RNA editing relates to those molecular processes by which the RNA nucleotide sequence is conspicuously modified (Fig. 13.1). To date such changes have been observed in tRNA, rRNA, and mRNA molecules of eukaryotes, but not prokaryotes. RNA editing can modify an A-to-I (inosine) by the action of adenosine deaminase that acts on RNA (ADAR), and similarly a C-to-U modification can be elicited by a protein complex composed by APOBEC-1 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1), an RNA cytidine deaminase, and APOBEC-1 complementation factor (ACF). This C to U editing holoenzyme (APOBEC-1/ACF) is also in part regulated by CELF2 [53, 54].

Inosine is an essential modification introduced by specialized enzymes in a highly regulated manner generating thereafter transcriptome diversity. Adenosine to inosine (A-to-I) modification by the ADAR (i.e., ADAR1 and ADAR2) enzymes performs the most common type of RNA editing in metazoans [55], while C-to-U modifications seem to be confined to more discrete transcripts [53, 56–59]. A-to-I RNA editing most frequently targets repetitive RNA sequences located within introns and 5′ and 3′ untranslated regions (UTRs). ADARs use double-stranded RNA as substrates but allow structure interruptions such as bulges and loops. It is well known that these enzymes can use messenger RNA as targets for A-to-I editing and thereby recode the transcript. Both ADAR1 and ADAR2 have been proven to be able to also target short double-stranded RNA molecules, i.e., microRNAs and their precursors. Since the editing activity is found both in the nucleus and the cytoplasm, there are several steps during the microRNA maturation pathway that can be targeted for modification [60]. Although the biological significance of non-coding RNA editing remains largely unknown, several possibilities have been proposed, including its role in the control of endogenous short interfering RNAs [61].

RNA editing involving C-to-U modifications has been reported extensively to play a pivotal role in virus-associated human diseases, including human T lymphotropic virus (HTLV), hepatitis C virus (HCV), hepatitis B virus (HBV), and Epstein-Barr virus (EBV), among others [62, 63]. Furthermore, more recently a possible role in cancer development has also been proposed [63]. However, to date, no abnormalities in C-to-U RNA editing have been reported in cardiovascular diseases.

A-to-I RNA defective editing has been reported in various human diseases including viral infection susceptibility and cancer and neurological and psychiatric disorders [64–68]. Involvement of defective RNA editing in cardiovascular diseases is indirect and scarce [69, 70], yet an involvement in congenital heart diseases is likely to soon emerge.

RNA splicing is the molecular process by which introns are deleted from nascent immature mRNA providing the means to successfully liked exons back together and thus form a single mature mRNA molecule. RNA splicing is carried out by the assembly of over a hundred core proteins and five small nuclear RNAs into large ribonucleoprotein complexes, named spliceosomes [71]. Regulation of splicing is a complex process [72–74], and alterations of splicing potential have major consequences in distinct human diseases [75].

Alternative splicing is a major driver of protein diversity and allows the generation of distinct proteins from a single gene. It is estimated that almost 85 % of genes within the human genome undergo alternative splicing. Distinct mechanisms such as exon exclusion, intron retention, and the usage of alternative splice sites contribute to modify protein structure, localization, regulation, and function [76, 77]. Interestingly, genetic mutations in distinct spliceosome components have been reported in human families with distinct cardiac diseases such as myocardial infarction [78, 79] and dilated cardiomyopathy [80, 81], suggesting a functional link. Importantly, alternative splicing also plays a pivotal role during embryonic development. Differential expression of distinct spliceosome components has been reported during heart development [82]. Postnatal excitation-contraction coupling impairment has been reported in genetically engineered mice lacking ASF/SF2 spliceosome component [83], and mutant mice for SRp38, a spliceosome regulator, display early embryonic cardiac resulting in impaired calcium handling [84].

On the other hand, alternatively spliced variants have been documented widely in cardiovascular diseases such as cardiomyopathies, arrhythmias, and vascular defects leading to differential expression of sarcomeric proteins, ion channels, and cell signaling proteins [76, 77, 85–89]. An example of the impact of alternative splicing in adult heart physiology is illustrated by the diversity and functional consequences of alternative spliced variants of the troponin-tropomyosin complex (see for a review [90]). Multiple alternatively spliced variants are formed from each of the troponin isoforms, and deregulation of spliced variant expression is linked to dilated cardiomyopathy in different species [91–93]. Similarly, impaired ion channel splice variants also contribute to cardiac arrhythmogenesis, as reported for distinct components of the calcium handling and plasma membrane cardiac pumps [86, 88].

Multiple transcription factors, with critical roles in cardiac development, are alternatively spliced, such as T-box genes [94–96], myocardin [97], myocyte enhancer factor (Mef)-2 [98, 99], pituitary homeobox (Pitx)-2 [100–102], and GATA binding protein 4 (Gata4) [103]. In this context, Yehya et al. [104] identified an intronic retention variant of the NFATC1 (nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent 1) gene in patients with ventricular septal defects, suggesting that such a spliced variant might be a VSD-susceptibility gene. Bedard et al. [105] reported spliced variants of ZIC3 (Zic family member 3) linked to patients with heterotaxy and congenital heart diseases. McCright et al. [106] reported that aberrant Notch2 alternative spliced variants leads to myocardial hypoplasia as well as eye and kidney defects. More recently, Ricci et al. [107] demonstrate that multiple genes were differentially spliced in hypoplastic left heart syndrome, suggesting a deregulation of cell metabolism and cytoskeleton and cell adherence. Interestingly, impaired alternative splicing in other genes also result in cardiac alterations. Impaired fibronectin splicing is associated with thoracic aortic aneurysm in patients with bicuspid aortic valve [108], while abnormal SCN5A (sodium channel, voltage gated, type V, alpha subunit) alternative spliced variants leads to fetal arrhythmias [109]. Furthermore, impaired expression of alternatively spliced NXT2 (nuclear transport factor 2-like export factor 2) variants, a protein involved in nuclear RNA export, also has been proven to affect cardiac development, particularly valve formation [110]. Ver Heyen et al. [111] reported that genetic engineered disruption of SERCA2a/2b (sarcoplasmic/endoplasmic reticulum calcium ATPase 2a/b) alternative splicing leads to 20 % increase in embryonic and neonatal mortality, as consequence of severe cardiac malformations. Buyon et al. [112] describes a spliced variant of congenital heart block-associated 52 kb autoantigen which is maximal at the time of fetal heart block, suggesting a putative role in its pathophysiology. These reports exemplify the potential causative role of impaired alternative spliced variants as key regulatory modulators of cardiac development. Increasing evidence of this is expected in the coming years as deep-sequencing technologies depict the magnitude of the alternative spliced transcriptome in congenital heart diseases.