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Inbreeding can lead to the accumulation of homozygous single nucleotide polymorphisms (SNPs) in the genome, which can significantly affect gene expression and phenotype. In this study, we examined the impact of homozygous SNPs resulting from inbreeding on alternative polyadenylation (APA) site selection and the underlying genetic mechanisms using inbred Luchuan pigs. Genome resequencing revealed that inbreeding results in a high accumulation of homozygous SNPs within the pig genome. 3' mRNA-seq on leg muscle, submandibular lymph node, and liver tissues was performed to identify differences in APA events between inbred and outbred Luchuan pigs. We revealed different tissue-specific APA usage caused by inbreeding, which were associated with different biological processes. Furthermore, we explored the role of polyadenylation signal (PAS) SNPs in APA regulation under inbreeding and identified key genes such as PUM1, SCARF1, RIPOR2, C1D, and LRRK2 that are involved in biological processes regulation. This study provides resources and sheds light on the impact of genomic homozygosity on APA regulation, offering insights into genetic characteristics and biological processes associated with inbreeding.
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Disruption of sleep and circadian rhythms are a comorbid feature of many pathologies, and can negatively influence many health conditions, including neurodegenerative disease, metabolic illness, cancer, and various neurological disorders. Genetic association studies linking sleep and circadian disturbances with disease susceptibility have mainly focused on changes in gene expression due to mutations, such as single-nucleotide polymorphisms. The interaction between sleep and/or circadian rhythms with the use of Alternative Polyadenylation (APA) has been largely undescribed, particularly in the context of other disorders. APA is a process that generates various transcript isoforms of the same gene affecting its mRNA translation, stability, localization, and subsequent function. Here we identified unique APAs expressed in rat brain over time-of-day, immediately following sleep deprivation, and the subsequent recovery period. From these data, we performed a secondary analysis of these sleep- or time-of-day associated PASs with recently described APA-linked human brain disorder susceptibility genes.
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Microcrystalline cellulose (MCC) is one of the essential functional excipients in the formulation of tablets. The need for cheaper MCC sources has drawn significant attention to exploring renewable sources. In this study, MCC was produced from soybean hull (SBH), the primary by-product of the soy industry, using a novel, simplified, and cost-effective approach. Various characterization techniques were used to study the physicochemical properties and micromeritics of the SBH-based MCC powders and compare them to those of the commercial Avicel PH-101. SBH MCCs had a larger particle size, a broader particle size distribution, a higher degree of polymerization, a higher degree of crystallinity, better thermal stability, and slightly superior flowability and compressibility than Avicel PH-101. The tableting blends (containing 60 % MCC) were prepared, and the post-compression out-of-die Heckel analysis showed that formulations with aggregated SBH MCCs were less ductile than those made with Avicel PH-101, resulting in a lower porosity (better compressibility) of the latter at higher compression pressures. The hardness values for all formulations were above 6 kg, with higher values for those made with Avicel PH-101. The lubricant sensitivity was lower for SBH MCCs. All tablets made using developed formulations showed very low friability (<0.1 %) and short disintegration times (<90 s), making them well-suited candidates for manufacturing orally disintegrating tablets (ODTs).
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Celulosa , Excipientes , Glycine max , Polvos , Comprimidos , Celulosa/química , Glycine max/química , Excipientes/química , Tamaño de la Partícula , Composición de Medicamentos/métodosRESUMEN
Two cylindrical section hydrocyclones can suppress particle misplacement by regulating the circulation flow, but few researchers have investigated the effect of the cylindrical height ratio. In this paper, numerical simulations and physical tests were conducted to investigate the effect of height ratio on the particle motion behavior and separation performance of the two cylindrical section hydrocyclone. According to the numerical simulation results, with increasing height ratio, the separation cut size decreased, the separation accuracy and recovery rate of medium and coarse particles in the underflow increased, the coarse particle misplacement in overflow decreased significantly, and the proportion of medium particle circulation flow gradually increased. According to the test results, the number of misplaced fine particles in underflow could be effectively reduced when H1/H0 = 0.30. With increasing height ratio, the number of misplaced coarse particles in the overflow decreased and the classification efficiency of fine particles increased. The maximum separation efficiencies of medium and coarse particles could be obtained at H1/H0 values of 0.47 and 0.17, respectively. Therefore, increasing the height ratio could inhibit coarse particle misplacement in overflow and improve the separation performance of two cylindrical section hydrocyclones.
