A genome-wide study reveals a pathway for small RNA-mediated recognition of UV-induced DNA lesions (smallRNAs)
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE86401 | GEO | 2017/03/01
SECONDARY ACCESSION(S): PRJNA341692
REPOSITORIES: GEO
Similar Datasets
Project description:This study reports that the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) form a chromatin-bound complex, which facilitates recognition of photo-lesions.
2017-03-01 | GSE86395 | GEO
Project description:Conventional RNA interference (RNAi) pathways suppress eukaryotic gene expression at the post-transcriptional or transcriptional level. At the core of RNAi are small RNAs (sRNAs) and effector Argonaute proteins. Arabidopsis AGO1 is known to bind microRNAs (miRNAs) and post-transcriptionally repress target genes via mRNA cleavage and/or translational inhibition in the cytoplasm. Here, we report that AGO1 binds to the chromatin of transcriptionally active genes and promotes their transcription. We show that sRNAs and SWI/SNF are required for AGO1 binding to chromatin and its function in promoting gene transcription. Moreover, we show that various stimuli including plant hormones and stresses specifically trigger AGO1 binding to the stimulus-responsive genes. Finally, we show that AGO1 facilitates the induction of genes in the jasmonate (JA) signaling pathways and the activation of JA responses. Our findings reveal an unsuspected role for AGO1 in facilitating gene transcription in response to plant hormones and stresses.
2018-01-04 | GSE95301 | GEO
Project description:The therapeutical efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection. Using a combination of genetic, transcriptomic and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.
2023-12-14 | GSE227871 | GEO
Project description:MicroRNA (miRNA) are well known to target 3’ untranslated regions (3’UTR) in mRNAs to silence gene expression at post-transcriptional levels. Multiple reports have also indicated the capability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function in a similar mechanism(s) regardless of the location of their action sites. We herein report a class of miRNA recognition elements (MREs) that exclusively function in CDS regions in humans. Through functional and mechanistic characterization of these “unusual” MREs, we demonstrate that CDS-targeted miRNAs require extensive base pairings in the 3’ side rather than the 5’ seed; cause gene silencing in an Argonaute-dependent, but GW182-independent manner; and repress translation by inducing transient ribosome stalling instead of mRNA destabilization. These findings reveal distinct mechanisms and functional consequences for miRNAs to target CDS versus 3’UTR and suggest that CDS-targeted miRNAs may enlist a translational quality control (QC)-related mechanism to regulate translation in mammalian cells.
2018-08-21 | GSE115146 | GEO
Project description:Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis or kala-azar, the most severe form of leishmaniasis in humans. To date, our understanding of the molecular mechanisms associated with the pathogenicity of Leishmania infection is still limited. RNA interference—collectively RNA silencing pathways—participates in the regulation of various biological processes in most eukaryotic cells. Complexes of Argonaute proteins with small RNAs are core components of the RNA interference system and play a key role in silencing gene expression. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference pathways to promote their survival. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Western blot analysis showed that protein abundance of infected macrophage Argonaute 1 (Ago1) was selectively and significantly higher than that of non-infected control at 24 h post-infection, suggesting that Ago1 plays a role in pathogenicity. In fact, siRNA-mediated downregulation of Ago1 enhanced Leishmania clearance from infected host cells, linking macrophage Ago1 to Leishmania virulence. To investigate the mechanisms of host Ago1 in Leishmania pathogenesis, a stable isotope labeling by amino acids in cell culture (SILAC)-based whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins were dependent on the level of macrophage Ago1. Moreover, the proteomic-based detailed biochemical analysis showed that Leishmania modulated host RNA-induced silencing complex (RISC) composition during infection, strongly suggesting macrophage RISC targeting. Strikingly, Leishmania proteins were detected as part of host RISC in infected cells. Together, our results demonstrate that Leishmania targets host RNA interference machinery to promote its survival inside the host macrophage.
2024-01-26 | PXD037042 | Pride
Project description:Global genome repair (GGR), a subpathway of nucleotide excision repair (NER), corrects bulky helix-distorting DNA lesions across the whole genome, and is essential for preventing mutagenesis and skin cancer. Here we show that METTL14 (methyltransferase-like 14), a critical component of the m6A RNA methyltransferase complex, promotes GGR through regulating m6A mRNA methylation-mediated DDB2 translation and suppresses UV-induced skin tumorigenesis. Ultraviolet B irradiation (UVB) down-regulates METTL14 protein through NBR1-dependent selective autophagy. METTL14 knockdown decreases GGR and DDB2 abundance. Conversely, overexpression of wild-type METTL14, but not its enzymatically inactive mutant, increases GGR and DDB2 abundance. METTL14 knockdown decreases m6A methylation and translation of the DDB2 transcripts. Adding DDB2 reverses the GGR repair defect in METTL14 knockdown cells, indicating that METTL14 facilitates GGR through regulating DDB2 m6A methylation and translation. Similarly, knockdown of YTHDF1, an m6A reader promoting translation of m6A modified transcripts, decreased DDB2 protein levels. Both METTL14 and YTHDF1 bind to the DDB2 transcript. In mice, skin-specific heterozygous METTL14 deletion increases UV-induced skin tumorigenesis. Furthermore, METTL14 as well as DDB2 is down-regulated in human and mouse skin tumors and by chronic UV irradiation in mouse skin, and METTL14 level is associated with the DDB2 level, suggesting a tumor-suppressive role of METTL14 in UV-associated skin tumorigenesis in association with DDB2 regulation. Taken together, these findings demonstrate that METTL14 is a target for selective autophagy and acts as a critical epitranscriptomic mechanism to regulate GGR and suppresses UVB-induced skin tumorigenesis.
