Biological Functions Of Genes Research Articles

Genes divided according to the relative position of the longest intron show increased representation in different KEGG pathways

Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and regulation of protein production. As a common feature of eukaryotic genomes, it has been reported that in protein-coding genes, the longest intron is usually one of the first introns. The goal of our work was to find a possible difference in the biological function of genes that fulfill this common feature compared to genes that do not. Data on the lengths of all introns in genes were extracted from the genomes of six vertebrates (human, mouse, koala, chicken, zebrafish and fugu) and two other model organisms (nematode worm and arabidopsis). We showed that more than 40% of protein-coding genes have the relative position of the longest intron located in the second or third tertile of all introns. Genes divided according to the relative position of the longest intron were found to be significantly increased in different KEGG pathways. Genes with the longest intron in the first tertile predominate in a range of pathways for amino acid and lipid metabolism, various signaling, cell junctions or ABC transporters. Genes with the longest intron in the second or third tertile show increased representation in pathways associated with the formation and function of the spliceosome and ribosomes. In the two groups of genes defined in this way, we further demonstrated the difference in the length of the longest introns and the distribution of their absolute positions. We also pointed out other characteristics, namely the positive correlation between the length of the longest intron and the sum of the lengths of all other introns in the gene and the preservation of the exact same absolute and relative position of the longest intron between orthologous genes.

Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs.

Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56kb (15.11 to 15.17Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45kb (137.55 to137.56Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.

A framework for identifying fertility gene targets for mammalian pest control.

Fertility-targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression and results from mouse knockout models. This framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non-drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. In addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives.

Genome-wide association study identifies variants associated with semen volume in white-feathered broilers.

Semen is a measure of the reproductive efficiency of roosters, which affects the economic benefits of white-feathered broilers. Over the years, research in this field has mainly focused on hens, while there have been fewer studies on the reproductive traits of roosters. To identify the genes related to the semen traits of roosters, we used a chicken 55 K SNP chip to genetically type the white-feathered population (220) and performed imputation with resequencing data from 97 roosters. In total, 1 048 576 SNPs were obtained and used for genome-wide association analysis of semen volume, from which 197 genome-wide significant markers were identified, all within the interval of 13.82-16.12 Mb on chromosome 7. By combining our results with the biological functions of genes in the interval, four candidate genes were identified that potentially relate to semen volume: FAPP1, OSBPL6, SESTD1 and SSFA2. Our findings may provide a basis for further research on the genetic mechanism and marker-assisted selection of semen volume in white-feathered broilers.

Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans.

Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.

Potential role of exitron-containing homeobox genes in cancer.

Homeobox genes are protagonists in developmental and cancer biology, making comprehending their regulation pivotal in multiple molecular pathways. Exitrons, also known as intronic exons, are new players in the transcriptional organization, providing additional splicing variants whose functions are still vastly unknown. Exitron splicing sites were identified in eight homeobox genes, which has not been yet debated in the scientific literature. Due to the intimate connection between homeobox genes and tumorigenesis, it is worth investing more time in understanding how these less explored exitron-containing transcriptional isoforms could play a role in modulating the homeobox gene's biological functions. The perspectives devised in this article are meant to instigate fresh debates on how the transcriptional variants retaining exitrons identified in the human homeobox genes HOXA1, HOXA9, HOXD8, NKX3.1, and DLX6 can be examined in the context of tumorigenesis. This article is categorized under: Cancer > Genetics/Genomics/Epigenetics.

HIF-1α-regulated stanniocalcin-1 mediates gemcitabine resistance in pancreatic ductal adenocarcinoma via PI3K/AKT signaling pathway.

