GEO DataSets

(Submitter supplied) We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. more...

Organism:

Thermoplasma acidophilum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26243

16 Samples

Download data: CSV, XLSX

(Submitter supplied) Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. more...

Organism:

Escherichia coli; Thermoplasma acidophilum; synthetic construct

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19604 GPL18133 GPL26243

12 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

synthetic construct; Escherichia coli; Thermoplasma acidophilum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26243 GPL19604 GPL18133

51 Samples

Download data

(Submitter supplied) We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. more...

Organism:

Thermoplasma acidophilum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26243

23 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Methanothermus fervidus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18133 GPL26241 GPL16085

74 Samples

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(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Methanothermus fervidus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26241

6 Samples

Download data: BW

(Submitter supplied) Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. more...

Organism:

Haloferax volcanii DS2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30888

8 Samples

Download data: WIG

(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

50 Samples

Download data: CSV

(Submitter supplied) Since their discovery, archaea have not only proven a fascinating domain in their own right, but also helped us understand the evolution and function of molecular components they share with bacteria or eukaryotes. Archaeal histones are homologous to their eukaryotic counterparts, but operate in a less constrained bacterial-like cellular environment and their role in transcription and genome function remains obscure. more...

Organism:

Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16085

18 Samples

Download data: BW

(Submitter supplied) We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

12 Samples

Download data: TXT

(Submitter supplied) Histones are the primary building blocks of chromatin in eukaryotes and many archaea. Bacteria are thought to rely on an orthogonal set of proteins to organize their chromosomes. Several bacterial genomes do, however, encode proteins with putative histone fold domains. Whether these proteins adopt a bona fide histone fold, assemble into higher order complexes that bind DNA, and play a central role in bacterial nucleoid physiology is not known. more...

Organism:

Bdellovibrio bacteriovorus; Aquifex aeolicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25581 GPL28567

5 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Halobacterium salinarum

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL30532 GPL28343

64 Samples

Download data: TXT, WIG

(Submitter supplied) Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. more...

Organism:

Halobacterium salinarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30532

24 Samples

Download data: CSV, TXT

(Submitter supplied) Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. more...

Organism:

Halobacterium salinarum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28343

40 Samples

Download data: WIG

(Submitter supplied) Using the model organism Thermococcus kodakarensis, we genetically alter the chromatin landscape and quantify the resultant changes in gene expression, including unanticipated and significant impacts on provirus transcription. Global transcriptome changes resultant from varying chromatin landscapes reveal the regulatory importance of higher-order histone-based chromatin architectures in regulating gene expression.

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27055 GPL28639

10 Samples

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(Submitter supplied) 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. more...

Organism:

Bdellovibrio bacteriovorus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL33833 GPL33834

27 Samples

Download data: BIGWIG, HIC