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PURPOSE: This study aims to analyze the clinicopathological characteristics and survival outcomes of tongue cancer in the pediatric population, a topic with limited existing data, using a population-based cohort. METHODS: Pediatric patients diagnosed with tongue cancer from 1975 to 2018 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. Survival rates were assessed using Kaplan-Meier analysis. Univariate survival analysis was conducted with the log-rank test, while multivariate analysis involved Cox proportional-hazards regression to identify factors influencing overall survival (OS). A predictive nomogram was developed based on Cox regression findings. RESULTS: In total, 97 pediatric patients with tongue cancer were identified, with a median age at diagnosis of 15 years (range: 1-19 years). Tumors were classified as squamous cell carcinoma (45.4%), rhabdomyosarcoma (RMS) (13.4%), and others (41.2%). Of the patients, squamous cell carcinoma was more common in older children, whereas rhabdomyosarcoma was more common in younger children. The Cox proportional hazard regression revealed that histology and surgery were significant independent predictors of overall survival. The chance of death increased with no surgery. Moreover, patients with squamous cell carcinoma or rhabdomyosarcoma have a poorer survival percentage than patients with other subtypes. CONCLUSIONS: Tongue cancer in children is rare and associated with poor survival outcomes. This study highlights the significance of tumor histology and surgical intervention in determining overall survival, offering valuable insights for clinical decision-making in pediatric tongue cancer.
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BACKGROUND: The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. RESULTS: A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. CONCLUSIONS: These validated results show significant improvement over current bovine genome annotations.
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Perfilación de la Expresión Génica , Genómica , Bovinos/genética , Animales , Análisis de Secuencia de ARN , Transcriptoma , Sitios de Carácter Cuantitativo , ARN , Isoformas de Proteínas , Anotación de Secuencia MolecularRESUMEN
PURPOSE: Adrenocortical carcinoma (ACC) is an uncommon adrenal gland endocrine tumor that has a poor prognosis in children. We aimed to conduct a population-based cohort study to predict overall survival (OS) in pediatric patients with ACC. METHODS: We used the Surveillance, Epidemiology, and End Results (SEER) database to conduct a retrospective cohort research on pediatric patients diagnosed with ACC between 1975 and 2018. We examined demographic characteristics, tumor stage and size, treatment options, and survival results. Kaplane-Meier estimations were used to generate survival curves based on several parameters. To compare survival curves, the log-rank test was applied.Cox proportional-hazards regression was used to determine the variables related with OS. In addition, we created a nomogram to predict overall survival in pediatric ACC patients. RESULTS: A total of 143 pediatric ACC patients were identified. Females were the most impacted (60.8%). Overall 1 year, 3 year, and 5 year survival rates were 75.0%, 57.6%, and 53.7% for all patients, respectively. In comparison to older patients (5-19 years), younger patients (≤ 4 years) were shown to have more positive characteristics, including a higher likelihood of local disease (29.4% vs. 14%, P < 0.001), tumors less than 10 cm (23.1% vs. 14.7%, P < 0.001), and improved overall survival (5 year OS 89.6% vs. 27.7%, P < 0.001). Age at diagnosis, SEER stage, and surgery were significant independent predictors of OS in this model, according to the results of Cox proportional hazard regression. After that, we developed a nomogram for predicting OS in children with ACC. Patients older than 4 years old had a higher chance of dying. Furthermore, the higher the SEER stage, the higher the risk of death. Patients who do not have surgery have a worse survival rate than those who do. CONCLUSIONS: Our study revealed that age at diagnosis, SEER stage, and surgery were found to be the most important predictors of the overall survival of pediatric ACC. These findings contribute to the existing body of knowledge and emphasize the importance of continued research to advance our understanding of pediatric ACC and improve patient care.
