Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.

The understanding of anti-tumor drug effects requires specific experimental settings which model clinical scenarios. We describe a protocol for 10-day treatment of lowly aggressive tumor cell lines with antineoplastic agents at concentrations which do not affect cell growth. We describe steps for seeding cells and treating cells with anti-tumor drugs. We then detail steps for cell sensitivity, cell proliferation, and mRNA and protein expression assays. We also detail assays to determine modifications in compound efflux. For complete details on the use and execution of this protocol, please refer to Rios Medrano et al.1.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is a significant health issue worldwide, and the expression of long non-coding RNAs (lncRNAs) are altered in these malignancies. The present study evaluated the expression level of ATXN1 CDC42EP1 genes and the lncRNAs related to these genes (lnc-ATXN1L, lnc-ATXN1, lnc-ATXN10, and lnc-CDC42EP1) in paraffin blocks of oral and pharyngeal squamous cell carcinoma (SCC) samples from patients referred to Amir Alam Hospital in Tehran, Iran.
RESULTS: This cross-sectional study was conducted on 76 paraffin blocks of oral and pharyngeal squamous cell carcinoma (SCC) samples from patients referred to Amir Alam Hospital in Tehran. The expression levels of ATXN1, CDC42EP1, lnc-ATXN1L, lnc-ATXN1, lnc-ATXN10, and lnc-CDC42EP1 were measured in all samples using a qPCR Master Mix kit. Real-time PCR was used to perform the reactions, and GAPDH was considered the housekeeping gene. Statistical analyses were conducted utilizing the Statistical Package for the Social Sciences (SPSS) version 22.0. The expression of lnc-ATXN1, lnc-ATXN10, and lnc-CDC42EP1 significantly differed between the two groups. All of them were downregulated (p < 0.05), and no significant difference was observed between the SCC samples and the adjacent tissue in other genes (p > 0.05). The expression of genes was not related to age, sex, size, and tumor location (p > 0.05).
CONCLUSIONS: Dysexpression of lnc-ATXN1, lnc-ATXN10, and lnc-CDC42EP1 can be used for diagnosing OSCC.

The present study describes the expression of genes in the Longissimus dorsi muscle related to meat quality of hair lambs finished in an Integration Crop-Livestock system. Twenty-eight non-castrated lambs of two breeds, Somalis Brasileira and Santa Inês, at 120 ± 15 days of age, with an average initial live weight of 18 ± 3.1 kg, were kept in a pasture-based finishing system with supplementation. Upon reaching 28 kg body weight, animals were sent for slaughter. Samples of the Longissimus dorsi and Biceps femoris muscle were harvested for analyses of gene expression and physicochemical properties. Significant differences were detected between the breeds for tissue and chemical composition, whereas the physical aspects did not differ. We observed the expression of six genes related to lipid synthesis (acetyl-CoA carboxylase [ACACA], fatty acid synthase [FAS], stearoyl-CoA desaturase [SCD], lipoprotein lipase [LPL], cell death-inducing DFFA-like effector A [CIDEA], and thyroid hormone responsive [THRSP]) and six genes related to molecular synthesis (myostatin [MSTN], growth differentiation factor 8 [GDF8], insulin-like growth factor 1 [IGF1], insulin-like growth factor 2 [IGF2], delta-like 1 homolog [DLK1], and growth hormone receptor [GHr]) in both breeds. The Santa Inês breed and the Somalis Brasileira showed similar expression patterns of genes related to lipogenesis and myogenesis of the Longissimus dorsi muscle, with the exception of the THRSP gene, in which the Somalis Brasileira have more receptors for the action of thyroid hormones, which resulted in greater thickness of fat in the carcass (subcutaneous fat) and higher lipid content in the chemical composition of the meat.

BACKGROUND: Colorectal cancer (CRC) is the second most deathly worldwide and third most common cancer, CRC is a very heterogeneous disease where tumors can form by both environmental and genetic risk factors and includes epigenetic and genetic alternations. Inhibitors of DNA binding proteins (ID) are a class of helix-loop-helix transcription regulatory factors; these proteins are considered a family of four highly preserved transcriptional regulators (ID1-4), shown to play significant roles in many processes that are associated with tumor development. ID family plays as negatively dominant antagonists of other essential HLH proteins, concluding the creation of non-functional heterodimers and regulation of the transcription process.
METHODS: 120 Fresh tissue and blood samples Forty (40) samples of fresh tissue and blood were collected from patients diagnosed with CRC, twenty (20) samples were collected from a patient diagnosed as healthy. The (qRT-PCR) method is a sensitive technique for the quantifying of steady-state mRNA levels that used to evaluation the expression levels of ID (1-4) gene.
RESULTS: The findings indicate downregulation in ID1 in tissue with a highly significant change between patients and control groups, where upregulation in the ID1 gene is shown in blood samples.ID2 gene also demonstrated high significant change where show upregulation in tissue and downregulation in blood sample. ID3 and ID4 genes show downregulation in tissue and blood samples with a significant change in ID3 blood samples between patient and blood groups.
CONCLUSIONS: Because of the regulation function of the ID family in many processes, the up or down regulation of IDs genes in tumors Proves how important its tumor development, and therefore those proteins can be used as an indicator for CRC.

