ORC binding profile in Candida albicans
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE54923 | GEO | 2014/02/13
SECONDARY ACCESSION(S): PRJNA238039
REPOSITORIES: GEO
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Project description:Map ORC binding sites to identify replication origins in C. albicans by using polyclonal ORC antibodies (gift from Stephen Bell Lab). Due to the unsynchronized nature of Candida cells, log-phase cultures were taken to perfoem ChIP-chip experiments to find the genome-wide ORC binding sites. ChIP-chip experiments from log-phase C. albicans culture. 7 different unsynchronized log-phase cultures as replicates.
2014-02-13 | E-GEOD-54923 | biostudies-arrayexpress
Project description:The budding yeast genome is marked by 250-350 origins of DNA replication. These origins are bound by the origin recognition complex (ORC) throughout the cell cycle. ORC has known DNA binding sequence preferences which, though necessary for binding, are not sufficient to fully specify a genomic locus as being bound by ORC, indicating that the cell must use additional chromosomal cues to specify ORC binding sites and origins of replication. Using high-throughput sequencing to precisely locate both ORC binding sites and nucleosome locations genome-wide, we find that a nucleosome depleted region (NDR) and precisely positioned nucleosomes are a ubiquitous feature of yeast replication origins. The ARS consensus sequence (ACS) and adjacent sequences are sufficient to maintain the nucleosome-free properties of the NDR. We use a temperature sensitive ORC1 mutant to demonstrate that ORC is required to maintain precisely positioned nucleosomes at origins of replication. These findings demonstrate the importance of local nucleosome positioning at replication origins, and that chromatin organization is an important determinant of origin selection.
2010-03-19 | GSE16926 | GEO
Project description:The budding yeast genome is marked by 250-350 origins of DNA replication. These origins are bound by the origin recognition complex (ORC) throughout the cell cycle. ORC has known DNA binding sequence preferences which, though necessary for binding, are not sufficient to fully specify a genomic locus as being bound by ORC, indicating that the cell must use additional chromosomal cues to specify ORC binding sites and origins of replication. Using high-throughput sequencing to precisely locate both ORC binding sites and nucleosome locations genome-wide, we find that a nucleosome depleted region (NDR) and precisely positioned nucleosomes are a ubiquitous feature of yeast replication origins. The ARS consensus sequence (ACS) and adjacent sequences are sufficient to maintain the nucleosome-free properties of the NDR. We use a temperature sensitive ORC1 mutant to demonstrate that ORC is required to maintain precisely positioned nucleosomes at origins of replication. These findings demonstrate the importance of local nucleosome positioning at replication origins, and that chromatin organization is an important determinant of origin selection. Examination of nucleosome positioning in wild-type and orc1-161ts mutant S. cerevisiae at room temperature and heatshock temperatures. Examination of ORC binding locations by ChIP-seq. All reported coordinates are based on the SGD genome build released 12/16/2005.
2010-03-19 | E-GEOD-16926 | biostudies-arrayexpress
Project description:The origin recognition complex (ORC) binds specific sites in mammalian genomes, from which DNA replication is initiated. Here, we address ORC binding selectivity in vivo by mapping ~52,000 ORC2 binding sites throughout the human genome. The ORC binding profile is broader than that of sequence-specific transcription factors, suggesting that it does not bind to specific DNA sequences. Instead, ORC binds to open (DNase I hypersensitive) regions in which histone H3 tails are hyperacetylated and also di-methylated at lysine 4. Our results suggest that ORC binding selectivity in vivo is determined by a novel mechanism involving non-specific interaction with accessible DNA and recognition of modified histones. ORC sites are far more prevalent in early replicating regions, suggesting that replication timing is primarily due to ORC density and stochastic firing of origins. Large genomic regions lacking ORC2 binding sites are strongly associated with common fragile sites and recurrent deletions in cancers.
2016-06-01 | GSE70165 | GEO
Project description:Ubiquitination and epigenetic modification both play essential roles in regulating cell fates and development, but little is known how two pathways crosstalk. A known chromatin-binding protein BRWD3, Bromodomain repeats and WD40 repeats domain contain protein 3, has been shown involved both in ubiquitination and histone modification regulation. BRWD3 has roles in multiple chromatin-related processes, including transcription, DNA replication, and chromatin modification. However, how ubiquitination is involved and what’s BRWD3’s ubiquitination targets are barely known. Here, we study the single Drosophila homolog dBRWD3 to uncover its mechanism. To find dBRWD3’s ubiquitination targets, we performed both dBRWD3 IP-MS and BRWD3 dependent ubiquitination IP-MS. Expectedly, the whole BRWD3-Cul4-DDB1 E3 ubiquitination complex and multiple histones are significantly enriched in dBRWD3-IP. Interestingly, multiple histone modification writers and the DNA replication initiation factor origin recognition complex (ORC) are among the intersection of two MS. ORC’s function is highly dependent on chromatin signature. dBRWD3 could provide a perspective on how chromatin signature is regulated by ubiquitination to regulate ORC function. In support of this, about 35% of ORC2 binding sites overlap with dBRWD3 binding sites among the genome. The H3K27ac occupancy rate of dBRWD3 related ORC sites is about 50% higher than that of dBRWD3 irrelevant ORC sites. Depletion of dBRWD3 significantly reduces DNA proliferation in the S phase. Further study will focus on determining which histone modification writer is targeted for ubiquitination and how does it contribute to the chromatin signature and ORC function.
2023-10-24 | PXD039708 | Pride
Project description:The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with several subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decrease ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.
2022-10-19 | GSE199896 | GEO
Project description:Origin Recognition Complex (ORC) is composed of six subunits, ORC1-6, and the entire complex loads excess MCM2-7 on chromosomes to promote initiation of DNA replication in organisms ranging from S. cerevisiae to humans. ORC is also believed to be important for origin specification. Mapping of origins in the cancer cell lines engineered to delete three of the subunits, ORC1, ORC2 or ORC5 shows that origin specification continues at mostly the same sites in the absence of ORC. The few hundred origins that were up-regulated in the absence of ORC suggest that GC/TA skewness and simple repeat sequences facilitate origin selection in the absence of the six-subunit ORC. In the absence of ORC, MCM2-7 association with chromatin continues to be sufficiently in excess to license reserve origins, used under replication stress, and to permit re-replication, which requires repeated loading of MCM2-7 at origins in the same cell-cycle. Thus, origin specification and excess MCM2-7 loading on origins can be executed in mammalian cancer cells in the absence of the six-subunit ORC.
2025-03-25 | GSE278065 | GEO
Project description:The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we performed immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we found that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis revealed that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, results in decreased ORC2 loading onto chromatin. Depleting Elys also sensitized cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a new connection between ORC, replication initiation and nucleoporins, highlighting a previously unrecognized function of nucleoporins in metazoan replication initiation.
2022-10-19 | PXD033045 | Pride
Project description:Determination of the genome-wide distribution of ORC by chromatin immunoprecipitation in the Drosophila Kc167 cell line at the beginning of S phase. Kc167 cells were arrested at the G1/S transition with hydroxyurea (HU). Goal was to test whether the ORC binding distribution remained the same between G1 and S. ChIP-Chip of ORC in HU compared to input genomic DNA. Biological Replicates: 1
2014-12-05 | E-GEOD-63914 | biostudies-arrayexpress