Ontology highlight
ABSTRACT:
PROVIDER: PRJNA910794 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22719883_1.fastq.gz | Fastqsanger.gz | |||
| SRR22719883_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:5-methyl-cytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisfulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methyl-cytosine DNA methylation as an integral part of its epigenetic arsenal.
2018-04-01 | GSE111621 | GEO
Project description:Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. These two factors bind both the promoters of RP genes and the rDNA locus; Tbf1 activates transcription at these loci and is essential. Orthologs of Tbf1 bind TTAGGG telomeric repeats in most eukaryotes, and TTAGGG cis-elements are present upstream of RP genes in plants and fungi, suggesting that Tbf1 was involved in both functions in ancestral eukaryotes. In all Hemiascomycetes, Rap1 substituted Tbf1 at telomeres and in the S. cerevisiae lineage this substitution also occurred independently at RP genes, illustrating the extreme adaptability and flexibility of transcriptional regulatory networks. This SuperSeries is composed of the following subset Series: GSE10458: Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation_ChIP-CHIP GSE10499: Transcription Factor Substitution during the Evolution of Fungal Ribosome Regulation_expression profiling Keywords: SuperSeries Refer to individual Series
2010-05-25 | E-GEOD-10622 | biostudies-arrayexpress
Project description:Signal amplification of the initial small RNA trigger is important to ensure the silencing of repetitive transposable elements (TEs). Curiously, secondary small RNA biogenesis occurs by various mechanisms that are coupled with distinct steps of TE silencing in different eukaryotes, such as nucleolytic cleavage of TE transcripts, recruitment of RNA-dependent RNA polymerase, and heterochromatin-directed transcription. How such a variety of small RNA amplification mechanisms has evolved has not been thoroughly elucidated to date. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after primary small RNAs induce the excision of IESs. To examine whether such post-excision production of secondary small RNAs is conserved, we investigate the causality between the excision of IESs and the biogenesis of secondary small RNAs in another ciliate, Tetrahymena. We show that secondary small RNAs accumulate at least a few hours before their derived IESs are excised and that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike the situation in Paramecium, small RNA amplification occurs prior to IES excision in Tetrahymena. This study reveals remarkable mechanistic diversity of secondary small RNA biogenesis mechanisms, even among ciliates showing similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.
2019-06-30 | GSE125297 | GEO
Project description:In eukaryotes, ribosomal RNA biogenesis consists of ribosomal DNA transcription to pre-rRNA, which must be modified and processed in the nucleus resulting in the 18S, 5.8S, and 28S ribosomal units. Molecular components involved in this process comprise the catalytic ribonucleoproteins complexes (snoRNPs) formed by non-coding RNAs classified as box C/D and box H/ACA snoRNA that associates to at least four proteins highly conserved through evolution and combined to multiple transient proteins. Taking advantage of computational and multidisciplinary experimental approaches, we determine that the orphan EhARPv2, a member of the Actin-related family from Entamoeba histolytica, interacts with nucleolar proteins. EhARPv2 and its partners here identified colocalize in the nuclear periphery, considered the nucleolus, and interact with both box C/D and H/ACA snoRNAs. Moreover, we find the reassortment of some components of snoRNPs from C/D- or H/ACA complexes mixed in vitro and in entire cells indicating that in E. histolytica snoRNP of C/D or H/ACA machineries alternate using common elements and that EhARPv2 is a part of this peculiar snoRNP. Our findings substantiate a role for EhARPv2 in the biogenesis of ribosomal RNA.
2020-08-16 | GSE156303 | GEO
Project description:Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.
2017-07-20 | GSE98408 | GEO
Project description:The evolution and diversification of proteins capable of remodelling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodelling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologues have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast-evolving under positive selection, while PKL is evolving under purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein’s intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis of gene expression in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights on gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.
2023-09-06 | GSE236025 | GEO
Project description:The tumor evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1-3, the mechanisms behind why only a small number of clones transform into malignant tumors remain enigmatic. Here, we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programs at single-cell transcriptomic resolution. We uncover a TNF-α signaling module, dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF-α signaling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF-α gene program, associated with epithelial-mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF-α gene program is sufficient to mediate invasive properties and show that the TNF-α signature correlates with shorter overall survival in human squamous cell carcinoma patients. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF-α programs in tumor evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
2024-07-17 | GSE235325 | GEO
Project description:A family of MATH-BTB proteins is known to act as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin proteasome pathway. The BTB domain binds a CUL3 scaffold protein and the less conserved MATH domain targets a highly diverse collection of substrate proteins to promote their ubiquitination and subsequent degradation. Among plants, a significant expansion of the MATH-BTB family occurred in grasses. Here, we functionally describe TaMAB2, a wheat MATH-BTB protein expressed exclusively in the zygote and two-celled proembryo. The overexpression of TaMAB2 in Arabidopsis plants provoked microtubular bundling and re-orientation together with retarded growth. In model BY-2 cells, TaMAB2 showed a microtubule and a ubiquitin-related localization which together with direct interaction with CUL3 pointed out its function in targeting specific substrates for ubiquitin-dependent degradation. Results of protein interaction analyses indicated eukaryotic translation initiation factors 3 and 4 as the most likely substrates of TaMAB2, while the interaction with cytoskeletal element, particularly actin 11 hints at the possible TaMAB2 mediated intreplay between cytoskeleton and translation initiation machinery during the first division of the zygote.
2019-10-24 | PXD014358 | Pride
Project description:Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.
2013-01-30 | E-SMDB-2855 | biostudies-arrayexpress