CTCF is a highly conserved DNA-binding protein involved in transcription regulation, chromatin insulation, genomic imprinting, X-chromosome inactivation, higher-order chromatin organization, and alternative splicing. These multifunctional properties of CTCF suggest an essential role in development and disease. CTCF is unique protein that known to mediate insulation function in vertebrates. Recent studies proposed that CTCF can be a heritable component in epigenetic and regulating the interaction between DNA methylation, higher-order chromatin structure, and developmentally regulated gene expression. In this review, we discuss roles of CTCF in these critical aspects of genome regulation. All information indicates that CTCF can emerge as a master weaver of the mammalian genome.

Background & Objective: Luminal B breast cancer (LBBC) is on the rise worldwide, with both incidence and mortality rates steadily increasing. Early detection proves difficult due to its aggressive characteristics, most notably its heightened proliferation rate and the complex interplay of molecular biomarkers, particularly in more advanced stages.Methods: Data Sources: In the present study, we conducted an in-silico analysis of LBBC cell lines using the Gene Expression Omnibus (GEO) microarray dataset, which includes 30 LBBC and 11 normal samples. Analysis Tools: Differentially expressed genes (DEGs) were identified using RStudio. A series of analyses, including cancer data interrogation via pan-cancer analysis, eXpression2Kinases (X2K), and the Cancer Dependency Map (DepMAP), was carried out to elucidate the underlying signaling pathways, transcription factors (TFs), and kinases, as well as to perform stemformatics analysis. Protein–protein interaction (PPI) networks were reconstructed using STRING and Cytoscape, enabling the identification of co-expressed and hub genes through the cytoHubba plug-in.Results: Of note, FGF2, EGFR, ADIPOQ, LIPE, MET, IGF1, FGF1, EGF, FGF7, and PPARG were identified as the top 10 hub genes; RELA, PPARG, CTCF, EGR1, and NFE2L2 were detected as predominant TFs in LBBC; and CDK1, CDK2, MAPK3, CSNK2A1, and MAPK14 were identified as potential biomarkers through hub gene clustering. Further analysis indicated hsa-mir-221-3p and hsa-mir-29a-3p as key miRNAs targeting LBBC-related genes.Conclusion: Collectively, our findings highlighted LBBC-associated genes, TFs, miRNAs, and pathways as prospective biomarkers, providing insights into LBBC diagnosis and therapeutic approaches.

The complement system is one of the main components of the immune system in many organisms. Existence of this system has been confirmed in numerous organisms, but there is no information about the mechanisms regulating the expression of it in some of them. In this study, we are focused on the upstream element of salmon fish C3 gene. Different tissues of the fish were prepared and DNA was extracted with a modified phenol-chloroform method. Target sequence was amplified using unclassical PCR method by using of designed degenerate primers and PCR product was purified and sequenced and finally confirmed sequence was recorded in Genomic Bank Database. In the next step, full anatomy of obtained sequence was examined for the presence of regulatory elements by application of different servers and software. Salmon fish C3 gene promoter region sequence was recorded in NCBI genomic data bank with access number JQ799884. 1. Presence of conserved TATA box and abaA, C/EBP, CTCF, IL-6, GR and PPAR transcription factors responsive elements were confirmed, however responsive element sequence for factors such as Sp1, CRE, ERE were not detected. Our results can confirm the existence of an evolutionary well-developed regulatory system on the complement system in bony fishes and support ancestral nature of complement system genes. This study is the first detailed report on the regulatory elements controlling gene expression of the C3 gene and may suggest involvement of complement derivatives in the early embryonic development steps that have been reported in some study.

Introduction: Polycystic ovary syndrome (PCOS) is the cause of 75% of infertility due to lack of ovulation. This study aimed to investigate the possible association between exon 1 polymorphisms of the NOEY2 gene in women with PCOS and diabetes. Material & Methods: This study was conducted on 240 blood samples (1 cc each) from women in four groups: polycystic, diabetes, polycysticdiabetes, and control. Genomic DNA extraction was performed using the extraction kit, according to the protocol. A primer pair was designed and synthesized for the exon 1 sequence of the NOEY2 gene. After gene amplification by polymerase chain reaction (PCR) and evaluation of band quality, Sanger sequencing was performed on PCR products. Sequencing results were analyzed using Chromas, GeneRunner, and Alignment software, and statistical calculations were performed by SNPAlyze, SPSS, and Web-Assotest program. (Ethic code: IR. IAU. TON. REC. 137031) Findings: Sequence analysis confirmed two polymorphisms: 5'UTR c. 156G> A polymorphism was observed in exon 1 of NOEY2 and second polymorphism of 5'UTR c. 207+76 G>A, 76 nucleotides farther from exon 1 and in the intron region of NOEY2 gene. Statistical analysis showed a statistically significant difference between 5'UTR c. 156G> A and susceptibility to PCOS and diabetes. Discussion & Conclusion: No report on this region was available in genetic databases and this polymorphism was reported for the first time in the present study. Bioinformatics studies showed that this polymorphism can affect the affinity to bind in certain transcription factors by allelic changes due to its location in the CTCF overlapping promoter region.

