Analysis of Pig Vomeronasal Receptor Type 1 (V1R) Promoter Region Reveals a Common Promoter Motif but Poor CpG Islands

Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072

Background

In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements.

Result

The present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome.

Conclusions

This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment.

Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation

SARS-CoV-2 is a new virus responsible for an outbreak of respiratory illness known as COVID-19, which has spread to several countries around the world and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In silico analysis of the transcription start sites, promoter regions, transcription factors and their binding sites, gene ontology, CpG islands for SARS-CoV-2 viral genome are a first step to understand the regulation mechanisms of gene expression and its association with genetic variations in the genomes. For this purpose, we first computationally surveyed all SARS-CoV-2 virus genes with the open reading frames from NCBI database and found eleven sequences to accomplish the mentioned features by using bioinformatics tools. Our analysis revealed that all (100%) of the SARS-CoV-2 virus genes have more than one TSS. By taking all TSSs with the highest predictive score we determined promoter regions and identified five common candidate motifs (MVI, MVII, MVIII, MVIV and MVV) of which MVI was found to be shared by all promoter regions of SARS-CoV-2 virus genes with the least E-value (3.8e-056, statistically highly significant). In our further analysis of MVI we showed MVI serve as binding sites for a single transcription factor (TF) family, EXPREG, involved in the regulatory mode of these genes. From EXPREG family four TFs that belongs to Cyclic AMP (cAMP) receptor protein (CRP) and Catabolite control protein A (CcpA) group mostly serve as transcriptional activator whereas two TFs that belong to LexA group always serve as transcriptional repressor in different kinds of cellular processes and molecular functions. Therefore, we unfolded SARS-CoV-2 viral genome to shed light on its gene expression regulation that could help to design and evaluate diagnostic tests, to track and trace the ongoing outbreak and to identify potential intervention options.

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Computationally surveyed all SARS-CoV-2 genes with the open reading frames from NCBI database showed eleven gene sequences

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Our analysis revealed that all (100%) of the SARS-CoV-2 genes have more than one TSS.

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We determined promoter regions and identified five common candidate motifs of which MVI was found to be shared by all promoter regions of SARS-CoV-2 genes.

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We showed MVI serve as binding sites for a single transcription factor family, EXPREG, involved in the regulatory mode of these genes.

In silico analysis of the promoter region of olfactory receptors in cattle (Bos indicus) to understand its gene regulation

Identifications of transcription start sites (TSSs) and promoter regions are first step to understand the regulation mechanisms of gene expression and association with genetic variations in the regions. This analysis was conducted with the objectives to identify TSSs, determine the promoter regions, identify common candidate motifs and transcription factors (TFs), and search for CpG islands (CGIs) in cattle olfactory receptors (ORs) genes promoter regions. In the analysis, TSSs of cattle olfactory genes were first identified. The locations for 60% of the TSSs were below -500 bp relative to the start codon and five candidate motifs (MOR1, MOR2, MOR3, MOR4, and MOR5) were identified that are shared by at least 50% of the cattle ORs promoter input sequences from both strands. Among the five candidate motifs, MOR4 was revealed as the common promoter motif for 85.71% of cattle ORs genes that serves as binding sites for TFs involved in the expression regulation of these genes. MOR4 was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF by using the TOMTOM web application. Hence, it was revealed that MOR4 may serve as the binding site mainly for the Zinc finger (ZNF) TF gene family to regulate expression of cattle ORs genes. Further gene ontology analysis for MOR4 demonstrated ORs belong to the G-protein-coupled receptor superfamily and MOR4 tend to be located near the genes involved in the detection of chemical stimulus involved in sensory perception and in innate immune responses such as cytokine-mediated signaling. In silico digestion of cattle OR sequences was performed using restriction enzyme MspI. CGIs from OR10K1 and OR2L13 gene was found. In the present analysis, the poor CGIs observed might suggest their gene expression regulation pattern is in tissue specific manner.

Comparative Genomic Analysis of the Pheromone Receptor Class 1 Family (V1R) Reveals Extreme Complexity in Mouse Lemurs (Genus, Microcebus) and a Chromosomal Hotspot across Mammals

Sensory gene families are of special interest for both what they can tell us about molecular evolution and what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within primates, with a special focus on the small-bodied nocturnal mouse and dwarf lemurs of Madagascar (genera Microcebus and Cheirogaleus, respectively). By doubling the existing genomic resources for strepsirrhine primates (i.e. the lemurs and lorises), we find that the highly speciose and morphologically cryptic mouse lemurs have experienced an elaborate proliferation of V1Rs that we argue is functionally related to their capacity for rapid lineage diversification. Contrary to a previous study that found equivalent degrees of V1R diversity in diurnal and nocturnal lemurs, our study finds a strong correlation between nocturnality and V1R elaboration, with nocturnal lemurs showing elaborate V1R repertoires and diurnal lemurs showing less diverse repertoires. Recognized subfamilies among V1Rs show unique signatures of diversifying positive selection, as might be expected if they have each evolved to respond to specific stimuli. Furthermore, a detailed syntenic comparison of mouse lemurs with mouse (genus Mus) and other mammalian outgroups shows that orthologous mammalian subfamilies, predicted to be of ancient origin, tend to cluster in a densely populated region across syntenic chromosomes that we refer to as a V1R "hotspot."