DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1194016 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31596703_1.fastq.gz | Fastqsanger.gz | |||
| SRR31596703_2.fastq.gz | Fastqsanger.gz | |||
| SRR31596704_1.fastq.gz | Fastqsanger.gz | |||
| SRR31596704_2.fastq.gz | Fastqsanger.gz | |||
| SRR31596705_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 34 |
Similar Datasets
Project description:Monocots possess a fibrous root system comprising an embryonic root (ER), crown roots (CR), and lateral roots (LR), which share striking similarities in adult anatomical structures and functions across the three root types. Nonetheless, their distinct cellular origins highlight the diversity of the initiation mechanism. Through our study, we conducted a comprehensive transcriptome and DNA methylome assay of these root types during their initiation. Our findings indicated significant divergence in transcriptome regulation trajectories with apparent transcriptional activation in post-embryonic root initials (CR and LR) contrasted by suppression in embryonic root (ER) generation. Additionally, CHH methylation was found dynamically and differentially regulated across the initiation stages of the various root types, and significantly associated with the short transposon element within the promoter regions of functional genes, which played crucial roles in determining the genes’ spatiotemporal transcription. Moreover, our work revealed that the activation of DNG702 and repression of DRM2 played important roles in the erasure of CHH methylation and activation of functional genes during the processes, such as a novel identified key regulatory bZip65, thus directly impacting the initiation of post-embryonic roots in rice. In conclusion, our extensive analysis delineates the landscapes of spatiotemporal transcriptomes and DNA methylomes during the initiation of the three root types in rice, shedding light on the pivotal role of CHH methylation in the spatiotemporal regulation of various key genes, ensuring the successful initiation of distinct root types in rice.
2024-12-04 | GSE283466 | GEO
Project description:Maternal protein rbpms2 play a crucial role in mouse blastocyst formation
| PRJNA835702 | ENA
Project description:Positive-strand RNA viruses replicate their genomes on membranes with virus-induced rearrangements such as single- or double-membrane vesicles, but the mechanisms of such rearrangements, including the role of host proteins, are poorly understood. Brome mosaic virus (BMV) RNA synthesis occurs in ?70 nm, negatively curved endoplasmic reticulum (ER) membrane invaginations induced by multifunctional BMV protein 1a. We show that BMV RNA replication is inhibited 80-90% by deleting the reticulon homology proteins (RHPs), a family of membrane-shaping proteins that normally induce and stabilize positively curved peripheral ER membrane tubules. In RHP-depleted cells, 1a localized normally to perinuclear ER membranes and recruited the BMV 2a(pol) polymerase. However, 1a failed to induce ER replication compartments or to recruit viral RNA templates. Partial RHP depletion allowed formation of functional replication vesicles but reduced their diameter by 30-50%. RHPs coimmunoprecipitated with 1a and 1a expression redirected >50% of RHPs from peripheral ER tubules to the interior of BMV-induced RNA replication compartments on perinuclear ER. Moreover, RHP-GFP fusions retained 1a interaction but shifted 1a-induced membrane rearrangements from normal vesicles to double membrane layers, a phenotype also induced by excess 1a-interacting 2a(pol). Thus, RHPs interact with 1a, are incorporated into RNA replication compartments, and are required for multiple 1a functions in replication compartment formation and function. The results suggest possible RHP roles in the bodies and necks of replication vesicles.
| S-EPMC2941330 | biostudies-literature
Project description:Background/objectivesFathers have been largely understudied in feeding research, as most studies have focused on mothers. This study aims to explore the relationship between paternal feeding practices and child eating behaviors.MethodsThis study employed a cross-sectional observational design. Fathers (n = 114) completed one-off self-reported questionnaires using the Child Feeding Practices Questionnaire and the Child Eating Behaviors Questionnaire from October 2023 to February 2024. Variations in feeding practices across sociodemographic factors were explored using correlational statistics. The generalized linear model was used to identify relationships between paternal feeding practices and child eating behaviors.ResultsFor young children, the availability of healthy food at home was positively associated with food approach behaviors, while paternal practices of pressuring and child control were linked to increased food avoidance. Among school-aged children, using food as a reward was positively associated with food approach behaviors, while using food to regulate emotions was linked to increased food avoidance. Restriction for weight control was associated with both food approach and avoidant behaviors. In adolescents, paternal monitoring of their diet and certain socioeconomic conditions were observed to be associated with their eating behaviors.ConclusionsThe findings provide valuable insights into the role of paternal feeding practices in shaping children's eating behaviors and highlight the potential for interventions targeting modifiable paternal behaviors to support healthy eating habits.
