Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610719 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11249200_1.fastq.gz | Fastqsanger.gz | |||
| SRR11249200_2.fastq.gz | Fastqsanger.gz | |||
| SRR11249201_1.fastq.gz | Fastqsanger.gz | |||
| SRR11249201_2.fastq.gz | Fastqsanger.gz | |||
| SRR11249202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 128 |
Similar Datasets
Project description:Although Sm-like proteins (LSMs) form the core of U6 RNPs and function in pre-mRNA splicing, little is known regarding their regulatory role in selection of splice sites, alternative splicing (AS) and splicing efficiency in eukaryotes. The Arabidopsis SAD1 locus encodes the LSM5 protein and was defined in a genetic screen for components that regulate the expression of stress-responsive gene. To further investigate regulatory role of the protein SAD1 in pre-mRNA splicing, we performed RNA sequencing (RNA-seq) to examine the changes of the global alternative splicing (AS) among the wildtype Arabidopsis plant (C24), the mutant plant (sad1) and the sad1-overexpressed plant (SAD1-OE). Our work not only provided novel insights into the regulatory role of SAD1 or LSM proteins in splicing, but also provided new cues to improving splicing efficiency and optimizing biological functions and screening the stress-resistant plant.
2013-11-01 | E-MTAB-4336 | biostudies-arrayexpress
Project description:Cytosine DNA methylation (mC) can silence transposable elements (TEs) and regulate gene expression. However, the mechanism and function of DNA methylation reprogramming during plant development are still largely unknown. To explore the DNA methylation dynamics during the male sexual-lineage development in the Brassicaceae family, we assessed the mC level in meiocyte, microspore and pollen of a Brassica rapa doubled haploid (DH) line by whole genome bisulfite sequencing (WGBS). Analysis of global mC profiles showed that significant reprogramming of CHH methylation occurred in the Brassica rapa male sex cells, similar to that observed in Arabidopsis. Analysis of differential methylation sites identified specific methylation loci in sex cells that can target and possibly regulate gene expression, suggesting a mechanism consistent with that of Arabidopsis. Quite a few long terminal repeat (LTR) transposable elements were activated in meiocyte and microspore, which correlated with reduced DNA methylation. Expression analysis of key genes that affect DNA methylation showed that active methylation and demethylation occurred during male sexual lineage development. These results suggest a conserved DNA methylation reprogramming mechanism during Brassica rapa male sex lineage development. The transcriptome and DNA methylome data obtained will also be useful for other mechanism studies in Brassica rapa.
2024-09-01 | GSE248075 | GEO
Project description:The effectiveness of microspore embryogenesis and plant formation from in vitro cultivated microspores is determined by a complex network of internal and environmental factors. Plant breeding and genetic engineering widely use haploids/doubled haploids (DHs) derived from in vitro-cultured microspores, but the mechanism of ME induction remains poorly defined. Here, RNA-sequencing was used to characterize the transcriptional landscapes of four early stages of ME in two barley cultivars (Golden Promise and Igri) that are contrastingly responsive in the microspore-derived plant formation. Our experimental setup revealed fundamental regulatory networks, key marker genes of ME (628 stage-specific markers), and 160 candidate genes crucial for genotype-dependent responsiveness/resistance to ME. We found that transcription factors probably give rise to embryo-like structure and callus formation at stage III and determine their further development. Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies aiming at unravelling the genetic control of microspore transition.
2024-12-29 | GSE233486 | GEO
Project description:Dissecting genetic components associated with eye disease using integrative genomic analysis
| PRJNA832664 | ENA
Project description:Highly coordinated pollen wall patterning is essential for male reproductive development. However, the regulatory mechanisms involved in these processes remain poorly understood. Here, we report the identification of Defective Microspore Development1 (DMD1), which encodes a nuclear-localized protein possessing transactivation activity. DMD1 is preferentially expressed in the tapetum and microspores during postmeiotic anther development. Mutations in DMD1 cause a male sterile phenotype with impaired microspore cell integrity. The mutants display abnormal callose degradation, and primexine thickening is inhibited in the newly released microspores. The expression levels of several genes associated with callose degradation and primexine formation are down-regulated in dmd1 anthers. Moreover, irregular Ubisch body morphology and discontinuous endexine is observed in dmd1, and the baculum is completely absent. DMD1 interacts with Tapetum Degeneration Retardation (TDR), a basic helix-loop-helix transcription factor required for exine formation. Taken together, our results suggest that DMD1 is responsible for microspore cell integrity, primexine formation, and exine pattern formation during rice microspore development, and is a potential approach for manipulating male fertility in hybrid rice breeding.
2021-05-01 | GSE149191 | GEO
Project description:Although many genetic studies on thyroid cancers using different approaches have been conducted, just a few loci have been systematically associated. Given the difficulties to obtain single-loci associations this work focuses on the study of epistatic interactions that could help to understand the genetic architecture of complex diseases and explain new heritable components of genetic risk. To our knowledge, this is the first genome-wide epistatic screening for epistasis ever performed in thyroid cancer. Here, we analyzed both sporadic medullary thyroid cancer (sMTC) and juvenile papillary thyroid cancer (PTC) patients. We have identified two significant epistatic gene interactions in sMTC (CHFR-AC016582.2 and C8orf37-RNU1-55P) and three in juvenile PTC (RP11-648k4.2-DIO1, RP11-648k4.2-DMGDH and RP11-648k4.2-LOXL1). Interestingly, each interacting gene pair included a non-coding RNA, providing thus support to the relevance that these elements are increasingly gaining to explain cancer development and progression. Overall, this study contributes to the understanding of the genetic basis of thyroid cancer susceptibility in two different case scenarios such as sMTC and juvenile PTC. It opens further ways of knowledge of new heritable components of genetic risk to disease through association and statistical viewpoints.
2016-02-01 | GSE67047 | GEO
Project description:PURPOSE:To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line ‘CX001’ and Chinese cabbage DH line ‘FT’, obtained from isolated microspore culture, were used in the experiments. Transcriptome analysis indicated that BraA09g066480.3C was expressed in ‘FT’ but not in ‘CX001’.The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage ‘CX001’
2022-12-29 | GSE221778 | GEO
Project description:Clubroot (Plasmodiophora brassicae) is a pathogen of Brassicaceae that causes significant reductions in yield as a consequence of gall formation in the root and hypocotyl of infected plants. The pathogen manipulates host cell cycle regulation in order to drive proliferation in early stages of infection and endoreduplication in later stages. Microarrays were used to profile changes in the expression of cell cycle control components at the onset (16 DPI) and late (26 DPI) stages of gall formation.
2023-06-01 | E-MTAB-5599 | biostudies-arrayexpress
Project description:UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.
2023-08-01 | GSE239314 | GEO