Pancreatic ductal adenocarcinoma (PDAC) has a poor response to the first-line chemotherapy drug gemcitabine. We previously identified stanniocalcin-1 as a gemcitabine-resistant-related gene, but its specific role and function in pancreatic cancer remain unclear. RT-qPCR and Western blot were used to evaluate differential protein and mRNA expressions. The biological functions of genes were determined using proliferation and drug-resistance experiments. Subcutaneous tumorigenesis experiment was performed on nude mice. Prognostic analysis was performed using public databases and our clinical data. We found HIF-1α-regulated STC1 expression mediated chemoresistance in pancreatic cancer. Deeper, we explored the action mechanism of STC1 and identified PI3K/AKT as the downstream signaling pathway of STC1. Furthermore, we analyzed clinical data and found that STC1 expression was related to the prognosis of gemcitabine-treated patients after surgery. In general, we proved the HIF-1α/STC1/PI3K-AKT axis participated in PDAC progression and chemoresistance, and STC1 may serve as a potential prognostic factor and therapeutic target for PDAC treatment.

A Signature for Smoking Status of Coronary Heart Disease Patients through Weighted Gene Coexpression Network Analysis

Background Smoking is one of the risk factors of coronary heart disease (CHD), while its underlying mechanism is less well defined. Purpose To identify and testify 6 key genes of CHD related to smoking through weighted gene coexpression network analysis (WGCNA), protein-protein interaction (PPI) network analysis, and pathway analysis. Methods CHD patients' samples were first downloaded from Gene Expression Omnibus (GEO). Then, genes of interest were obtained after analysis of variance (ANOVA). Thereafter, 23 coexpressed modules that were determined after genes with similar expression were incorporated via WGCNA. The biological functions of genes in the modules were researched by enrichment analysis. Pearson correlation analysis and PPI network analysis were used to screen core genes related to smoking in CHD. Results The violet module was the most significantly associated with smoking (r = −0.28, p = 0.006). Genes in this module mainly participated in biological functions related to the heart. Altogether, 6 smoking-related core genes were identified through bioinformatics analyses. Their expressions in animal models were detected through the animal experiment. Conclusion This study identified 6 core genes to serve as underlying biomarkers for monitoring and predicting smoker's CHD risk.

Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis

IntroductionStaphylococcus aureus is a gram-positive bacterium that causes serious infection. With the increasing resistance of bacteria to current antibiotics, it is necessary to learn more about the molecular mechanism and cellular pathways involved in the Staphylococcus aureus infection.MethodsWe downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were applied to illustrate the biological functions of genes in these modules. We constructed the protein-protein interaction (PPI) network by Cytoscape and selected five candidate hub genes. Five potential hub genes were validated in GSE30119 by GraphPad Prism 8.0. The diagnostic values of these genes were calculated and present in the ROC curve based on the GSE13670 dataset. Their gene functions were analyzed by Gene Set Enrichment Analysis (GSEA).ResultsA co-expression network was built with 5000 genes divided into 11 modules. The genes in green and turquoise modules demonstrated a high correlation. According to the KEGG and GO analyses, genes in the green module were closely related to ubiquitination and autophagy. Subsequently, we picked out the top five hub genes in the green module. And UBB was determined as the hub gene in the GSE30119 dataset. The expression level of UBB, ASB, and MKRN1 could significantly differentiate between Staphylococcus aureus infection and healthy controls based on the ROC curve. The GSEA analysis indicated that lower expression levels of UBB were associated with the P53 signal pathway.ConclusionsWe identified some hub genes and significant signal enrichment pathways in Staphylococcus aureus infection via bioinformatics analysis, which may facilitate the development of potential clinical therapeutic strategies.

