Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401800 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:SETDB1 disruption leads to an increase in the expression of transposable elements as determined by our standard RNAseq, where bidirectional transcription has been reported. We repeated RNA seq on our samples with a stranded prep to determine whether bidirectional transcription occurs of transposable elements following depletion of SETDB1 in THP-1 AML Cells Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits. Results: Consensus sequences for elements for upregulated TEs were downloaded from the Dfam database (Hubley et al., 2016). Stranded RNA-seq data was then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count(Anders et al., 2015; Li, 2013). Reads were visualized using the IGV genome browser, using a custom pseudogenome that was generated from the Dfam consensus sequences (Robinson et al., 2011; Thorvaldsdottir et al., 2013). Conclusions: Our data determined that following the disruption of SETDB1, there is increased bidirectional transcription over a subset of transposable elements.
2017-09-06 | GSE103410 | GEO
Project description:RNAseq to determine gene expression changes following depletion of SETDB1 in THP-1 AML Cells
| PRJNA401801 | ENA
Project description:Purpose: To determine how loss of SETDB1 effects gene expression in THP-1 AML cells. Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits. Results: Using an optimized data analysis workflow, we mapped 23 million or more sequence reads per sample to the human genome (GRCh38) with GSNAP for obtaining standard gene expression measurements. Since SETDB1 is also know to regulate repetitive elements we also mapped sequences to a pseudogenome containing tranposable elements from hg19 repeatmasker annotations using RepEnrich and following the pipeline published on GitHub (https://github.com/nskvir/RepEnrich). Conclusions: Our data determined that immediately following the disruption of SETDB1, a strong type I Interferon response can be observed at day 4. In addition, many repetitive elements are also significanly induced, including L1 LINEs, Endogenous Retroviruses, and Satellite repeats.
2017-09-06 | GSE103409 | GEO
Project description:We performed H3K9me3 chIP-seq 5 days following disruption of the SETDB1 H3K9 trimethylase with two different sgRNAs (6, and 9) or non-targeting control. Our data suggests that H3K9me3 is modestly reduced over transposable elements and some ZNF genes following disruption of SETDB1.
2017-09-06 | GSE103408 | GEO
Project description:To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases. Microarrays were used to determine whether circadian regulation occurs at the transcriptional level in response to Salmonella Typhimurium infection.
2013-04-25 | GSE46356 | GEO
Project description:Von Hippel-Lindau (VHL) is a tumor suppressor that functions as the substrate recognition subunit of the CRL2VHL E3 complex. While substrates of VHL have been identified, its tumor suppressive role remains to be fully understood. For further determination of VHL substrates, we analyzed the physical interactome of VHL and identified the histone H3K9 methyltransferase SETBD1 as a novel target. SETDB1 undergoes oxygen-dependent hydroxylation by prolyl hydroxylase domain proteins (PHD) and the CRL2VHL complex recognizes hydroxylated SETDB1 for ubiquitin-mediated degradation. Under hypoxic conditions, SETDB1 accumulates by escaping CRL2VHL activity. Loss of SETDB1 in hypoxia compared with that in normoxia escalates the production of transposable element (TE)-derived double-stranded RNAs (dsRNAs), thereby hyperactivating the immune-inflammatory response. In addition, strong derepression of TEs in hypoxic cells lacking SETDB1 triggers DNA damage-induced death. Our collective results support a molecular mechanism of oxygen-dependent SETDB1 degradation by the CRL2VHL E3 complex and reveal a role of SETDB1 in genome stability under hypoxia.
2024-01-26 | PXD037104 | Pride
Project description:To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases. Microarrays were used to determine whether circadian regulation occurs at the transcriptional level in response to Salmonella Typhimurium infection. Cecal tissues from wild type mice and Clock mutant mice infected with S. Typhimurium or mock control at two circadian times (10am and 10pm) were used for RNA extraction and hybridization on Affymetrix microarrays.
2013-04-25 | E-GEOD-46356 | biostudies-arrayexpress
Project description:Epigenetic regulators play a critical role in normal and malignant hematopoiesis. We recently showed that the Histone 3 Lysine 9 (H3K9) methyltransferase SETDB1 negatively regulates the expression of the pro-leukemic genes HoxA9 and its cofactor Meis1 through deposition of promoter H3K9 trimethylation (H3K9me3) in MLL-AF9 AML cells. Here, we investigated the microbiological impact of altered SETDB1 expression in AML cells. We explored changes in transcription using RNA-seq, promoter associated histone modifications using ChIP-seq, and chromatin accessibility using ATAC-seq. Next generation sequencing of AML cells with or without overexpression of SETDB1 shows that high expression of SETDB1 induces repressive changes to the promoter epigenome and downregulation of genes linked with AML, including Dock1 and the MLL-AF9 target genes Hoxa9, Six1, and others. These data reveal novel targets of SETDB1 in AML that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and suppressing AML.
2019-10-03 | GSE136850 | GEO
Project description:We performed RNAseq analysis of primary human osteoblasts co-cultured with the human THP-1 AML cell-line and, in parallel, RNAseq analysis on the THP-1 AML cells exposed to the human primary osteoblasts.
2020-07-15 | GSE154374 | GEO
Project description:To compare the global gene expressions between KLF4-expressed AML cells and albendazole-treated AML cells, we conducted gene expression arrays in THP-1 cells lentivirally-transduced with doxycycline-inducible KLF4 or in THP-1 cells treated with albendazole in different concentrations. We identified that albendazole induces prominent differentiation in THP-1 cells through up-regulating KLF4 and DPYSL2A expressions. Considering the guaranteed safety and tolerability of albendazole in humans, this drug could easily be repositioned to AML patients once its anti-tumor efficacy is clarified.
2021-03-09 | GSE101784 | GEO