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| 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
Other
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| 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.
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| 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.
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| Contributor(s) |
Hocher A, Warnecke T |
| Citation(s) |
31710291 |
| |
| Submission date |
Oct 08, 2019 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Tobias Warnecke |
| E-mail(s) |
molecular.systems.laboratory@gmail.com
|
| Organization name |
Imperial College
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platforms (3) |
| GPL18133 |
Illumina HiSeq 2500 (Escherichia coli) |
| GPL19604 |
Illumina HiSeq 2500 (synthetic construct) |
| GPL26243 |
Illumina HiSeq 2500 (Thermoplasma acidophilum) |
|
| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE127728 |
The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog |
|
| Relations |
| BioProject |
PRJNA576437 |
| SRA |
SRP224761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138576_Zscore_Merged_replicates_CR_1X_40_65bp.bw |
10.5 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_CR_1X_70_100bp.bw |
11.0 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_CR_1X_total_fragments.bw |
11.3 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_ChrDig_40_65bp.bw |
26.5 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_ChrDig_70_100bp.bw |
27.3 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_ChrDig_total.bw |
29.5 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_gDNA_40_65bp.bw |
21.6 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_gDNA_70_100bp.bw |
25.1 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Ecoli_gDNA_total.bw |
28.4 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Tacidophilum_gDNA_40_65bp.bw |
8.4 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Tacidophilum_gDNA_70_100bp.bw |
9.3 Mb |
(ftp)(http) |
BW |
| GSE138576_Zscore_Merged_replicates_Tacidophilum_gDNA_total_fragments.bw |
10.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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