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The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

ABSTRACT: The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

PROVIDER: PRJNA525128 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8650280.fastq.gz	Fastqsanger.gz
	SRR8650281.fastq.gz	Fastqsanger.gz
	SRR8650282.fastq.gz	Fastqsanger.gz
	SRR8650273.fastq.gz	Fastqsanger.gz
	SRR8650283.fastq.gz	Fastqsanger.gz

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The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

Project description: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. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-03-11 | GSE127727 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (RNA-Seq)

2019-03-11 | GSE127726 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

Project description: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. We confirm and extend prior results showing that T. acidophilum harbours a HU family protein, HTa, that protects part of the genome from MNase digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization behaviour. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-10-08 | GSE138576 | GEO

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

| PRJNA525121 | ENA

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-Seq)

| PRJNA525129 | ENA

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

Project description:The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)

| PRJNA576437 | ENA

Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

2011-09-27 | GSE21956 | GEO

Transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions

Project description:Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted). Total RNA of T. acidophilum was isolated with the RNeasy Protect Bacteria Kit (Qiagen). The transcriptomics analysis was performed on TI273075 60mer chips of Roche NimbleGen microarrays (NimbleGen Systems of Iceland, LLC). Probes were selected for all protein sequences (1482) and labelled with Cy3. The median number of probes per sequence is 20, and each probe is replicated 5 times on the chip. The probes are randomly distributed over the surface of the array. Unused features are filled with randomly generated probes of comparable GC content. ArrayStar v2.0 software (DNASTAR, Inc.) was used for the data analysis. Three independent biological replicates were processed for aerobic and anaerobic conditions, respectively.

2011-09-26 | E-GEOD-21956 | biostudies-arrayexpress

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog.

Project description:Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are widespread but not universal: several lineages have lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

| S-EPMC6877293 | biostudies-literature

The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-11 | GSE127728 | GEO