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Series GSE138576 Query DataSets for GSE138576
Status Public on Oct 08, 2019
Title The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog (Mnase-seq and EMSA-seq)
Organisms Escherichia coli; Thermoplasma acidophilum; synthetic construct
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design Examination of Mnase digestion products along the course of T.acidophilum growth phase, In E.coli cells expressing Hta. Digestion of T.acidophilum and E.coli genomic DNA by MNase. Relative migration of DNA oligo in EMSA-seq assay using purified HTa.
Contributor(s) Hocher A, Warnecke T
Citation(s) 31710291
Submission date Oct 08, 2019
Last update date Dec 03, 2019
Contact name Tobias Warnecke
Organization name Imperial College
Street address Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
Platforms (3)
GPL18133 Illumina HiSeq 2500 (Escherichia coli)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
GPL26243 Illumina HiSeq 2500 (Thermoplasma acidophilum)
Samples (12)
GSM4113865 Ecoli_Chr1
GSM4113866 Ecoli_Chr2
GSM4113867 Ecoli_gDNA1
This SubSeries is part of SuperSeries:
GSE127728 The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog
BioProject PRJNA576437
SRA SRP224761

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 10.5 Mb (ftp)(http) BW 11.0 Mb (ftp)(http) BW 11.3 Mb (ftp)(http) BW 26.5 Mb (ftp)(http) BW 27.3 Mb (ftp)(http) BW 29.5 Mb (ftp)(http) BW 21.6 Mb (ftp)(http) BW 25.1 Mb (ftp)(http) BW 28.4 Mb (ftp)(http) BW 8.4 Mb (ftp)(http) BW 9.3 Mb (ftp)(http) BW 10.7 Mb (ftp)(http) BW
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