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Neoplasias de la Corteza Suprarrenal , Carcinoma Corticosuprarrenal , Humanos , Femenino , Masculino , Carcinoma Corticosuprarrenal/mortalidad , Carcinoma Corticosuprarrenal/terapia , Niño , Adolescente , Neoplasias de la Corteza Suprarrenal/mortalidad , Neoplasias de la Corteza Suprarrenal/terapia , Estudios Retrospectivos , Preescolar , Pronóstico , Tasa de Supervivencia , Estudios de Cohortes , Adulto Joven , Programa de VERF , LactanteRESUMEN
As a byproduct of dairy production, the disposal of acid whey poses severe environmental challenges. Herein, an innovative solution involving metabolically engineering Clostridium saccharoperbutylacetonicum to convert all carbon sources in acid whey into sustainable biofuels and biochemicals was presented. By introducing several heterologous metabolic pathways relating to metabolisms of lactose, galactose, and lactate, the ultimately optimized strain, LM-09, exhibited exceptional performance by producing 15.1 g/L butanol with a yield of 0.33 g/g and a selectivity of 89.9%. Through further overexpression of alcohol acyl transferase, 2.7 g/L butyl acetate along with 6.4 g/L butanol was generated, resulting in a combined yield of 0.37 g/g. This study achieves the highest reported butanol titer and yield using acid whey as substrate in clostridia and marks pioneering production of esters using acid whey. The findings demonstrate an innovative bioprocess that enhances renewable feedstock biotransformation, thereby promoting economic viability and environmental sustainability of biomanufacturing.
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Biocombustibles , Clostridium , Ingeniería Metabólica , Suero Lácteo , Suero Lácteo/metabolismo , Clostridium/metabolismo , Ingeniería Metabólica/métodos , Butanoles/metabolismo , FermentaciónRESUMEN
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined â¼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Genoma , Genómica , Ratas , Animales , Genoma/genética , Anotación de Secuencia Molecular , Secuenciación Completa del Genoma , Variación Genética/genéticaRESUMEN
The neurobiological mechanisms that regulate the appetite-stimulatory properties of cannabis sativa are unresolved. This work examined the hypothesis that cannabinoid-1 receptor (CB1R) expressing neurons in the mediobasal hypothalamus (MBH) regulate increased appetite following cannabis vapor inhalation. Here we utilized a paradigm where vaporized cannabis plant matter was administered passively to rodents. Initial studies in rats characterized meal patterns and operant responding for palatable food following exposure to air or vapor cannabis. Studies conducted in mice used a combination of in vivo optical imaging, electrophysiology and chemogenetic manipulations to determine the importance of MBH neurons for cannabis-induced feeding behavior. Our data indicate that cannabis vapor increased meal frequency and food seeking behavior without altering locomotor activity. Importantly, we observed augmented MBH activity within distinct neuronal populations when mice anticipated or consumed food. Mechanistic experiments demonstrated that pharmacological activation of CB1R attenuated inhibitory synaptic tone onto hunger promoting Agouti Related Peptide (AgRP) neurons within the MBH. Lastly, chemogenetic inhibition of AgRP neurons attenuated the appetite promoting effects of cannabis vapor. Based on these results, we conclude that MBH neurons contribute to the appetite stimulatory properties of inhaled cannabis.
