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Genome-wide profiling of Argonaute-chromosome interactions [ChIP-Seq]

ABSTRACT: Argonuate proteins are the central components of the RNA-induced silencing complex (RISC) which execute small RNA-mediated gene regulation mainly in the cytoplasm and their nuclear functions in mammalian cells remain largely unknown. Here we show that in human cancer cells Ago1 is pervasively associated with chromosomal loci throughout the genome with the association centered mostly on actively transcribed promoters. Ago1 but not Ago2 physically interacts with RNA polymerase II (RNAP II) in the nucleus. Moreover, genes bound by Ago1 are significantly enriched for several cancer related pathways. Detailed analysis of these genes including PIK3CA, PRKCH, CDC6 and RRM1 verified Ago1-mediated transcriptional gene regulation through Ago1-promoter interactions. We also found a strong correlation between Ago1-bound genes and genes downregulated by Ago1 depletion which, phenotypically, leads to inhibition of proliferation in different cancer cells. Therefore, our findings reveal the first landscape of human Ago1-chromosomal interactions which may drive oncogenic programs in cancer cells Examination of Ago-DNA interactions in human cancer cells

ORGANISM(S): Homo sapiens

SUBMITTER: Vera Huang

PROVIDER: E-GEOD-40536 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide profiling of Argonaute-chromosome interactions [ChIP-Seq]

Project description:Argonuate proteins are the central components of the RNA-induced silencing complex (RISC) which execute small RNA-mediated gene regulation mainly in the cytoplasm and their nuclear functions in mammalian cells remain largely unknown. Here we show that in human cancer cells Ago1 is pervasively associated with chromosomal loci throughout the genome with the association centered mostly on actively transcribed promoters. Ago1 but not Ago2 physically interacts with RNA polymerase II (RNAP II) in the nucleus. Moreover, genes bound by Ago1 are significantly enriched for several cancer related pathways. Detailed analysis of these genes including PIK3CA, PRKCH, CDC6 and RRM1 verified Ago1-mediated transcriptional gene regulation through Ago1-promoter interactions. We also found a strong correlation between Ago1-bound genes and genes downregulated by Ago1 depletion which, phenotypically, leads to inhibition of proliferation in different cancer cells. Therefore, our findings reveal the first landscape of human Ago1-chromosomal interactions which may drive oncogenic programs in cancer cells

2013-09-27 | GSE40536 | GEO

Gene expression profiling in cells with Ago1 knockdown (Affymetrix)

Project description:Argonautes, a family of highly evolutionarily conserved proteins, are the central platform for small RNA-mediated gene regulatory mechanisms which occur mainly in the cytoplasm. To understand a potential role of Argonaute 1 (Ago1) protein in the nucleus of mammalian cells in regulating gene transcription and epigenetics, we performed integrated analyses of Ago1 ChIP-sequencing (GSE40536) and gene expression profiling in cells depleted of Ago1. For gene expression profiling, we knocked down the expression of Ago1 by siRNA in PC-3 cells and compared gene expression profiles in the cells depleted of Ago1 and cells receiving control treatments. We found that Ago1 depletion resulted in more downregulated genes which were enriched in gene responsible for promoting cell cycle progression, DNA replication and repair, and response to endogenous stimuli. Integrated analyses of Ago1-chromosomal interactions and gene expression changes in response to Ago1 depletion reveal a significant correlation between Ago1-bound genes and genes altered by Ago1 depletion. These genes are significantly enriched in cancer-related pathways. Our data suggests a nuclear function of Ago1 in regulating gene transcription. PC-3 cells were mock transfected or transfected with an Ago1 specific siRNA or a control siRNA. Each treatment was done in duplicates.

2013-09-27 | E-GEOD-42600 | biostudies-arrayexpress

Gene expression profiling in cells with Ago1 knockdown (Affymetrix)

2013-09-27 | GSE42600 | GEO

Cross-linking MS of S. cerevisiae ORC bound to DNA and Cdc6

Project description:During DNA replication initiation, the Origin Recognition Complex (ORC) and Cdc6 co-associate on DNA to load replicative helicases onto origins of replication. We apply DSSO crosslinking mass spectrometry of reconstituted ORC-DNA-Cdc6 to identify interactions between different subunits and domains in the complex.

2022-02-28 | PXD031033 | Pride

Arabidopsis thaliana

Project description:Arabidopsis AGO1 and AGO10 bound sRNAs

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Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen) Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq. Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA. Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

2019-09-06 | GSE136907 | GEO

Profile of mRNAs associated with Ago (Argonaute) 1 in normoxic and hypoxic endothelial cells

2013-06-30 | GSE43165 | GEO

Farnesylated Heat Shock Protein 40 is a component of membrane-bound RISC in Arabidopsis

Project description:ARGONAUTE1 (AGO1) binds directly to small regulatory RNA and is a key effector protein of post-transcriptional gene silencing mediated by microRNA (miRNA) and small interfering RNA (siRNA). The formation of an RNA induced silencing complex (RISC) of AGO1 and small RNA requires the function of the Heat Shock Protein 70/90 chaperone system. Some functions of AGO1 occur in association with endomembranes, in particular the rough endoplasmic reticulum (rER), but proteins interacting with AGO1 in membrane fractions remain unidentified. In this study, we show that the farnesylated Heat Shock Protein 40 homologs, J2 and J3, associate with AGO1 in membrane fractions in a manner that involves protein farnesylation. We also show that three changes in AGO1 function are detectable in mutants in protein farnesylation and J2/J3. First, perturbations of the HSP40/70/90 pathway by mutation of j3, hsp90 and farnesyl transferase affect the amounts of AGO1 associated with membranes. Second, miRNA association with membrane-bound AGO1, and with membrane-bound polysomes is increased in farnesyl transferase and farnesylationdeficient J2/J3 mutants. Third, silencing by non-cell autonomously acting short interfering RNAs (siRNAs) is impaired. These observations highlight the involvement of farnesylated J2/J3 in small RNA-mediated gene regulation, and suggest that the importance of chaperone-AGO1 interaction is not limited to the RISC assembly process.

2018-09-10 | PXD010197 | Pride

Genome-wide maps of AGO1-bound small RNA in Arabidopsis leaves

Project description:We report flg22 regulate the accumulation of AGO1-bound small RNA in arabidopsis. We find that a number of miRNAs are up- or down-regulated by flg22, a well-studied PAMP. Examination of AGO1-bound small RNAs with or without flg22 treatment.

2010-02-25 | E-GEOD-20448 | biostudies-arrayexpress

Profile of mRNAs associated with Ago (Argonaute) 1 in normoxic and hypoxic endothelial cells

Project description:Messenger RNAs that are bound to Ago1 is to be transcriptionally or translational suppressed. Therefore the changes in Ago1-associated transcripts indicate the changes of suppression of these genes. We used microarrays to detail changes of mRNA transcripts that are associated with Ago1 in endothelial cells under normoxia and hypoxia conditions. Human umbilical vein endothelial cells pooled from 8 different sources were subjected to normoxia (21% oxygen, Nx) or hypoxia (2% hypoxia, Hx) for 24 hr. Ago1 was immunoprecipitated with mouse anti-human Ago1 using a lysis buffer containing 0.1% NP-40. The associated RNA was extracted and hybridized on Affymetrix Human Gene 1.0 ST arrays.

2013-06-30 | E-GEOD-43165 | biostudies-arrayexpress

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