Fine mapping and functional activity of the adenosine deaminase origin in murine embryonic fibroblasts

Sibani, Sahar; Rampakakis, Emmanouil; Paola, Domenic Di; Zannis‐Hadjopoulos, Maria

doi:10.1002/jcb.21662

Cited by 2 publications

(1 citation statement)

References 55 publications

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“…We also measured the activity of several well-characterized mouse origins of DNA replication in Myc-ER fibroblasts. 33,34 Dhx9 suppression significantly reduced the frequency of firing at several origins and also blocked the ability of Myc to increase origin activity ( Figure 6F). Em-myc/Bcl-2 lymphomas expressing the indicated shRNAs.…”

Section: /2mentioning

confidence: 95%

RNAi screening uncovers Dhx9 as a modifier of ABT-737 resistance in an Eμ-myc/Bcl-2 mouse model

Mills

Malina

Lee

et al. 2013

Blood

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• A focused RNAi screen identifies Dhx9 as a regulator of ABT-737 sensitivity in Em-myc/Bcl-2 lymphomas.• Dhx9 suppression activates an apoptotic signal through the Chk1/p53 replicative stress pathway in Myc-driven cells.ABT-737 is a promising chemotherapeutic agent that promotes apoptosis by acting as a selective BH3 mimetic to neutralize Bcl-2-like family members. One shortcoming with its use is that Mcl-1, a member of the Bcl-2 family, is poorly inhibited by ABT-737 and thus is a major cause of resistance. We performed a short hairpin RNA (shRNA)-based drop-out screen to identify novel genes and pathways that could reverse resistance to ABT-737 treatment in Em-myc/Bcl-2 lymphoma cells engineered to rely on endogenous Mcl-1 for survival. Several drug-sensitive shRNAs were identified that were selectively depleted in the presence of ABT-737. Of these, 2 independent shRNAs targeting the RNA/DNA helicase Dhx9 were found to sensitize lymphomas to ABT-737 to an extent comparable to control Mcl-1 shRNAs. Although Dhx9 suppression sensitized both mouse and human cells to ABT-737 treatment, it did so without altering MCL-1 levels. Rather, loss of Dhx9 appeared to activate a p53-dependent apoptotic program, through aggravation of replicative stress, which was found to be both necessary and sufficient for the ABT-737-shDhx9 synthetic lethal relationship. (Blood. 2013; 121(17):3402-3412)

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Section: /2mentioning

confidence: 95%

RNAi screening uncovers Dhx9 as a modifier of ABT-737 resistance in an Eμ-myc/Bcl-2 mouse model

Mills

Malina

Lee

et al. 2013

Blood

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Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

et al. 2012

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We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels ($1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G 1 and the probability of firing during S.[Supplemental material is available for this article.] DNA replication is a highly orchestrated process that ensures fidelity of genomes during duplications, as well as their adaptation to variations in cell division, DNA damage, and, in metazoa, chromatin changes associated with development and differentiation. It initiates from multiple chromosomal loci, called replication origins (ORIs), which are selected in the G 1 phase of the cell cycle by sequential recruitment of the origin recognition complex (ORC), CDC6, CDT1, and the MCM complex (the pre-replicative complex; pre-RC). Selected pre-RCs are then sequentially activated during the S phase, following a tight temporally ordered program (Mechali 2010).In Saccharomyces cerevisiae, ORIs contain a 12-bp consensus for ORC binding (Bell and Stillman 1992). Genome-wide analyses of ORIs by chromatin immunoprecipitation and parallel sequencing (ChIP-seq) using anti-ORC or -MCM antibodies showed that this consensus is essential but not sufficient for origin activity and identified other features that influence selection and replication timing, including transcription and/or chromatin structure (Eaton et al. 2010). In metazoa, instead, pre-RC does not exhibit sequence specificity, and the number of potential ORIs is considerably larger, following a process of selection that differs according to cell type, functional status, or stress conditions (Mechali 2010).These further levels of complexity allow DNA replication to adapt to the unique expression patterns of individual cell types. Little is known, however, about the regulation of ORI selection and replication timing in metazoa.

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Fine mapping and functional activity of the adenosine deaminase origin in murine embryonic fibroblasts

Cited by 2 publications

References 55 publications

RNAi screening uncovers Dhx9 as a modifier of ABT-737 resistance in an Eμ-myc/Bcl-2 mouse model

RNAi screening uncovers Dhx9 as a modifier of ABT-737 resistance in an Eμ-myc/Bcl-2 mouse model

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

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