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Drosophila zinc finger proteins CG9609, AEF1 and CG10543 are colocalized with SAGA, SWI/SNF and ORC complexes on gene promoters and involved in transcription regulation

ABSTRACT: Drosophila zinc finger proteins CG9609, AEF1 and CG10543 are colocalized with SAGA, SWI/SNF and ORC complexes on gene promoters and involved in transcription regulation

PROVIDER: PRJNA1052617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27206500_1.fastq.gz	Fastqsanger.gz
	SRR27206500_2.fastq.gz	Fastqsanger.gz
	SRR27206501_1.fastq.gz	Fastqsanger.gz
	SRR27206501_2.fastq.gz	Fastqsanger.gz
	SRR27206495_1.fastq.gz	Fastqsanger.gz

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Drosophila zinc finger proteins CG9609, AEF1 and CG10543 are colocalized with SAGA, SWI/SNF and ORC complexes on gene promoters and involved in transcription regulation

Project description:We purified the DUB module of the Drosophila SAGA complex and found that a number of zinc proteins interact with it, including CG9609, Aef1 and CG10543. A genome-wide study showed that CG9609, Aef1 and CG10543 proteins are localized predominantly on the promoters of active genes. The binding sites of these proteins colocalize with the SAGA, dSWI/SNF and ORC complexes. It has been shown that CG9609, Aef1 and CG10543 proteins are involved in transcription regulation.

2023-12-20 | GSE250183 | GEO

Drosophila Zinc Finger Protein CG9890 Is Colocalized with Chromatin Modifying and Remodeling Complexes on Gene Promoters and Involved in Transcription Regulation.

Project description:In this work, we conducted a genome-wide study of the zinc finger protein CG9890 and showed that it is localized mostly on the promoters of active genes. The CG9890 binding sites are low-nucleosome-density regions and are colocalized with the chromatin modifying and remodeling complexes SAGA and dSWI/SNF, as well as with the ORC replication complex. The CG9890 protein was shown to be involved in the regulation of the expression of some genes on the promoters of which it is located, with the ecdysone cascade genes accounting for a significant percentage of these genes. Thus, the CG9890 protein is a new member of the transcriptional network which is localized on active promoters, interacts with the main transcription and replication complexes, and is involved in the regulation of both basal and inducible transcription.

| S-EPMC7800599 | biostudies-literature

ORC binding profile in Candida albicans

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.

2014-02-13 | GSE54923 | GEO

Kc167 ORC Localization in hydroxyurea (HU)

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.

2014-12-05 | GSE63914 | GEO

ORC binding profile in Candida albicans

2014-02-13 | E-GEOD-54923 | biostudies-arrayexpress

Kc167 ORC Localization in hydroxyurea (HU)

2014-12-05 | E-GEOD-63914 | biostudies-arrayexpress

ORC precisely positions nucleosomes at origins of replication

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

Yeast ORC sumoylation status fine-tunes origin activity

Project description:Sumoylation is emerging as a post-translation modification important for chromosome duplication and stability. The origin recognition complex (ORC), which directs DNA replication initiation by loading the MCM replicative helicases onto origins, is sumoylated in both yeast and human cells. However, the biological consequences of ORC sumoylation are largely unclear. Here we report the effects of hyper- and hypo-sumoylation of yeast ORC using multiple approaches. We show that ORC hyper-sumoylation preferentially reduces the activity of a subset of early origins, while Orc2 hypo-sumoylation has an opposing effect. Mechanistically, ORC hyper-sumoylation leads to reduced MCM loading in vitro and diminished MCM chromatin association in vivo. The importance of an appropriate level of ORC sumoylation is suggested by the data that either hyper- or hypo-sumoylation of ORC results in genome instability and a dependence on other genome maintenance factors for cell fitness. Thus, yeast ORC sumoylation status needs to be fine-tuned to achieve optimal origin activity control and genome stability.

2023-03-11 | PXD032977 | Pride

Genome-wide EMSA (gEMSA) of ORC and yeast genomic DNA

Project description:Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal DNA, triggering a series of molecular events that culminate in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome requires multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern with relevance to differentiation, genome stability and evolution. It is unclear whether ORC-origin interactions are relevant to the regulation of origin activation time. Here we applied a novel genome-wide strategy to classify origins in the model eukaryote Saccharomyces cerevisiae based on the types of molecular interactions used for ORC-origin binding. Specifically, origins were classified as DNA-dependent when the strength of ORC-origin binding in vivo could be explained by the affinity of ORC for origin DNA in vitro, and, conversely, as ‘chromatin-dependent’ when the ORC-DNA interaction in vitro was insufficient to explain the strength of ORC-origin binding in vivo. The two classes of origins were distinct in terms of local nucleosome architecture and dependence on origin-flanking sequences in plasmid replication assays, consistent with local features of chromatin promoting ORC binding at ‘chromatin-dependent’ origins. Importantly, origins that fired in late S-phase, but not those that fired in early S-phase, showed a significant dependence on the ORC-origin DNA interaction for ORC binding in vivo. Therefore we demonstrate for the first time a connection between ORC-origin binding mechanisms and the regulation of origin activation time at a genome-wide level.

2013-09-30 | GSE48440 | GEO

MOT1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Project description:An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

2016-11-11 | GSE81480 | GEO

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