The Role of scaRNAs in Adjusting Alternative mRNA Splicing in Heart Development

Abstract

Congenital heart disease (CHD) is a leading cause of death in children <1 year of age. Despite intense effort in the last 10 years, most CHDs (~70%) still have an unknown etiology. Conotruncal based defects, such as Tetralogy of Fallot (TOF), a common complex of devastating heart defects, typically requires surgical intervention in the first year of life. We reported that the noncoding transcriptome in myocardial tissue from children with TOF is characterized by significant variation in levels of expression of noncoding RNAs, and more specifically, a significant reduction in 12 small cajal body-associated RNAs (scaRNAs) in the right ventricle. scaRNAs are essential for the biochemical modification and maturation of small nuclear RNAs (spliceosomal RNAs), which in turn are critical components of the spliceosome. This is particularly important because we also documented that splicing of mRNAs that are critical for heart development was dysregulated in the heart tissue of infants with TOF. Furthermore, we went on to show, using the zebrafish model, that altering the expression of these same scaRNAs led to faulty mRNA processing and heart defects in the developing embryo. This review will examine how scaRNAs may influence spliceosome fidelity in exon retention during heart development and thus contribute to regulation of heart development.

2’-O-methylation alters the RNA secondary structural ensemble

“…The same approach was used to estimate pES1 for site-labeled G34-C8 TAR (pES1 = 7.3%) and TAR-C24U25A35 (pES1 = 14.5%) in 1 mM Mg 2+ using the dGS and dES1 values calculated for TAR in the absence of Mg 2+ (Table S2). 13 C/ 15 N R1ρ experiments. 13 C/ 15 N R1ρ RD measurements were performed on site-labeled TAR and TAR-C24U25A35 RNA in the presence or absence of 1 mM Mg 2+ as described previously (55).…”

“…13 C/ 15 N R1ρ experiments. 13 C/ 15 N R1ρ RD measurements were performed on site-labeled TAR and TAR-C24U25A35 RNA in the presence or absence of 1 mM Mg 2+ as described previously (55). RD measurements on the unmodified chemically synthesized site-labeled TAR were used to confirm reproducibility with previously published data on uniformly 13 C/ 15 N labeled TAR prepared using in vitro transcription (66,67).…”

“…Geometry optimization was performed using the B3LYP functional (84) with two runs using the 3-21G (85) and 6-311+G (2d, p) basis sets (86). 13 C chemical shifts were then calculated using the GIAO method (87) using the B3LYP/6-311+G (2d, p) basis sets. The calculated chemical shifts were then referenced to isotropic magnetic shielding of TMS.…”

“…It can be added to the ribose sugar moiety of all four nucleotides (Nm = Am, Um, Cm and Gm) ( Figure 1A) either via stand-alone methyltransferases (6) or by the enzyme fibrillarin when guided by box C/D small nucleolar RNAs (snoRNAs) (7,8). Nm modifications are important for the cellular activity of diverse RNAs (9,10) and have been linked to diseases (11)(12)(13)(14). For example, ribosomal RNAs (rRNA) contain more than 100 Nm sites (15), many in the decoding and peptidyltransferase centers (16).…”

“…The loss of Nm modifications on snRNA U6 due to knockout of the La-related protein, which helps load U6 snRNA onto the box C/D snoRNA protein complex (20), changes splicing fidelity, impairs spermatogenesis in mice (20), and contributes to the Alazami syndrome (21). Loss of snoRNA-guided Nm modifications on snRNAs also leads to profound defects in cardiac mRNA splicing and development (13,22,23).…”