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Cannabis , Alucinógenos , Ratones , Ratas , Animales , Apetito , Cannabis/metabolismo , Proteína Relacionada con Agouti/metabolismo , Ingestión de Alimentos/fisiología , Hipotálamo/metabolismo , Neuronas/metabolismo , Alucinógenos/farmacologíaRESUMEN
PURPOSE: To study the safety of patients with moderately advanced esophageal cancer during their hospital stay after undergoing surgery. METHODS: The clinical and pathological data of 66 patients with locally advanced esophageal cancer discharged from the Department of Thoracic Surgery of Jiangsu University Hospital from January 2017 to October 2022 were selected, of whom 32 underwent direct surgery (control group) and 34 underwent neoadjuvant therapy followed by surgery (experimental group), to retrospectively analyze whether there were differences in surgical outcomes, complication rates, biochemical and infection indicators between the two groups. RESULTS: The number of lymph node dissections, lymph node dissection rate, and hemoglobin value on the first day after the operation in the experimental group were smaller than those in the control group, and the difference was statistically significant (P < 0.05). The thoracic drainage volume of the experimental group was more than that of the control group, and the difference was statistically significant (P < 0.05). The incidence of pulmonary complications in the experimental group was higher than that in the control group, especially pulmonary infection, and the difference was statistically significant (P < 0.05). Compared with the control group, the experimental group was more prone to anastomotic leakage, and the difference was statistically significant (P < 0.05). CONCLUSION: Neoadjuvant therapy combined with surgery for patients with advanced esophageal cancer is generally safe during hospitalization.
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Neoplasias Esofágicas , Terapia Neoadyuvante , Humanos , Terapia Neoadyuvante/efectos adversos , Estudios Retrospectivos , Fuga Anastomótica/etiología , Tiempo de Internación , Neoplasias Esofágicas/cirugíaRESUMEN
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Empalme Alternativo , Poliadenilación , Humanos , ARN Mensajero/genética , Poliadenilación/genética , Empalme Alternativo/genética , Exones , Diferenciación CelularRESUMEN
Background: It has been reported that hepatitis B virus (HBV) double mutations (A1762T, G1764A) are an aetiological factor of hepatocellular carcinoma (HCC). However, it is unclear who is prone to develop HCC, among those infected with the mutant. Exploring HBV quasispecies, which are strongly influenced by host immune pressure, may provide more information about the association of viral factors and HCC. Materials and methods: Nine HCC cases and 10 controls were selected from the Long An cohort. Serum samples were collected in 2004 and 2019 from subjects with HBV double mutations and the complete genome of HBV was amplified and sequenced using next-generation sequencing (NGS). Results: The Shannon entropy values increased from 2004 to 2019 in most cases and controls. There was no significant difference in mean intrahost quasispecies genetic distances between cases and controls. The change in the values of mean intrahost quasispecies genetic distances of the controls between 2004 and 2019 was significantly higher than that of the cases (P<0.05). The viral loads did not differ significantly between cases and controls in 2004(p=0.086) but differed at diagnosed in 2019 (p=0.009). Three mutations occurring with increasing frequency from 2004 to 2019 were identified in the HCC cases, including nt446 CâG, nt514 AâC and nt2857TâC. Their frequency differed significantly between the cases and controls (P<0.05). Conclusions: The change in the values of mean intrahost quasispecies genetic distances in HCC was smaller, suggesting that HBV in HCC cases may be subject to low host immune pressure. Increasing viral loads during long-term infection are associated with the development of HCC. The novel mutations may increase the risk for HCC.
