Genes & genetic systems最新文献

Next-generation RNA sequencing analysis was performed to develop 13 novel expressed sequence tag-simple sequence repeat markers to evaluate the genetic variation in the near-threatened halophyte Limonium tetragonum (Thunb.) A. A. Bullock. In the four populations examined, the total number of alleles at each locus ranged from two to seven, with an average of 3.1. The average observed and expected heterozygosity ranged from 0.00 to 0.13 and 0.28 to 0.78, respectively. Three of the 13 loci had the same homozygous alleles within populations, but different alleles among populations. Compared to other halophytes, relatively low genetic diversity was observed in this species. Further studies are necessary to determine the population demography of L. tetragonum and to clarify the cause of its low genetic diversity.

Next-generation sequencing (NGS) has become widely available and is routinely used in basic research and clinical practice. The reference genome sequence is an essential resource for NGS analysis, and several population-specific reference genomes have recently been constructed to provide a choice to deal with the vast genetic diversity of human samples. However, resources supporting population-specific references are insufficient, and it is burdensome to perform analysis using these reference genomes. Here, we constructed a set of resources to support NGS analysis using the Japanese reference genome, JG. We created resources for variant calling, variant effect prediction, gene and repeat element annotations, read mappability and RNA-seq analysis. We also provide a resource for reference coordinate conversion for further annotation enrichment. We then provide a variant calling protocol with JG. Our resources provide a guide to prepare sufficient resources for the use of population-specific reference genomes and can facilitate the migration of reference genomes.

Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from Archaean homologs; however, how this occurred remains unclear. Our previous genetic analysis on the budding yeast nucleosome identified 26 histone residues conserved between S. cerevisiae and T. brucei; 15 that are lethal when mutated and 11 that are synthetically lethal with deletion of the FEN1 nuclease. These residues are partially conserved in nucleosomes of a variety of giant viruses, allowing us to follow the route by which they were established in the LECA (Last Eukaryote Common Ancestor). We analyzed yeast nucleosome genetic data to generate a model for the emergence of the eukaryotic nucleosome. In our model, histone H2B-H2A and H4-H3 doublets found in giant virus nucleosomes facilitated the formation of the acidic patch surface and nucleosome entry sites of the eukaryotic nucleosome, respectively. Splitting of the H2B-H2A doublet resulted in the H2A variant, H2A.Z., and subsequent splitting of the H4-H3 doublet led to a eukaryotic specific domain required for chromatin binding of H2A.Z. We propose that the LECA emerged when the newly-split H3 N-terminal horizontally acquired a common N-tail found in extinct pre-LECA lineages and some extant giant viruses. This hypothesis predicts that the emergence of the H3 variant CENP-A and establishment of CENP-A-dependent chromosome segregation occurred after the emergence of the LECA, implying that the root of all eukaryotes is assigned within Euglenida.

Background: β-sitosterol is a natural plant steroidal compound with anti-cancer properties against various tumors. This work attempts to explore the inhibitory effect of β-sitosterol on the progression of lung adenocarcinoma (LUAD) and further analyze its targets.

Methods: In this work, we applied network pharmacology to obtain the components and targets of Ganoderma spore powder. The biological functions of β-sitosterol and CHRM2 were studied using the homograft mouse model and a series of in vitro experiments including quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blot (WB), CCK-8, flow cytometry, immunohistochemistry (IHC), and immunofluorescence (IF) experiments. The regulatory influence of β-sitosterol on the glycolysis pathway was validated by detecting glucose consumption and lactate production, as well as extracellular acidification rate (ECAR) and oxygen consumption rate (OCR).

Results: In this project, we unearthed that CHRM2 was a protein that directly binds to β-sitosterol. In vitro, CHRM2 overexpression repressed the apoptosis rate and expression of apoptosis-related proteins and promoted glycolysis, while the addition of lonidamine attenuated the inhibitory effect conferred by CHRM2 overexpression on LUAD apoptosis. Furthermore, β-sitosterol hindered glycolysis as well as the growth of tumors in vitro and in vivo. CHRM2 overexpression reversed the effect of β-sitosterol on the biological behavior of LUAD cells.

Conclusion: Our project emphasized that CHRM2 is a direct target of β-sitosterol in LUAD cells. β-sitosterol can repress the glycolysis pathway, exerting an anti-tumor effect. These findings can provide new evidence for supporting the potential use of β-sitosterol as a therapeutic agent for LUAD.

