Termite of palm trees
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1140375 | ENA |
REPOSITORIES: ENA
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Project description:Spatial genome organization is essential to direct fundamental DNA-templated biological processes (e.g. transcription, replication, and repair), but the 3D in situ nanometer-scale structure of accessible cis-regulatory DNA elements within the crowded nuclear environment remains elusive. Here, we combined the recently developed Assay for Transposase-Accessible Chromatin with visualization (ATAC-see), PALM super-resolution imaging and lattice light-sheet microscope (a method termed 3D ATAC-PALM) to selectively image and quantitatively analyze key features of the 3D accessible genome in single cells. 3D ATAC-PALM reveals that accessible chromatin are non-homogeneously organized into spatially segregated clusters or accessible chromatin domains (ACDs). To directly link imaging and genomic data, we optimized multiplexed imaging of 3D ATAC-PALM with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence. We found that ACDs colocalize with active chromatin and enclose transcribed genes. By applying these methods to analyze genetically purterbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight the 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
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Project description:Purpose: To identify conserved and novel miRNAs in date palm and, most importantly, to identify miRNAs that could play a role in salt tolerance Methods: we generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm,then Deep sequencing of these four sRNA libraries,last The bioinformatics analysis,further validated using semi-quantitative PCR (qPCR). Results: Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of most miRNAs in date palm. In leaves, all of the identified miRNAs were affected by the salinity treatment, and the majority (75%) of them were upregulated, whereas in roots, only 33% of the miRNAs were upregulated, but 44% of them were downregulated, while the remaining miRNAs (22%) were unaffected by the treatment. The salt responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, and calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world with a wide range of abiotic stress tolerance, date palm contains a large population of conserved and nonconserved miRNAs that function at the posttranscriptional level. Conclusions: This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.
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Project description:We aim to investigate chromatin accessibility in the keratinocytes of hip and palm
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Project description:Oil palm (Elaeis guineensis Jacq.) is one of the most important oil-producing crops in the world. However, the demand for oil from this crop will increase in the future. A comparative gene expression profile of the oil palm leaves was needed in order to understand the key factors that influence the oil production. Here, we reported an RNA-seq dataset from three different oil yields and three different genetic populations of oil palm. All raw sequencing reads were obtained from an Illumina NextSeq 500 platform. We also provide a list of the genes and their expression levels resulting from the RNA-sequencing. This transcriptomic dataset will provide a valuable resource for increasing oil yield.
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Project description:single cell RNA-seq profiling of palm and hip
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Project description:Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.
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Project description:Oil palm rhizosphere R059GS3 Metagenomic assembly
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