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Recombinant proteins have broad applications. However, there is a lack of a recombinant protein expression system specifically for large-scale production in anaerobic hosts. Here, we developed a powerful and stringently inducible protein expression system based on the bacteriophage T7 system in the strictly anaerobic solvent-producing Clostridium saccharoperbutylacetonicum. With the integration of a codon optimized T7 RNA polymerase into the chromosome, a single plasmid carrying a T7 promoter could efficiently drive high-level expression of the target gene in an orthogonal manner, which was tightly regulated by a lactose-inducible system. Furthermore, by deleting beta-galactosidase genes involved in lactose metabolism, the transcriptional strength was further improved. In the ultimately optimized strain TM-07, the transcriptional strength of the T7 promoter showed 9.5-fold increase compared to the endogenous strong promoter Pthl. The heterologous NADP+-dependent 3-hydroxybutyryl-CoA dehydrogenase (Hbd1) from C. kluyveri was expressed in TM-07, and the yield of the recombinant protein reached 30.4-42.4% of the total cellular protein, surpassing the strong protein expression systems in other Gram-positive bacteria. The relative activity of Hbd1 in the crude enzyme was 198.0 U/mg, which was 8.3-fold higher than the natural activity in C. kluyveri. The relative activity of the purified enzyme reached 467.4 U/mg. To the best of our knowledge, this study represents the first application of the T7 expression system in Clostridium species, and this optimized expression system holds great potential for large-scale endotoxin-free recombinant protein production under strictly anaerobic conditions. This development paves the way for significant advancements in biotechnology and opens up new avenues for industrial applications.
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Bacteriófago T7 , Lactosa , Bacteriófago T7/genética , Proteínas Recombinantes/metabolismo , ARN Polimerasas Dirigidas por ADN/genética , Clostridium/genética , Clostridium/metabolismoRESUMEN
BACKGROUND: Heritable rumen microbiota is an important modulator of ruminant growth performance. However, no information exists to date on host genetics-rumen microbiota interactions and their association with phenotype in sheep. To solve this, we curated and analyzed whole-genome resequencing genotypes, 16S rumen-microbiota data, and longitudinal body weight (BW) phenotypes from 1150 sheep. RESULTS: A variance component model indicated significant heritability of rumen microbial community diversity. Genome-wide association studies (GWAS) using microbial features as traits identified 411 loci-taxon significant associations (P < 10-8). We found a heritability of 39% for 180-day-old BW, while also the rumen microbiota likely played a significant role, explaining that 20% of the phenotypic variation. Microbiota-wide association studies (MWAS) and GWAS identified four marker genera (Bonferroni corrected P < 0.05) and five novel genetic variants (P < 10-8) that were significantly associated with BW. Integrative analysis identified the mediating role of marker genera in genotype influencing phenotype and unravelled that the same genetic markers have direct and indirect effects on sheep weight. CONCLUSIONS: This study reveals a reciprocal interplay among host genetic variations, the rumen microbiota and the body weight traits of sheep. The information obtained provide insights into the diverse microbiota characteristics of rumen and may help in designing precision microbiota management strategies for controlling and manipulating sheep rumen microbiota to increase productivity. Video Abstract.
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Estudio de Asociación del Genoma Completo , Microbiota , Masculino , Ovinos , Animales , Rumen , Genotipo , Microbiota/genética , Peso CorporalRESUMEN
SCOPE: This study aims to investigate the anticancer properties of Citrus grandis 'Tomentosa' (CGT) in non-small cell lung cancer (NSCLC). METHODS AND RESULTS: The ethanol extract of CGT (CGTE) is prepared by using anhydrous ethanol and analyzed by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), revealing that the main chemical components in CGTE are flavonoids and coumarins, such as naringin, rhoifolin, apigenin, bergaptol, and osthole. CGTE at concentrations without inducing cell death significantly inhibits cell proliferation via inducing cell cycle G1 phase arrest by MTT, colony formation, and flow cytometry assays, implying that CGT has anticancer potential. CGTE markedly inhibits the activity of Skp2-SCF E3 ubiquitin ligase, decreases the protein level of Skp2, and promotes the accumulation of p27 by co-immunoprecipitation (co-IP) and in vivo ubiquitination assay; whereas Skp2 overexpression rescues the effects of CGTE in NSCLC cells. In subcutaneous LLC allograft and A549 xenograft mouse models, CGTE, without causing obvious side effects in mice, significantly inhibits lung tumor growth by targeting the Skp2/p27 signaling pathway. CONCLUSION: These findings demonstrate that CGTE efficiently inhibits NSCLC proliferation both in vitro and in vivo by targeting the Skp2/p27 signaling pathway, suggesting that CGTE may serve as a therapeutic candidate for NSCLC treatment.
