GEO DataSets

(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) 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) 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) 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:

GPL18133 GPL19604 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

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(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) 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) 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 GPL16085 GPL26241

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) 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

(Submitter supplied) Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts. To date, such studies have investigated primarily Bacteria. more...

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18473

5 Samples

Download data: WIG

(Submitter supplied) Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15749 GPL15750

10 Samples

Download data: TAR

(Submitter supplied) The protozoan pathogen Toxoplasma gondii relies on tight regulation of gene expression to invade and establish infection in its host. The divergent gene regulatory mechanisms of Toxoplasma and related apicomplexan pathogens rely heavily on regulators of chromatin structure and histone modifications. The important contribution of histone acetylation for Toxoplasma in both acute and chronic infection has been demonstrated, where histone acetylation increases at active gene loci. more...

Organism:

Toxoplasma gondii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25973

6 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. more...

Organism:

Haloferax volcanii DS2

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL32418 GPL30888

34 Samples

Download data: BIGWIG

(Submitter supplied) Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. more...

Organism:

Mus musculus

Type:

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

4 related Platforms

41 Samples

Download data: BED, TXT

(Submitter supplied) Genome wide mapping of five histone marks (H3K4me2, H3K9me2, H3K9me3, H3K27me3 and H3AcK9/14) as well as nucleosome occupancy was generated by chromatin immunoprecipitation followed by deep sequencing. To gain insights into the dynamic nature of the P. tricornutum epigenome in response to an environmental cue, we analyzed the impact of nitrate depletion. We specifically examined three histone modifications (H3K4me2, H3K9/14Ac and H3K9me3) using Chip-seq.

Organism:

Phaeodactylum tricornutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20142

10 Samples

Download data: GFF3