyopathy

“…Titin and its 145-kDa interacting partner myopalladin located in the sarcomeric Z-band both bind to cardiac ankyrin-repeat protein (CARP), an early differentiation marker of cardiac myogenesis expressed during embryonic and fetal heart development and in end-stage heart failure in the adult heart. [6][7][8][9] CARP is localized in the cytoplasm in the sarcomeric I-region through its interaction with the N2A domain of titin and the N-terminal domain of myopalladin. In addition, CARP was detected in the nucleus, where it functions as a transcriptional regulator involved in gene expression.…”