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Carcinoma de Pulmón de Células no Pequeñas , Citrus , Neoplasias Pulmonares , Humanos , Animales , Ratones , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/patología , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/patología , Citrus/química , Cromatografía Liquida , Espectrometría de Masas en Tándem , Proteínas Ligasas SKP Cullina F-box , Inhibidor p27 de las Quinasas Dependientes de la Ciclina/metabolismoRESUMEN
Since its discovery in 1991, genomic imprinting has been the subject of numerous studies into its mechanisms of establishment and regulation, evolution and function, and presence in multiple genomes. Disturbance of imprinting has been implicated in a range of diseases, ranging from debilitating syndromes to cancers to fetal deficiencies. Despite this, studies done on the prevalence and relevance of imprinting on genes have been limited in scope, tissue types available, and focus, by both availability and resources. This has left a gap in comparative studies. To address this, we assembled a collection of imprinted genes available in current literature covering five species. Here we sought to identify trends and motifs in the imprinted gene set (IGS) in three distinct arenas: evolutionary conservation, across-tissue expression, and health phenomics. Overall, we found that imprinted genes displayed less conservation and higher proportions of non-coding RNA while maintaining synteny. Maternally expressed genes (MEGs) and paternally expressed genes (PEGs) occupied distinct roles in tissue expression and biological pathway use, while imprinted genes collectively showed a broader tissue range, notable preference for tissue specific expression and limited gene pathways than comparable sex differentiation genes. Both human and murine imprinted genes showed the same clear phenotypic trends, that were distinct from those displayed by sex differentiation genes which were less involved in mental and nervous system disease. While both sets had representation across the genome, the IGS showed clearer clustering as expected, with PEGs significantly more represented than MEGs.
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Fenómica , Transcriptoma , Humanos , Animales , Ratones , Transcriptoma/genética , Impresión Genómica/genética , Perfilación de la Expresión Génica , GenómicaAsunto(s)
Integrasas , Tamoxifeno , Animales , Ratones , Alelos , Integrasas/genética , Ratones TransgénicosRESUMEN
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Obesity's complex etiology due to the interplay of environment and genetics makes it a more challenging research and health problem. Some of the contributing genetic factors that have not yet been examined in detail entail mRNA polyadenylation (PA). Genes with multiple PA sites express mRNA isoforms differing in coding sequence or 3'UTR through alternative polyadenylation (APA). Alterations in PA have been associated with various diseases; however, its contribution to obesity is not well-researched. Following an 11-week high-fat diet, the APA sites in the hypothalamus of two unique mouse models for polygenic obesity (Fat line) and healthy leanness (Lean line) were determined using whole transcriptome termini site sequencing (WTTS-seq). We found 17 genes of interest with differentially expressed APA (DE-APA) isoforms, among which seven were previously associated with obesity or obesity-related traits (Pdxdc1, Smyd3, Rpl14, Copg1, Pcna, Ric3, Stx3) but have not yet been studied in the context of APA. The remaining ten genes (Ccdc25, Dtd2, Gm14403, Hlf, Lyrm7, Mrpl3, Pisd-ps3, Sbsn, Slx1b, Spon1) represent novel candidates associated with obesity/adiposity due to variability brought about by differential usage of APA sites. Our results provide insights into the relationship between PA and the hypothalamus in the context of obesity, by being the first study of DE-APA sites and DE-APA isoforms in these mouse models. Future studies are needed further to explore the role of APA isoforms in polygenic obesity by expanding the scope of research to other metabolically important tissues (such as liver and adipose tissues) and investigating the potential for targeting PA as a therapeutic strategy for obesity management.