Ontology highlight
ABSTRACT:
PROVIDER: PRJNA601664 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10902724_1.fastq.gz | Fastqsanger.gz | |||
| SRR10902724_2.fastq.gz | Fastqsanger.gz | |||
| SRR10902725_1.fastq.gz | Fastqsanger.gz | |||
| SRR10902725_2.fastq.gz | Fastqsanger.gz | |||
| SRR10902726_1.fastq.gz | Fastqsanger.gz |
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Project description:The genomes of many vertebrates show a characteristic variation in GC content. To explain its origin and evolution mainly three mechanisms have been proposed, selection for GC content, mutation bias and GC-biased gene conversion. At present the mechanism of GC-biased gene conversion, i.e. short-scale, unidirectional exchanges between homologous chromosomes in the neighborhood of recombination-initiating double-strand breaks in favor for GC nucleotides, is the most widely accepted hypothesis. We here suggest that DNA methylation also plays an important role in the evolution of GC content in vertebrate genomes. To test this hypothesis we investigated one mammalian (human; GSE30340) and one avian (chicken) genome. We used bisulfite sequencing to generate a whole-genome methylation map of chicken sperm. Human processed data files (spermdonor1, #reads>=1) were downloaded from the NGSmethDB database (http://bioinfo2.ugr.es/NGSmethDB/database.php). Inclusion of these methylation maps into a model of GC content evolution provided significant support for the impact of DNA methylation on the local equilibrium GC content. Moreover, two different estimates of equilibrium GC content, one which neglects and one which incorporates the impact of DNA methylation and the concomitant CpG hypermutability, give estimates that differ about 15% in both genomes, arguing for a strong impact of DNA methylation on the evolution of GC content. Thus, our results put forward that previous estimates of equilibrium GC content, which neglect the hypermutability of CpG dinucleotides, need to be reevaluated. Genomic DNA from chicken mature sperm was isolated, bisulfite converted and sequenced on a Illumina HiSeq instrument
2015-01-23 | E-GEOD-56639 | biostudies-arrayexpress
Project description:Phosphorus, in its orthophosphate form (Pi), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole genome molecular mechanisms contributing to plant acclimation to Pi deficiency remain largely unknown. White lupin (Lupinus albus L.) has evolved unique adaptations for growth in Pi deficient soils including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 cDNA libraries to build the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences 50,734 were transcriptionally active (RPKM = 3) representing approximately 7.8% of the Lupinus albus genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to Pi deficiency with a = 2-fold change and a p-value = 0.05. Twelve sequences were consistently differentially expressed due to Pi deficiency stress in three species, making them ideal candidates to monitor the Pi status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in Pi deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to Pi deficiency. Examination of 2 different tissue types (roots and leaves) under phosphorus (P) -sufficient or P-deficient condition with 3 biological replications per condition in white lupin (Lupinus albus).
2012-11-29 | E-GEOD-31132 | biostudies-arrayexpress
Project description:Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organization of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order gain a better understanding of the epigenetic organization of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n=40), L. albus (2n=50) and L. luteus (2n=52), and the legume model plant Medicago truncatula (2n=16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG, CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n=32), L. digitatus (2n=36), L. micranthus (2n=52) and L. pilosus (2n=42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome.
2017-08-17 | GSE98637 | GEO
Project description:Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.
2012-11-29 | GSE31132 | GEO
Project description:In mammals, DNA methylation is essential for protecting repetitive sequences from aberrant transcription, translocation, and homologous recombination. However, DNA hypomethylation occurs during specific developmental stages (e.g. preimplantation embryos) and in certain cell types (e.g., primordial germ cells). The absence of dysregulated repetitive elements in these cells suggests the existence of alternative mechanisms that prevent genome instability triggered by DNA hypomethylation. In this report, we seek to elucidate the factors that play a critical role in ensuring genome stability by focusing on DAXX and ATRX, two proteins that have been linked to transcriptional control and epigenetic regulation. We carried out ChIP-seq and RNA-seq analyses to compare the genome-wide binding and transcriptome profiles of DAXX and ATRX in mouse ES (mES) cells triple knocked out for the three mammalian DNA methyltransferases (DNMTs) (TKO cells) to those in wildtype mES cells. Our data indicate that DAXX and ATRX are distinct in their chromatin-binding profiles and highly co-enriched at tandem repetitive elements. Global DNA hypomethylation, as was the case in TKO cells, further promoted the recruitment of the DAXX/ATRX complex to tandem repeat sequences including IAP (intracisternal A‐particle) retrotransposons and telomeres. Inhibition of DAXX or ATRX in cells with hypomethylated genomes (e.g., TKO cells, mES cells cultured in ground-state conditions, and preimplantation embryos) increased aberrant transcriptional de-repression of repeat elements and dysfunction at telomeres. Furthermore, we provide evidence that DAXX/ATRX-dependent silencing may occur through DAXX’s interaction with SUV39H1 and increased H3K9me3 on repetitive sequences. Our study suggests that DAXX and ATRX are important for safeguarding the genome, particularly in silencing repetitive elements in the absence of DNA methylation. We tested the hypothesis that the DAXX/ATRX complex participates in protecting repetitive elements in the absence of DNA methylation. To this end, we investigated genome-wide chromatin targeting of DAXX and ATRX in wildtype mES cells, and in mES cells that exhibit extensive loss of DNA methylation due to homozygous knockout of all three DNA.
