Current Genomics - Volume 22, Issue 7, 2021

Circular RNA (circRNA) is a non-coding molecule produced through alternative splicing of one or more exons of a gene in the presence of an RNA-induced silencing complex (RISC). Its formation depends on complementary intron sequences on both sides of the circularized sequence. CircRNA functions as a sponge for miRNA, playing the role of the transcriptional regulator or potential biomarker. It has an impact on fetal growth and on synaptic facilitation in the brain. In this review, we illustrate biogenesis mechanisms, characteristics, and functions of cirRNAs. We also summarize methods using sequence feature and RNA next-generation sequencing data for circRNA prediction. Finally, we discuss the state of the research on circRNA in diseases, which will bring new contributions to future disease treatments.

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.

Background: Mycobacterium ulcerans is the fundamental agent of the third most common Mycobacterial disease known as Buruli Ulcer (BU). It is an infection of the skin and soft tissue affecting the human population worldwide. Presently, the vaccine is not available against BU. Objective: This study aimed to investigate the vaccine potential of virulence proteins of M. ulcerans computationally. Methods: Chromosome encoded virulence proteins of Mycobacterium ulcerans strain Agy99 were selected, which were available at the VFDB database. These proteins were analyzed for their subcellular localization, antigenicity, and human non-homology analysis. Ten virulence factors were finally chosen and analyzed for further study. Three-dimensional structures for selected proteins were predicted using Phyre2. B cell and T cell epitope analysis was done using methods available at Immune Epitope Database and Analysis Resource. Antigenicity, allergenicity, and toxicity analysis were also done to predict epitopes. Molecular docking analysis was done for T cell epitopes, those showing overlap with B cell epitopes. Results: Selected virulence proteins were predicted with B cell and T cell epitopes. Some of the selected proteins were found to be already reported as antigenic in other mycobacteria. Some of the predicted epitopes also had similarities with experimentally identified epitopes of M. ulcerans and M. tuberculosis which further supported our predictions. Conclusion: In-silico approach used for the vaccine candidate identification predicted some virulence proteins that could be proved important in future vaccination strategies against this chronic disease. Predicted epitopes require further experimental validation for their potential use as peptide vaccines.

Aims: Perform in-silico analysis of human SOS1 mutations to elucidate their pathogenic role in Noonan syndrome (NS). Background: NS is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, SOS1, RAF1, and KRAS genes. NS is thought to affect approximately 1 in 1000. NS patients suffer different pathogenic effects depending on the mutations they carry. Analysis of the mutations would be a promising predictor in identifying the pathogenic effect of NS. Methods: We performed computational analysis of the SOS1 gene to identify the pathogenic nonsynonymous single nucleotide polymorphisms (nsSNPs) th a t cause NS. SOS1 variants were retrieved from the SNP database (dbSNP) and analyzed by in-silico tools I-Mutant, iPTREESTAB, and MutPred to elucidate their structural and functional characteristics. Results: We found that 11 nsSNPs of SOS1 that were linked to NS. 3D modeling of the wild-type and the 11 nsSNPs of SOS1 showed that SOS1 interacts with cardiac proteins GATA4, TNNT2, and ACTN2. We also found that GRB2 and HRAS act as intermediate molecules between SOS1 and cardiac proteins. Our in-silico analysis findings were further validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying SOS1 gene variant c.1654A>G (NSiCMCs) and compared to control human skin fibroblast-derived iCMCs (C-iCMCs). Our in vitro data confirmed that the SOS1, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs when compared to C-iCMCs. Conclusion: This is the first in-silico and in vitro study demonstrating that 11 nsSNPs of SOS1 play deleterious pathogenic roles in causing NS.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that first occurred in Wuhan in December 2019. The spike glycoproteins and nucleocapsid proteins are the most common targets for the development of vaccines and antiviral drugs. Objective: We herein analyze the rate of evolution along with the sequences of spike and nucleocapsid proteins in relation to the spatial locations of their epitopes, previously suggested to contribute to the immune response caused by SARS-CoV-2 infections. Methods: We compare homologous proteins of seven human coronaviruses: HCoV-229E, HCoV- -OC43, SARS-CoV, HCoV-NL63, HCoV-HKU1, MERS-CoV, and SARS-CoV-2. We then focus on the local, structural order-disorder propensity of the protein regions where the SARS-CoV-2 epitopes are located. Results: We show that most of nucleocapsid protein epitopes overlap the RNA-binding and dimerization domains, and some of them are characterized by a low rate of evolutions. Similarly, spike protein epitopes are preferentially located in regions that are predicted to be ordered and wellconserved, in correspondence of the heptad repeats 1 and 2. Interestingly, both the receptor-binding motif to ACE2 and the fusion peptide of spike protein are characterized by a high rate of evolution. Conclusion: Our results provide evidence for conserved epitopes that might help develop broad- -spectrum SARS-CoV-2 vaccines.

Background: Behavioral genetic studies are important for the understanding of the contribution of genetic variations to human behavior. However, such studies might be associated with some ethical concerns. Methods: In the current study, ethical challenges related to studies of genetic variations contributing to human behavior were examined among researchers. To achieve the study purpose, the Middle East and North Africa (MENA) region researchers were taken as an example, where the aftermentioned ethical challenges were discussed among a group of researchers, who were the participants of an online forum. Discussions and responses of the participants were monitored and were later qualitatively analyzed. Results: Discussions revealed that several ethical challenges, including subjects’ recruitment, the difficulty of obtaining informed consents, and issues of privacy and confidentiality of obtained data as information leakage, in this case, will lead to social stigma and isolation of the participants and their immediate family members. Jordanian social and cultural norms, faith, and the tribal nature of the population were raised as a major challenge that might face conducting behavioral genetic studies in the Arab populations of the MENA. The lack of regulation related to the conduction of genetic studies, misunderstanding, and misuse of genetic information are other challenges. A full explanation of genetic research and the current and future possible benefits/risks of such research could be potential solutions. Conclusion: In conclusion, the MENA populations are tackled with major challenges in relation to conducting research studies in genetics/antisocial behavior field/s. Establishment of guidelines related to genetic studies, capacity building, increasing public awareness about the importance of genetic testing, and enhancing responsible conduct of research will facilitate the conduct of such sensitive studies in the future in the region.