2021-08-13 | GSE145924 | GEO
Project description:Rpn1 is the largest proteasomal receptor for polyubiquitin and shuttle proteins contains one known binding site for polyubiquitin and shuttle proteins. We used a combination of NMR spectroscopy, photo-crosslinking, mass spectrometry, and mutagenesis,to confirm the presence of additional ubiquitin recognition site on RPN1. This novel site is situated in the N-terminal section of Rpn1, a region previously surmised to be devoid of functionality.
2021-08-09 | PXD027128 | Pride
Project description:O2- and O4-alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic method to discover novel O2- and O4-n-butylthymidine (O2- and O4-nBudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for O2-nBudT- and O4-nBudT-bearing DNA probes, respectively. Among these proteins, DDB1 and DDB2 selectively bind to O2-nBudT-containing DNA, whereas three HMG-box-containing proteins (i.e. HMGB1, HMGB2 and TFAM) exhibit preferential binding to O4-nBudT-bearing DNA. We further confirmed, by employing electrophoretic mobility shift assay, that TFAM can bind selectively and directly with O4-alkyldT-harboring DNA, and the binding capacity depends mainly on the HMG box-A domain of TFAM. We also found that TFAM promotes transcriptional mutagenesis of O4-alkyldT lesions in vitro and in human cells. Together, we explored, for the first time, the interactomes of O-alkyldT lesions. Our study also expands the functions of TFAM by revealing its capability in binding to O4-alkyldT-bearing DNA, demonstrating the role of HMG-box A domain in this molecular recognition, and uncovering its modulation of transcriptional mutagenesis of these lesions in human cells.
2020-12-21 | PXD021719 | Pride
Project description:Protecting the integrity of their genome is critical to all species. The surveillance and maintenance of the genome of every organism is orchestrated by a highly regulated combination of DNA damage response and specific DNA repair pathways. Two of these critical pathways are base excision repair (BER) and ribonucleotide excision repair (RER). Here, we investigate the phylogenetic diversity in the recognition and repair of three well-established DNA lesions, primarily repaired by BER or RER: 1) 8-oxoguanine, 2) an abasic site, and 3) incorporated ribonucleotide in DNA in E. coli, B. subtilis, H. salinarum, T. brucei, T. thermophila, S. cerevisiae, S. pombe, C. elegans, human HeLa and HEK293 cells, A. thaliana, and Z. mays. Using quantitative mass spectrometry, we identified 337 enriched interactors across these species. Of these proteins, 140 were previously characterized to be involved in DNA repair, and 39 proteins were newly identified due to their homology to previously studied repair proteins. For 10 of the 11 species, we identify unique, uncharacterized proteins that lack homology to any protein within the included 11 species. Our study emphasizes strong crosstalk between RER and BER and highlights the evolutionary conservation of this cross recognition across all domains of life.
2023-07-20 | PXD036040 | Pride
Project description:The roles of Argonaute proteins in cytoplasmic miRNA and RNAi pathways are well established. However, their implication in small RNA-mediated transcriptional gene silencing in the mammalian cell nucleus is less understood. We have recently shown that intronic siRNAs cause chromatin modifications that inhibit RNA polymerase II elongation and modulate alternative splicing in an Argonaute-1 (AGO1) dependent manner. Here we used chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) to investigate the genome-wide distribution of AGO1 nuclear targets. Unexpectedly we found that about 80% of AGO1 clusters are associated with cell-type specific transcriptional enhancers, most of them (73%) overlapping active enhancers. This association seems to be mediated by long, rather than short, enhancer RNAs; and to be more prominent in intragenic, rather than intergenic, enhancers. Paradoxically, crossing ChIP-seq with RNA-seq data upon AGO1 depletion revealed that enhancer bound AGO1 is not linked to the global regulation of gene transcription but to the control of constitutive and alternative splicing, which was confirmed by an individual gene analysis explaining how AGO1 controls inclusion levels of the cassette exon 107 in the SYNE2 gene. Genome-wide analysis of AGO-1 and different histone modifications in 2 cell types
2014-09-29 | E-GEOD-56826 | biostudies-arrayexpress