Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42273 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1199430_1.fastq.gz | Fastqsanger.gz | |||
| ERR1199430_2.fastq.gz | Fastqsanger.gz | |||
| ERR1199440_1.fastq.gz | Fastqsanger.gz | |||
| ERR1199440_2.fastq.gz | Fastqsanger.gz | |||
| ERR1199450_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 216 |
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Project description:Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. Analysis of 625 million bases of sequenced cDNAs yielded a single-bp resolution map of transcription start sites and operon structures for more than 1000 transcriptional units. The analysis led to the discovery of 310 expressed non-coding RNAs, with an extensive expression of overlapping cis-antisense transcripts to a level unprecedented in any bacteria or archaea but resembling that of eukaryotes. As opposed to bacterial transcripts, most Sulfolobus transcripts completely lack 5' UTR sequences, suggesting that mRNA/ncRNA interactions differ between bacteria and archaea. The data also reveal internal hotspots for transcript cleavage linked to RNA degradation, and predict sequence motifs that promote RNA destabilization. This study emphasizes the importance of transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation for bacteria and archaea. 5 samples of cDNA sequencing (2 of these are replicates), and 3 samples of RACE-cDNA sequencing (described in the samples section).
2009-10-21 | E-GEOD-18630 | biostudies-arrayexpress
Project description:Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. Analysis of 625 million bases of sequenced cDNAs yielded a single-bp resolution map of transcription start sites and operon structures for more than 1000 transcriptional units. The analysis led to the discovery of 310 expressed non-coding RNAs, with an extensive expression of overlapping cis-antisense transcripts to a level unprecedented in any bacteria or archaea but resembling that of eukaryotes. As opposed to bacterial transcripts, most Sulfolobus transcripts completely lack 5' UTR sequences, suggesting that mRNA/ncRNA interactions differ between bacteria and archaea. The data also reveal internal hotspots for transcript cleavage linked to RNA degradation, and predict sequence motifs that promote RNA destabilization. This study emphasizes the importance of transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation for bacteria and archaea.
2009-10-21 | GSE18630 | GEO
Project description:Members of the third domain of life, the Archaea, are ubiquitous in all environments on Earth but remain understudied in many aspects including regulatory processes of the central dogma. Archaea present unique biology because they utilize a mosaic of molecular features from both Bacteria and Eukarya, along with unique features. The advent of a high-throughput view of the translation landscape via ribosome profiling in the Bacteria and the Eukarya has illuminated the complexity and previously underappreciated regulation of translation (i.e. translation efficiency, ribosome surveillance, etc.) that potentially has large scale effects on cellular functionality. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii and elucidated the translational landscape for the first time in the third domain of life. We coupled ribosome profiling with translation inhibitors to: (a) determine the size of the archaeal ribosome footprint, (b) systematically assign translation states of the ribosome to footprint lengths in a mostly leaderless transcriptome, (c) experimentally induce ribosome pauses and clarify the pausing landscape comprehensively, (d) identify putative novel proteins, including small open reading frames (smORFs), and (e) provide evidence that many genes initiate on putative alternative translation start sites (paTSS) around and within open reading frames (ORFs), demonstrating how a microorganism with a gene dense genome can produce proteins with distinct functions using the same gene.
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Project description:The rumen harbors a complex mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacteria populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen fauna. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to the initial stages of rumination, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated in nylon bags within the rumen of cannulated dairy cows for 48 hours.
2020-10-14 | PXD017007 | Pride
Project description:Small RNAs have been studied in detail in Bacteria and Eukarya domain, but in the case of Archaea domain the knowledge is scarce and the physiological function of the majority is still uncertain. To extend the knowledge of sRNAs in Archaea domain and its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. Bioinformatic approach has allowed to predict 295 putative sRNAs genes in the genome of H. mediterranei, 88 of which have been verified by means of RNA-seq. The secondary structure of putative sRNAs and its possible targets have been identified. Curiously, some of them present as possible targets genes related to the nitrogen assimilation, as glutamate dehydrogenase or regulatory nitrogen protein PII. Analysis of RNA-seq data has also revealed differences in the expression pattern of 16 sRNAs according to the nitrogen source. Consequently, RNomic and the bioinformatic approaches used in this work have allowed the identification of new sRNAs in Hfx. mediterranei, some of which show different expression pattern depending on the nitrogen source. It suggests that these sRNAs could be involved in the regulation of nitrogen assimilation, being able to constitute important gene regulatory network.
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Project description:The airway epithelium represents a critical component of the human lung that helps orchestrate defences against respiratory tract viral infections, which are responsible for more than 2.5 million deaths/year globally. Innate immune activities of the airway epithelium rely Toll-like receptors (TLRs), nucleotide binding and leucine-rich-repeat pyrin domain containing (NLRP) receptors, and cytosolic nucleic acid sensors. ATP Binding Cassette (ABC) transporters are ubiquitous across all three domains of life – Archaea, Bacteria, and Eukarya – and expressed in the human airway epithelium. ABCF1, a unique ABC family member that lacks a transmembrane domain, has been defined as a cytosolic nucleic acid sensor that regulates CXCL10, interferon-b expression, and downstream type I interferon responses. We tested the hypothesis that ABCF1 functions as a dsDNA nucleic acid sensor in human airway epithelial cells important in regulating antiviral responses.
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Project description:Recently the function and cellular importance of small proteins became more and more visible. Whereas many examples of small protein functions have been described in eukarya and bacteria, less is known about small protein functions in archaea. A previous determination of the proteome in the halophilic archaeon Haloferax volcanii by mass spectrometry confirmed the expression of several annotated genes for small proteins. One such protein is encoded by HVO_0582. To identify the biological function of the encoded small protein we attempted to generate a deletion strain. Since we were not successful in generating the deletion we repressed HVO_0582 using CRISPRi. The repression strain showed a severe growth defect as well as strong changes in morphology. ChIPSeq experiments revealed several binding sites for this putative transcription factor. Transcriptome and proteome analyses show a clear effect on RNA and protein expression in the CRISPRi strain. Based on our findings we conclude that the small protein CdrS is involved in regulation of cell division / cell morphology.
2021-08-09 | PXD017903 | Pride
Project description:Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, in recent years histone proteins have been identified in a few bacterial clades, in particular the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no experimental functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions, similar to what is observed in eukaryotes with compact genomes such as yeast, and also to some archaea. As in eukaryotes, chromatin accessibility positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that Bacteriovorax promoters exhibit very strong polymerase pausing, unlike in yeast, but similar to the state of mammalian and fly promoters. Finally, the Bacteriovorax genome exists in a three-dimensional (3D) conformation analogous to that of other bacteria without histones, organized by the parABS system and along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the deep evolution of chromatin organization across the tree of life.
2023-12-06 | GSE245010 | GEO