Extended Abstract Background: To date, one of the main areas of research is the creation of breeds with inherent resistance to digestive nematodes in sheep. In this context, resistance to digestive nematodes has exhibited significant phenotypic differences within and between sheep breeds, suggesting a genetic basis for these differences. According to the list of effective candidate genes and the identified gene network for parasite resistance in sheep, there are genes involved in the immune system, such as the interferon-γ gene (IFN-γ). Cytokinin is involved in biochemical immune system signaling pathways, parasite resistance, and immunological responses. In addition, certain mutations in this gene impair the ability of specialized cells of the immune system to fight off parasite invasion. One of the most popular approaches to generating gene expression data for genome function studies is DNA microarray technology, which allows the simultaneous expression of thousands of genes. Proteomics and genomics are two application areas of microarray technology. This research aims to identify and categorize some of the genes involved in the relative genetic resistance of sheep to nematode infection using microarray data. Methods: In this context, the GEO-Bank, part of the NCBI, was searched for access to open-access databases. Downloaded microarray data corresponded to infection with parasitic nematodes with the best replication (e.g., data in two resistant and sensitive groups), and the set of genes with differential expression was identified using R -based appropriate software packages (Biobase, GEOquery, limma, affy, Genfilter, Pheatmap, Plyr, Reshape2, and Ggplot2). Raw data were measured on a logarithmic scale, and the P-value fit statistics were used for expression comparisons between gene groups. Results: The main analysis was performed after precorrection and processing of the raw data because of the high intragroup variance of the data, as evidenced by the observed quality control results of the raw data and the quality control-related results of the integrated data. After pre-processing of the raw data, correlation analysis revealed a strong relationship between genes in the pre-Inf group (Pre-Inf) and the infected group (Inf) compared to the control group. Three heatmap reference charts, a PCA chart, and a volcano plot were used to verify data quality, and by verifying these charts, samples of unfavorable quality were removed from the next stages of analysis. After a bioinformatics analysis, the results showed significantly increased expression patterns (NACA, RPL4, NAGS, CTCF, GBP1, BHLHE, YTHDF3, PDHA1, and MXI1) and diminished expression patterns of PDHA1 and MXI1 genes. According to the results of this study, these genes play a role in the cellular metabolism process, molecular function, the formation of genetic connections, and cell life. Therefore, they were significant (p-value < 0.05) according to the magnitude of the change. The N-acryl glutamate synthetase (NAGS) gene is the cofactor of the first enzyme involved in the urea cycle in mammals. The functional role of this gene has been identified in many neurological diseases. The CTCF gene has a positive effect on the cells of the immune system and plays a special role in defending against viruses and pathogens that invade the host body. The guanylate binding protein 1 (GBP1) gene plays a role in the body's defense against many infectious pathogens. This gene causes oxidative reactions and autophagy of the host immune system as a barrier to invading pathogens. The methyl adenosine RNA binding 3 gene is more effective in antiviral immunity and is closely linked to the GBP1 gene, which plays a role in the body's resistance to many infectious agents. This gene causes oxidative responses and autophagy of the host immune system against invading pathogens. The PDHA1 pyruvate dehydrogenase gene is involved in immune system metabolism. This gene plays a role in allosteric factor-induced regulation, repair of covalent bonds, and relatively rapid changes in the level of expressed proteins, either through altered gene expression or proteolytic degradation. The MXI1 gene helps control the entry of invading pathogens into the host's body and promotes recovery and healing from infections. The results can be explained by several reasons, including the use of different sample breeds and laboratory techniques, the level of parasite contamination, the age of the test material, the variety of tested nematodes, and inconsistent techniques and tools of the current study with those of previous studies. Other reasons include the climatic differences between the test region and its physical location as well as the use of different RNA and microarray methods. However, the results of the study may be helpful under the related circumstances. Conclusion: The results of microarrays and differential expression patterns can be of great help to molecularly modify livestock to resist internal parasites. Using more advanced tools, such as next-gene sequencing, will provide more accurate and relevant information.