2015-07-15 | E-GEOD-70811 | biostudies-arrayexpress
Project description:Iron (Fe) and phosphorus (P) are essential nutrients for plants growth. Despite their abundance in soils, they are barely available for plants. In order to overcome these nutritional stresses, plants have evolved strategies including physiological, biochemical and morphological adaptations. Biosynthesis and release of low molecular weight compounds from the roots play a crucial role in P and Fe mobilization. White lupin (Lupinus albus L.) is considered a model plant for studying root exudates and for P-deficient adaptation. White lupin is able to markedly modify its root architecture by forming special structures called cluster roots, and modifies the rhizospheric soil characteristics by biosynthesising and releasing great amounts of exudates. These phenomena are quite well described in response to P deficiency, but there is few information on the adaptation of a cluster-root producing plant species to Fe deficiency. This prompted this work, aimed to characterize the physiological and transcriptomic responses of white lupin plants to Fe deficiency. Occurrence of Strategy I components and interactions with P nutrition has been also investigated in this work. Results showed a physiological and transcriptional link between the responses to Fe and P deficiency in white lupin roots. Phosphorus-deficient plants activated the Strategy I Fe acquisition mechanisms that lead to an enhanced Fe mobilization and translocation and that might help the P acquisition process. On the other hand, also the Fe deficiency enhanced the phosphate acquisition and some P-deficient-responsive genes were overexpressed.
2019-03-22 | GSE112220 | GEO
Project description:We have used repetitive elements, including retrotransposons, as model loci to address how and when heterochromatin forms during development. High throughput RNA-sequencing using a Nano-CAGE protocol throughout early embryogenesis revealed that the expression of repetitive elements is abundant in embryonic cells, highly dynamic and stage-specific, with most repetitive elements becoming repressed before implantation. Furthermore, we show that Line L1 elements and IAP retrotransposons become reactivated from both parental genomes in mouse embryos after fertilisation, indicating an open chromatin configuration at the beginning of development. Our data show that the reprogramming process that follows fertilisation is accompanied by a robust transcriptional activation of retrotransposons and suggests that expression of repetitive elements is initially regulated through an RNA-dependent mechanism in mammals. Genome Wide profiling of CAGE transcripts using Nano-CAGE and RNAseq in oocytes and 3 different stages of mouse pre-implantation development
2013-01-27 | E-GEOD-39849 | biostudies-arrayexpress
Project description:Heterochromatin is a pivotal element in the functional organization of genomes. In our study, we delve into the heterochromatin pattern of association by the PML (promyelocytic leukemia) protein. By using PML chromatin immunoprecipitation and sequencing data and comparing computational methodologies to depict PML chromatin association, we describe PML-associated domains or PADs as large heterochromatic regions that exhibit similar genomic features across cancer cell lines. We show that PADs are specifically enriched in non-coding genes, duplicated gene clusters, and repetitive DNA elements. Moreover, we find enriched binding motifs of KZFPs, which are involved in orchestrating epigenetic repression at repetitive DNA elements. Hence, our findings suggest that PML conservatively associates to heterochromatic domains enriched in repetitive DNA elements and duplicated gene clusters in cancer. These findings contribute to a broader understanding of the complex regulatory framework of genome organization by heterochromatin in cancer.
2024-08-22 | GSE261929 | GEO
Project description:Sequencing DNA from lupin seeds and lupin-containing cookies
| PRJNA532825 | ENA
Project description:To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.
2021-08-22 | GSE145600 | GEO