Identification of cell cycle as the critical pathway modulated by exosome-derived microRNAs in gallbladder carcinoma

Gallbladder cancer (GBC), the most common malignancy in the biliary tract, is highly lethal malignant due to seldomly specific symptoms in the early stage of GBC. This study aimed to identify exosome-derived miRNAs mediated competing endogenous RNAs (ceRNA) participant in GBC tumorigenesis. A total of 159 differentially expressed miRNAs (DEMs) was identified as exosome-derived miRNAs, contains 34 upregulated exo-DEMs and 125 downregulated exo-DEMs based on the expression profiles in GBC clinical samples downloaded from the Gene Expression Omnibus database with the R package. Among them, 2 up-regulated exo-DEMs, hsa-miR-125a-3p and hsa-miR-4647, and 5 down-regulated exo-DEMs, including hsa-miR-29c-5p, hsa-miR-145a-5p, hsa-miR-192-5p, hsa-miR-194-5p, and hsa-miR-338-3p, were associated with the survival of GBC patients. Results of the gene set enrichment analysis showed that the cell cycle-related pathways were activated in GBC tumor tissues, mainly including cell cycle, M phase, and cell cycle checkpoints. Furthermore, the dysregulated ceRNA network was constructed based on the lncRNA-miRNA-mRNA interactions using miRDB, TargetScan, miRTarBase, miRcode, and starBase v2.0., consisting of 27 lncRNAs, 6 prognostic exo-DEMs, and 176 mRNAs. Together with prognostic exo-DEMs, the STEAP3-AS1/hsa-miR-192-5p/MAD2L1 axis was identified, suggesting lncRNA STEAP3-AS1, might as a sponge of exosome-derived hsa-miR-192-5p, modulates cell cycle progression via affecting MAD2L1 expression in GBC tumorigenesis. In addition, the biological functions of genes in the ceRNA network were also annotated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Our study promotes exploration of the molecular mechanisms associated with tumorigenesis and provide potential targets for GBC diagnosis and treatment.

A consensus on the Aquaporin Gene Family in the Allotetraploid Plant, Nicotiana tabacum.

Aquaporins (AQPs) are membrane‐spanning channel proteins with exciting applications for plant engineering and industrial applications. Translational outcomes will be improved by better understanding the extensive diversity of plant AQPs. However, AQP gene families are complex, making exhaustive identification difficult, especially in polyploid species. The allotetraploid species of Nicotiana tabacum (Nt; tobacco) plays a significant role in modern biological research and is closely related to several crops of economic interest, making it a valuable platform for AQP research. Recently, De Rosa et al., (2020) and Ahmed et al., (2020), concurrently reported on the AQP gene family in tobacco, establishing family sizes of 76 and 88 members, respectively. The discrepancy highlights the difficulties of characterizing large complex gene families. Here, we identify and resolve the differences between the two studies, clarify gene models, and yield a consolidated collection of 84 members that more accurately represents the complete NtAQP family. Importantly, this consensus NtAQP collection will reduce confusion and ambiguity that would inevitably arise from having two different descriptive studies and sets of NtAQP gene names. This report also serves as a case study, highlighting and discussing variables to be considered and refinements required to ensure comprehensive gene family characterizations, which become valuable resources for examining the evolution and biological functions of genes.

A novel tissue specific alternative splicing variant mitigates phenotypes in\xa0Ets2\xa0frame-shift mutant models

E26 avian leukemia oncogene 2, 3′ domain (Ets2) has been implicated in various biological processes. An Ets2 mutant model (Ets2db1/db1), which lacks the DNA-binding domain, was previously reported to exhibit embryonic lethality caused by a trophoblast abnormality. This phenotype could be rescued by tetraploid complementation, resulting in pups with wavy hair and curly whiskers. Here, we generated new Ets2 mutant models with a frame-shift mutation in exon 8 using the CRISPR/Cas9 method. Homozygous mutants could not be obtained by natural mating as embryonic development stopped before E8.5, as previously reported. When we rescued them by tetraploid complementation, these mice did not exhibit wavy hair or curly whisker phenotypes. Our newly generated mice exhibited exon 8 skipping, which led to in-frame mutant mRNA expression in the skin and thymus but not in E7.5 Ets2em1/em1 embryos. This exon 8-skipped Ets2 mRNA was translated into protein, suggesting that this Ets2 mutant protein complemented the Ets2 function in the skin. Our data implies that novel splicing variants incidentally generated after genome editing may complicate the phenotypic analysis but may also give insight into the new mechanisms related to biological gene functions.