| S-EPMC11901718 | biostudies-literature
Project description:Magnaporthe oryzae, a fungal pathogen that causes rice blast, which is the most destructive disease of rice worldwide, has the potential to perform both asexual and sexual reproduction. MAT loci, consisting of MAT genes, were deemed to determine the mating types of M. oryzae strains. However, investigation was rarely performed on the development and molecular mechanisms of the sexual reproduction of the fungus. In the present work, we analyzed the roles of two MAT loci and five individual MAT genes in the sex determination, sexual development and pathogenicity of M. oryzae. Both of the MAT1-1 and MAT1-2 loci are required for sex determination and the development of sexual structures. MAT1-1-1, MAT1-1-3 and MAT1-2-1 genes are crucial for the formation of perithecium. MAT1-1-2 impacts the generation of asci and ascospores, while MAT1-2-2 is dispensable for sexual development. A GFP fusion experiment indicated that the protein of MAT1-1-3 is distributed in the nucleus. However, all of the MAT loci or MAT genes are dispensable for vegetative growth, asexual reproduction, pathogenicity and pathogenicity-related developments of the fungus, suggesting that sexual reproduction is regulated relatively independently in the development of the fungus. The data and methods of this work may be helpful to further understand the life cycle and the variation of the fungus.
| S-EPMC8539793 | biostudies-literature
Project description:Hide-and-seek game in pathogen genome: Transposon elements play an important role in shaping population diversification of rice blast fungus Magnaporthe oryzae
| PRJNA844564 | ENA
Project description:The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.
| S-EPMC10710418 | biostudies-literature
Project description:During development, cells craft an impressive array of actin-based structures, mediating events as diverse as cytokinesis, apical constriction, and cell migration. One challenge is to determine how cells regulate actin assembly and disassembly to carry out these cell behaviors. During Drosophila oogenesis diverse cell behaviors are seen in the soma and germline. We used oogenesis to explore developmental roles of two important actin regulators: Enabled/VASP proteins and Capping protein. We found that Enabled plays an important role in cortical integrity of nurse cells, formation of robust bundled actin filaments in late nurse cells that facilitate nurse cell dumping, and migration of somatic border cells. During nurse cell dumping, Enabled localizes to barbed ends of the nurse cell actin filaments, suggesting its mechanism of action. We further pursued this mechanism using mutant Enabled proteins, each affecting one of its protein domains. These data suggest critical roles for the EVH2 domain and its tetramerization subdomain, while the EVH1 domain appears less critical. Enabled appears to be negatively regulated during oogenesis by Abelson kinase. We also explored the function of Capping protein. This revealed important roles in oocyte determination, nurse cell cortical integrity and nurse cell dumping, and support the idea that Capping protein and Enabled act antagonistically during dumping. Together these data reveal places that these actin regulators shape oogenesis.
| S-EPMC2728145 | biostudies-literature
Project description:Mice with olfactry accessory protein RTP1 and RTP2 knocked out show severe bias in their olfactory receptor repertoire. Surprisingly, even though RTP1,2(-/-) animals have fewer OSNs, we discovered ~8% of the ORs are expressed in larger numbers than the wild type.
2017-03-01 | GSE87694 | GEO
Project description:Ulcerative colitis (UC) is a chronic inflammatory bowel disease that primarily affects the mucosal layer of the colon (large intestine). However, the relationship between Intercellular Adhesion Molecule-1 (ICAM1), SELL and UC is unclear. The UC datasets, GSE87466 and GSE36807, were downloaded from the gene expression omnibus database. The R package limma was utilized to identify differentially expressed genes (DEGs). Weighted gene co-expression network analysis was conducted. The construction and analysis of protein-protein interaction network, functional enrichment analysis, gene set enrichment analysis, and comparative toxicogenomics database analysis were performed. TargetScan was employed to screen miRNAs regulating central DEGs. Western blot (WB) was used to verify. A total of 2118 DEGs were identified in our study. Gene ontology analysis indicated their enrichment primarily in immune system processes, cellular responses to chemical stimuli, responses to organic substances, responses to external stimuli, and immune responses. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the target cells were mainly enriched in chemokine signaling pathways and TNF signaling pathways. Gene set enrichment analysis enrichment analysis showed significant enrichment in chemokine signaling pathways and cell adhesion molecules. In the Metascape enrichment project, gene ontology terms included regulation of cell activation and positive regulation of immune response. Through the construction and analysis of a protein-protein interaction network, we identified 11 core genes (ICAM1, SELL, CD44, CD40, CCR7, CXCL8, CD19, CCL4, CD274, IL7R, IL1B). We found that the core genes (ICAM1, SELL) were highly expressed in UC samples and lowly expressed in normal samples, suggesting their potential regulatory roles in UC. These core genes were associated with lymphoproliferative disorders, inflammation and necrosis. WB results confirmed the high expression of ICAM1 and SELL in UC. ICAM1 and SELL are highly expressed in UC, and the higher the ICAM1 and SELL genes, the worse the prognosis.
| S-EPMC10713187 | biostudies-literature