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, though the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.

The atavistic theory of cancer posits that cancer emerges and progresses through the reversion of cellular phenotypes to more ancestral types with genomic and epigenetic changes deactivating recently evolved genetic modules and activating ancient survival mechanisms. This theory aims at explaining the known cancer hallmarks and the paradox of cancer\'s predictable progression despite the randomness of genetic mutations. Lineweaver and colleagues recently proposed the Serial Atavism Model (SAM), an enhanced version of the atavistic theory, which suggests that cancer progression involves multiple atavistic reversions where cells regress through evolutionary stages, losing recently evolved traits first and reactivating primitive ones later. The Warburg effect, where cancer cells upregulate glycolysis and lactate production in the presence of oxygen instead of using oxidative phosphorylation, is one of the key feature of the SAM. It is associated with the metabolism of ancient cells living on Earth before the oxygenation of the atmosphere. This review addresses the question of whether cancer metabolism can be considered as an atavistic reversion. By analyzing several known characteristics of cancer metabolism, we reach the conclusion that this version of the atavistic theory does not provide an adequate conceptual frame for cancer research. Cancer metabolism spans a whole spectrum of metabolic states which cannot be fully explained by a sequential reversion to an ancient state. Moreover, we interrogate the nature of cancer metabolism and discuss its characteristics within the framework of the SAM.

GBM WHO CNS Grade 4 represents a major challenge for oncology due to its aggressive behavior. Conventional imaging has restrictions in detecting tumor recurrence. This prospective study aims to identify gene-based biomarkers in whole blood instead of isolating exosomes for the early detection of tumor recurrence. Blood samples (n = 33) were collected from seven GBM patients at time points before and after surgery as well as upon tumor recurrence. Four tumor tissue samples were assessed in parallel. Next-generation sequencing (NGS), including mRNA-seq and small RNA-seq, was used to analyze gene expression profiles in blood samples and tumor tissues. A novel filtering pipeline was invented to narrow down potential candidate genes. In total, between 6-93 mRNA and 1-19 small RNA candidates could be identified among the seven patients. The overlap of genes between the patients was minimal, indicating significant inter-individual variance among GBM patients. In summary, this prospective study supports the applicability of gene expression measurements in whole blood for the detection of tumor recurrence. It might provide an alternative to the challenging workflow of liquid biopsy after laborious exosome isolation from whole blood.

Egg quality in fishes is commonly determined by fertilisation success and cleavage patterns as a phenotypic outcome of underlying regulatory mechanisms. Although these phenotypic estimators of egg quality are useful in farming conditions, these \"good quality\" egg batches do not always translate to good larval growth and survival. The identification of genes involved in embryonic development may help find links between genetic factors of maternal origin and egg quality. Herein, the relative expression of seven stage-specific developmental genes of Atlantic cod was analysed using quantitative PCR to understand the function during embryogenesis and its relationship with egg quality. Genes ccnb2 and pvalb1 showed significant differential expression between developmental stages and significant upregulation from blastula and somite stages, respectively. The comparison of spawning batches showed that the relative gene expression of genes ccnb2, acta, tnnt3 and pvalb1 was significantly higher from the middle of the spawning season where phenotypic quality estimators establish the best egg quality. Moreover, a positive significant correlation was observed between quality estimators based on egg morphology and the genetic expression of genes acta and acta1 during somitogenesis. This study suggests that the combination of quality estimators, genetics and batch timing could help optimise reproductive protocols for commercial stocks of Atlantic cod.

Plant flowering time is affected by endogenous and exogenous factors, but its variation patterns among different populations of a species has not been fully established. In this study, 27 Arabidopsis thaliana accessions were used to investigate the relationship between autonomous pathway gene methylation, gene expression and flowering time variation. DNA methylation analysis, RT-qPCR and transgenic verification showed that variation in the flowering time among the Arabidopsis populations ranged from 19 to 55 days and was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway, FLOWERING LOCUS VE (FVE), FLOWERING LOCUS Y (FY), FLOWERING LOCUS D (FLD), PEPPER (PEP), HISTONE DEACETYLASE 5 (HAD5) and Pre-mRNA Processing Protein 39-1 (PRP39-1), as well as their relative expression levels. The expression of FVE and FVE(CS) was modified separately through degenerate codon substitution of cytosine and led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of methylated sites in FVE and FVE(CS) among those transgenic plants and the recipient Col-0 verified the close relationship between the number of methylation sites, expression and flowering time. Our findings suggest that the methylation variation of these six key upstream transcription factors was associated with the gene expression level of the autonomous pathway and flowering time in Arabidopsis. The FVE(CS) and FVE genes in transgenic plants tended to be hypermethylated, which could be a protective mechanism for plants. However, modification of gene sequences through degenerate codon substitution to reduce cytosine can avoid hypermethylated transferred genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology.