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ATAC-seq with and without SET8 in U2OS cells

ABSTRACT: ATAC-seq with and without SET8 in U2OS cells

PROVIDER: PRJNA486188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7699130_1.fastq.gz	Fastqsanger.gz
	SRR7699130_2.fastq.gz	Fastqsanger.gz
	SRR7699131_1.fastq.gz	Fastqsanger.gz
	SRR7699131_2.fastq.gz	Fastqsanger.gz
	SRR7699132_1.fastq.gz	Fastqsanger.gz

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ATAC-seq with and without SET8 in U2OS cells

Project description:We report that loss of SET8 from cells leads to a global decrease in chromatin compaction status in G1 phase.

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Stable Set8 effect on gene expression in U2OS cells

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Stable Set8 effect on gene expression in U2OS cells

Project description:Ubiquitin-mediated proteolysis play a significant role in various biological processes including transcription, DNA repair and cell cycle progression. The identification of Set8 and Set8b (a splice isoform) histone H4K20 methyl transferase as a substrate for the cullin-based ubiquitin ligase (CRL4-Cdt2) demonstrate that this pathway plays a significant role in promoting cell cycle progression, specifically promoting G2 progression. This study investigate the effect of failure to degrade Set8 in S-phase of the cell cycle via CRL4-Cdt2 on gene expression. We used microarrays to detail the effect of the expression of stable form of Set8b H4K20 mono-methyl transferase (Set8b_deltaPIP2) on gene expression Human osteosarcoma-derived human cells were transduced with retroviruses encoding either wt-Set8b or a mutant of Setb8 which is resistant to degradation via CRL4-Cdt2 ubiquitin ligase complex (Set8b_deltaPIP2) or with an a control pMSCV empty virus. 5 days after transduction, cells were harvested and the RNA was extracted by Trizol (Invitrogen) and hybridized to the affymetrix chips array.

2010-09-18 | E-GEOD-24170 | biostudies-arrayexpress

ATAC-seq in the U2OS-AR cell line comparing cells treated for 4 hours with 5 nM R1881 to vehicle (DMSO) control-treated cells

Project description:We performed ATAC-seq in the U2OS-AR cell line (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for human AR), upon androgen (R1881) or vehicle (DMSO) treatment for 4 hours.

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RNA-Seq of U2OS cells with and without IFNα2 pretreatment

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Studying changes in chromatin accessibility in U2OS-GR cells by ATAC-seq directly after 4-hour glucocorticoid treatment and following a 24-hour hormone washout

Project description:We performed ATAC-seq in the U2OS-GR cell line. The cell line is derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for rat GR. Cells were treated with dexamethasone (100 nM) or vehicle (ethanol) for 4 hours and either harvested immediately or washed 2x with PBS and subsequently cultured in hormone-free medium for 24 hours before harvest.

2021-05-03 | E-MTAB-9909 | biostudies-arrayexpress

Open chromatin profiling in the U2OS cell

Project description:In order to identify the open chromatin profiles in the U2OS cell, ATAC-seq technology was used to determine the accessible chromatin landscape in U2OS cell.

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Poly ADP-ribosylation of SET8 leads to aberrant H4K20 methylation domains in mammalian cells

Project description:In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle- dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised and it undergoes degradation via ubiquitylation pathway. Knockdown of PARP1 shifted the relative dynamic equilibrium of H4K20me2 to H4K20me3 in cells. Overexpression or knockdown of PARP1 led to aberrant H4K20me1 domains genome-wide, impacting Wnt signaling pathways genes and transcription factor binding site enrichment. Therefore, SET8 mediated chromatin remodeling in mammalian cells are influenced by poly ADP-ribosylation by PARP1.

2022-11-17 | GSE188744 | GEO

Histone 4 Lys-20 Mono-Methylation by SET8 Mediates Wnt Target Gene Activation

Project description:Histone methylation has an important role in transcriptional regulation. However, unlike H3K4 and H3K9 methylation, the role of H4K20 mono-methylation (H4K20me-1) in transcriptional regulation remains unclear. Here we show that Wnt3a specifically stimulates H4K20 mono-methylation at TBE (TCF-binding element) via the histone methylase SET8. Additionally, SET8 is crucial for activation of the Wnt reporter gene and target genes in both mammalian cells and zebrafish. Furthermore, SET8 interacts with TCF4/LEF1 directly, and this interaction is regulated by Wnt3a. Therefore, we conclude that SET8 is a Wnt signaling mediator and is recruited by LEF1/TCF4 to regulate the transcription of Wnt-activated genes, possibly via H4K20 mono-methylation at the target gene promoters. Our findings also indicate that H4K20me-1 is a marker for gene transcription activation, at least in canonical Wnt signaling. This chip experiment was carried out to find out how many genes would be regulated by SET8 after Wnt3a CM stimulated HEK293 cells. Total RNA was extracted from HEK293 cells after siRNA transfection (control or SET8 shRNA) for about 40 hours and then induced with Control or Wnt3a CM for 7 hours using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). Three pairs of samples: si-control + control CM / si-control + Wnt3a CM 7 h / si-SET8 + Wnt3a CM. Samples were amplified and labeled using a NimbleGen One-Color DNA Labeling Kit.

2010-12-29 | E-GEOD-24708 | biostudies-arrayexpress

U2OS-ERa, U2OS-ERb, and U2OS-ERab cells treated with 4HT or E2

Project description:U2OS-ERa, U2OS-ERb, and U2OS-ERab cells treated with 4HT or E2 Keywords: other

2005-04-06 | GSE2292 | GEO