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| Status |
Public on Mar 08, 2023 |
| Title |
A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea [ChIP-seq] |
| Organism |
Sulfolobus islandicus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Cell cycle regulation is of paramount importance for all forms of life. Here we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level of accr1 reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped viruses Acidianus two-tailed virus (ATV) and Sulfolobus monocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifested as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-folds) including cdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site in the promoters of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters of cdvA genes across Sulfolobales, suggesting that aCcr1-mediated cdvA repression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.
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| Overall design |
Chromatin immunoprecipitation (ChIP-Seq) was performed according to Takemata et al.(39) with slight modifications. Briefly, the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine. The cells were pelleted by centrifugation at 5,000 g for 10 minutes and washed with PBS. The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr1 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system
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| Contributor(s) |
Yang Y, Liu J, Krupovic M, Shen Y |
| Citation(s) |
36715325 |
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| Submission date |
Nov 25, 2022 |
| Last update date |
Mar 09, 2023 |
| Contact name |
yunfeng Yang |
| E-mail(s) |
[email protected]
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| Phone |
18382465184
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| Organization name |
Shandong University
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| Street address |
72 Binhaidadao, Aoshanwei, Jimo
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266237 |
| Country |
China |
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| Platforms (1) |
| GPL32733 |
Illumina NovaSeq 6000 (Sulfolobus islandicus) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE218793 |
A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea |
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| Relations |
| BioProject |
PRJNA905455 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE218790_RAW.tar |
50.3 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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