Eukaryote specific RNA and protein features facilitate assembly and catalysis of H/ACA snoRNPs

Small but strong: the emerging role of small nucleolar RNA in cardiovascular diseases

Cardiovascular diseases (CVDs) are the leading cause of mortality and disability worldwide. Numerous studies have demonstrated that non-coding RNAs (ncRNAs) play a primary role in CVD development. Therefore, studies on the mechanisms of ncRNAs are essential for further efforts to prevent and treat CVDs. Small nucleolar RNAs (snoRNAs) are a novel species of non-conventional ncRNAs that guide post-transcriptional modifications and the subsequent maturation of small nuclear RNA and ribosomal RNA. Evidently, snoRNAs are extensively expressed in human tissues and may regulate different illnesses. Particularly, as the next-generation sequencing techniques have progressed, snoRNAs have been shown to be differentially expressed in CVDs, suggesting that they may play a role in the occurrence and progression of cardiac illnesses. However, the molecular processes and signaling pathways underlying the function of snoRNAs remain unidentified. Therefore, it is of great value to comprehensively investigate the association between snoRNAs and CVDs. The aim of this review was to collate existing literature on the biogenesis, characteristics, and potential regulatory mechanisms of snoRNAs. In particular, we present a scientific update on these snoRNAs and their relevance to CVDs in an effort to cast new light on the functions of snoRNAs in the clinical diagnosis of CVDs.

iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework

Accumulating evidence indicates that the dysregulation of small nucleolar RNAs (snoRNAs) is relevant with diseases. Identifying snoRNA-disease associations by computational methods is desired for biologists, which can save considerable costs and time compared biological experiments. However, it still faces some challenges as followings: (i) Many snoRNAs are detected in recent years, but only a few snoRNAs have been proved to be associated with diseases; (ii) Computational predictors trained with only a few known snoRNA-disease associations fail to accurately identify the snoRNA-disease associations. In this study, we propose a ranking framework, called iSnoDi-MDRF, to identify potential snoRNA-disease associations based on multiple biological data, which has the following highlights: (i) iSnoDi-MDRF integrates ranking framework, which is not only able to identify potential associations between known snoRNAs and diseases, but also can identify diseases associated with new snoRNAs. (ii) Known gene-disease associations are employed to help train a mature model for predicting snoRNA-disease association. Experimental results illustrate that iSnoDi-MDRF is very suitable for identifying potential snoRNA-disease associations. The web server of iSnoDi-MDRF predictor is freely available at http://bliulab.net/iSnoDi-MDRF/.

The daunting task of modifying ribosomal RNA

One of the most basic tasks of every cell is the synthesis of ribosomes, yet the process is so complex that we are only beginning to comprehend it. In human cells, the final product contains four RNAs and 79 proteins forming a large ribonucleoprotein, the ribosome. About twice as many factors are involved in assembly of these protein synthesizing machines. Additionally, some 200 small nucleolar ribonucleoproteins (snoRNPs) function in the modification of pre-ribosomal RNA (pre-rRNA) at a similar number of ribonucleotides. Modification is essential for proper function and biogenesis of ribosomes (Decatur and Fournier 2002; Sloan et al. 2016). While abrogation of individual modifications has little to no measurable effects, removal of a combination of modifications or of all causes severe to lethal effects. Modifications mostly cluster around the functional centers of the ribosome and some modifications are important for ribosome assembly. The subject of this perspective is to raise awareness to how modification at so many sites can be achieved while the pre-rRNA is being processed, folded and re-folded, and assembled with ribosomal proteins to yield the pre-ribosomal subunits in the nucleolus (Baßler and Hurt 2019). This is not a comprehensive review but a simplification of complex issues providing access to the general reader.

iSnoDi-LSGT: identifying snoRNA-disease associations based on local similarity constraints and global topological constraints

Growing evidence proves that small nucleolar RNAs (snoRNAs) have important functions in various biological processes, the malfunction of which leads to the emergence and development of complex diseases. However, identifying snoRNA-disease associations is an ongoing challenging task due to the considerable time- and money-consuming biological experiments. Therefore, it is urgent to design efficient and economical methods for the identification of snoRNA-disease associations. In this regard, we propose a computational method named iSnoDi-LSGT, which utilizes snoRNA sequence similarity and disease similarity as local similarity constraints. The iSnoDi-LSGT predictor further employs network embedding technology to extract topological features of snoRNAs and diseases, based on which snoRNA topological similarity and disease topological similarity are calculated as global topological constraints. To the best of our knowledge, the iSnoDi-LSGT is the first computational method for snoRNA-disease association identification. The experimental results indicate that the iSnoDi-LSGT predictor can effectively predict unknown snoRNA-disease associations. The web server of the iSnoDi-LSGT predictor is freely available at http://bliulab.net/iSnoDi-LSGT.

Guide RNA acrobatics: positioning consecutive uridines for pseudouridylation by H/ACA pseudouridylation loops with dual guide capacity

Site-specific pseudouridylation of human ribosomal and spliceosomal RNAs is directed by H/ACA guide RNAs composed of two hairpins carrying internal pseudouridylation guide loops. The distal "antisense" sequences of the pseudouridylation loop base-pair with the target RNA to position two unpaired target nucleotides 5'-UN-3', including the 5' substrate U, under the base of the distal stem topping the guide loop. Therefore, each pseudouridylation loop is expected to direct synthesis of a single pseudouridine (Ψ) in the target sequence. However, in this study, genetic depletion and restoration and RNA mutational analyses demonstrate that at least four human H/ACA RNAs (SNORA53, SNORA57, SCARNA8, and SCARNA1) carry pseudouridylation loops supporting efficient and specific synthesis of two consecutive pseudouridines (ΨΨ or ΨNΨ) in the 28S (Ψ3747/Ψ3749), 18S (Ψ1045/Ψ1046), and U2 (Ψ43/Ψ44 and Ψ89/Ψ91) RNAs, respectively. In order to position two substrate Us for pseudouridylation, the dual guide loops form alternative base-pairing interactions with their target RNAs. This remarkable structural flexibility of dual pseudouridylation loops provides an unexpected versatility for RNA-directed pseudouridylation without compromising its efficiency and accuracy. Besides supporting synthesis of at least 6% of human ribosomal and spliceosomal Ψs, evidence indicates that dual pseudouridylation loops also participate in pseudouridylation of yeast and archaeal rRNAs.