To explore the oncogenic mechanism of FOXM1 in the tumor microenvironment (TME) regarding triple negative breast cancer (TNBC) promotion. The mRNA and protein levels of target genes in TNBC cells and their exosomes were detected by RT-qPCR and western blot. Co-culture models of TNBC cells and THP-1/M0 macrophages was established to detect the impact of co-culture on FOXM1 expression and macrophage polarization direction. The bioinformatics website was used to predict the binding sites between the FOXM1 and IDO1 promoter, which were further validated using dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay. Finally, after erastin-induced ferroptosis, Cell Counting Kit-8 (CCK-8), terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL), and other experiments were conducted to investigate whether the FOXM1/IDO1 axis regulates M2 macrophage polarization through ferroptosis. It was found that FOXM1 was highly expressed in exosomes derived from TNBC cells, and TNBC cells upregulated FOXM1 expression in THP-1 cells through exosomes to promote M2 macrophage polarization. Furthermore, FOXM1 upregulated IDO1 in M2-type TAMs by regulating transcription. Lastly, FOXM1/IDO1 inhibited ferroptosis, promoting M2 macrophage polarization, thereby advancing TNBC progression. In conclusions, FOXM1 derived from TNBC cell-derived exosomes activated IDO1 transcription in TAMs to inhibit ferroptosis, promoting TAMs' M2 polarization and exerting carcinogenic effects.

Mycoplasmas, autonomously culturable bacteria with the smallest genome, are an important organism to understand the minimal form of life. Mutagenesis using mutagens is a useful methodology for understanding the essential regions of genomic information. Ultraviolet light (UV) and trimethyl psoralen (TMP) are mutagens known to induce various mutations; the latter is reported to specifically induce deletions in nematodes. However, their mutagenic effects on mycoplasma are not known. Here, we exposed Metamycoplasma salivarium to UV-C light or TMP and UV-A as mutagens, and analyzed the mutational pattern after serial cultivation ranging from 34 to 56 rounds for different lineages. Our results showed that more deletions, but fewer point mutations, were induced with TMP and UV-A than with UV-C, indicating the usefulness of TMP in inducing deletions. In addition, we compared our results with mutational data from other studies, which suggested that the combination of TMP and UV-A or UV-C exposure both induced point mutations that were highly biased toward C→T and G→A transitions. These data provide useful basic knowledge for mutational studies on M. salivarium.

Response regulators (RRs) are implicated in various developmental processes as well as environmental responses by acting as either positive or negative regulators, and are crucial components of cytokinin signaling in plants. We characterized 36 RRs in rice (Oryza sativa L.; Os) using in silico analysis of publicly available data. A comprehensive analysis of OsRR family members covered their physicochemical properties, chromosomal distribution, subcellular localization, phylogeny, gene structure, distribution of conserved motifs and domains, and gene duplication events. Gene Ontology analysis indicated that 22 OsRR genes contribute mainly to the cytokinin response and signal transduction. Predicted cis-elements in RR promoter sequences related to phytohormones and abiotic stresses indicated that RRs are involved in hormonal and environmental responses, supporting previous studies. MicroRNA (miRNA) target analysis showed that 148 miRNAs target 29 OsRR genes. In some cases, multiple RRs are targets of the same miRNA group, and may be controlled by common stimulus responses. Based on the analysis of publicly available gene expression data, OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, OsPRR73 and OsPRR95 were found to be involved in responses to abiotic stresses. Using quantitative reverse transcription polymerase chain reaction we confirmed that six of these RRs, namely OsRR4, OsRR6, OsRR9, OsRR10, OsRR22 and OsPRR73, are involved in the response to salinity, osmotic, alkaline and wounding stresses, and can potentially be used as models to understand molecular mechanisms underlying stress responsiveness.

Intraspecific variation in specialized metabolites plays a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), which is required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine were preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variation in β-tyrosine may contribute to the defensive potential of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of the evolution of rice defense. However, their distribution patterns in O. rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine content in 110 genetically and geographically diverse O. rufipogon accessions and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine content in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into the evolution of rice defense.

We investigated the variation and geographical distribution of the Pseudo-regulator response 37 (Setaria italica PRR37; SiPRR37) gene, which is involved in heading time (photoperiodism) in foxtail millet. An allele of the SiPRR37 gene, in which an approximately 4.9-kb transposable element (designated TE1) is inserted (a loss-of-function or reduction-of-function type), is distributed sporadically in East Asia and broadly in Southeast Asia and South Asia, implying that this gene is important in latitudinal adaptation. In addition, we found a new allele of SiPRR37 with an insertion of a 360-bp TE (TE2) at this locus and investigated the geographical distribution of this new type. This SiPRR37 allele with TE2 is distributed in Japan, Korea, Nepal, Iran and Turkey. Both TE1 and TE2 are useful markers for tracing foxtail millet dispersal pathways in Asia.

Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.