Chromosome mapping of attP landing sites in the strains for phiC31 integrase-mediated transgenesis of Drosophila prolongata (Diptera: Drosophilidae)

Drosophila prolongata exhibits extreme sexual dimorphism in terms of different morphological, behavioral, and life-history traits. To clarify the biological function of genes underpinning such unique traits, the strains for phiC31 integrase-mediated transgenesis of D. prolongata have been established. This study aimed to make further use of the strains by identifying the chromosomal location of attP landing sites with reference to the D. melanogaster genome in silico. The results showed that some inverted orders of genes may have occurred between D. prolongata and D. melanogaster. Such chromosomal rearrangements might be important evolutionary driving forces for the emergence of unique traits in D. prolongata.

Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation.

BackgroundHuman embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation.MethodsWe utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs.ResultsA total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network.

Ferritin Light Chain (FTL) competes with long noncoding RNA Linc00467 for miR-133b binding site to regulate chemoresistance and metastasis of colorectal cancer.

Although the colorectal cancer (CRC) mortality rates are decreasing in virtue of CRC screening and improved therapeutic methods, CRC is still a leading cause of cancer deaths. One of the main causes is chemoresistance occurrence in CRC. Understanding of the molecular mechanisms of chemoresistance benefits to CRC diagnosis and treatment. In this study, gene expression was determined by western blot and qRT-PCR. The biological functions of genes in CRC cells were studied by knocking down or overexpressing the gene in CRC cells and then analyzing cell sensitivity to 5-Fu by the MTT assay and the flow cytometry, and analyzing cell migration and invasion by transwell assays. The luciferase reporter assay was used to examine microRNA regulation of target gene expression, and biotin pull-down assay was performed to detect interaction between RNA molecules. This study found that ferritin light chain (FTL) and long intergenic noncoding RNA Linc00467 were both upregulated in CRC tissues and cell lines, and inversely correlated to CRC patient survival. FTL and Linc00467 promoted CRC cells abilities to resistance against 5-fluor-ouracil (5-Fu), migration and invasion. These effects were compromised by miR-133b which targeted both FTL and Linc00467. miR-133b interacted with Linc00467 and miR-133b inhibitor prevented Linc00467 knockdown-induced alternations of FTL expression and biological functions. Both FTL and Linc00467 are oncogenes in CRC. FTL expression upregulated in CRC via Linc00467/ miR-133b axis, and leads to CRC cell resistance against 5-FU treatment and promotes CRC metastasis. FTL expression upregulated in CRC via Linc00467/miR-133b axis, and leads to CRC cell resistance to 5-FU treatment and promotes CRC metastasis.

B7-H3 modulates endothelial cell angiogenesis through the VEGF cytokine.

B7-H3 is a cell surface molecule in the immunoglobulin superfamily that has been shown to perform both immunological and non-immunological functions. It has also been found that vascular endothelial growth factor (VEGF) is an important molecule in the modulation of endothelial cell behavior. In this study, we analyzed the serum expression of B7-H3 in 113 rheumatoid arthritis and systemic lupus erythematous patients using the ELISA and found a positive correlation between B7-H3 and VEGF. Next, we investigated the involvement of B7-H3 in angiogenesis using human umbilical vein endothelial cells (HUVECs) with transient knockdown of B7-H3 and an in vivo Matrigel model. Data from the in vitro experiments showed that B7-H3 increased cell proliferation, migration, and tube formation, and correlated with the expression of VEGF. Furthermore, B7-H3 affected the formation of functional vascular networks in Matrigel plugs, which were dissected from mice injected with different HUVECs. Our data suggest that B7-H3 promotes angiogenesis through the enhancement of VEGF secretion. This is the first study proposing a significant role for B7-H3 in the promotion of angiogenesis and may provide further understanding of this gene's biological function.

Investigating the metabolome of resistant bacteria by high resolution mass spectrometry imaging with desorption electrospray ionization

Pathogenic bacteria remains a primary target of a study due to its prevalence in the environment, specifically the healthcare setting. The use of antibiotics and antimicrobials are essential to treat the symptoms of harmful strains of bacteria. However, although medicinal alternatives exist to kill harmful microorganisms, bacteria have the capability to evolve. Because of this, resistant properties have become a growing problem in the healthcare setting, thus creating various scientific interests of study. High resolution mass spectrometry and imaging analyzes specific ions within a sample thus providing further identification of potential metabolites in Staphylococcus aureus. Therefore, metabolites produced by both resistant and non-resistant strains of bacteria were compared and evaluated. Profiling the metabolic production between the two strains provides a further understanding on how these resistant characteristics were formed, their biological gene function, and how they can potentially be treated.

322 Evaluation of the biological function of genes linked to regions with distortion of Mendelian segregation and their relation to reproductive traits in dairy cattle.

322 Evaluation of the biological function of genes linked to regions with distortion of Mendelian segregation and their relation to reproductive traits in dairy cattle.

Functional characterization of transposon-tagged abiotic stress-responsive rice genes and their molecular polymorphisms among various stress-tolerant genotypes

Dissociation (Ds) insertional mutagenesis has been regarded as an efficient tool to generate insertion mutants for functional genomics and molecular breeding. However, little is known about the application of the tool on exploring biological functions of abiotic stress-related genes and their molecular breeding experience. In this study, a total of 833 Ds insertion lines have been obtained, which showed significantly higher tolerance or sensitivity to high salinity, drought or cold stress, by screening around 20,000 Ds lines. Analysis of Ds flanking sequence tags revealed that 165 rice genes were tagged by Ds insertion. Gene Ontology (GO) and gene set enrichment analysis showed that over-represented Ds-tagged genes might function in the response to exogenous stimuli. These Ds-tagged genes showed expression divergence among five high salinity and five drought tolerant rice lines under either high salinity or drought stress. Higher percentages of Ds-tagged genes were down- or up-regulated by these abiotic stresses. These Ds-tagged genes were also frequently reduced or suppressed by various phytohormones including abscisic acid and jasmonate. On the other hand, we have also detected single nucleotide polymorphisms (SNPs) and 1–10 base pairs of insertion and deletions (indels) of these Ds-tagged genes among ten high salinity/drought tolerant rice lines by comparing with the reference genome Nipponbare. Our data showed that SNPs were detected among 102 out of 165 genes and indels were identified in 39 out of 165 genes. All the data provided additional information to further explore the biological functions of these genes or to carry out molecular breeding.

Genome-wide association studies for two exterior traits in Chinese Dongxiang spotted pigs.

Pigs show extensive variation in exterior appearance. This variation has been explored as one of the selection targets to form breeding features in the pig industry. In this study, a customized Affymetrix Axiom Pig1.4M array plate was used to conduct genome-wide association studies (GWAS) for two exterior traits-spotted coat color (SC) and facial type (FT)-in Chinese Dongxiang spotted pigs. Two and 12 single nucleotide polymorphisms (SNPs) were identified to be associated with SC and FT at the 5% genome-wide significant level, respectively. Of these SNPs, two associated with SC were located around the DACH1 gene on Sus Scrofa chromosome (SSC)11. Eleven SNPs associated with FT were located within a 7.68Mb region (29.03-36.71Mb) on SSC7. Based on the GWAS results and the biological functions of genes, we highlight EDNRB as a candidate gene for SC and HMGA1 and RPS10 as the potential genes affecting facial variation. The findings contribute to the final characterization of causative genes and mutations underlying the effects of the SSC7 and SSC11 loci and improve our understanding of the genetic basis of phenotypic variation in Chinese indigenous pigs.