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USP16 KO

ABSTRACT: CRISPR-Cas9 editing of human histone deubiquitinase gene USP16 in human monocytic leukemia cell line THP-1

PROVIDER: PRJEB43087 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5295300.fastq.gz	Fastqsanger.gz
	ERR5295310.fastq.gz	Fastqsanger.gz
	ERR5295301.fastq.gz	Fastqsanger.gz
	ERR5295311.fastq.gz	Fastqsanger.gz
	ERR5293892.fastq.gz	Fastqsanger.gz

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Genome-wide maps of Usp16, ubH2A and gene expression profiles in wild type and Usp16 knock out mouse embryonic stem cells (ESCs) and embryoid bodies (EBs)

Project description:Polycomb Repressive Complex 1 and histone H2A ubiquitination (ubH2A) contribute to embryonic stem cell (ESC) pluripotency by repressing lineage-specific gene expression. However, whether active deubiquitination co-regulates ubH2A levels in ESCs and during differentiation is not known. Here, we report that the histone H2A deubiquitinase Usp16 regulates H2A deubiquitination and gene expression in ESCs, and importantly, is required for ESC differentiation. Usp16 knockout is embryonic lethal in mice, but does not affect ESC viability or identity. Usp16 binds to the promoter regions of a large number of genes in ESCs and Usp16 binding is inversely correlated with ubH2A levels and positively correlated with gene expression levels. Intriguingly, Usp16-/- ESCs fail to differentiate due to ubH2A-mediated repression of lineage-specific genes. Finally, Usp16, but not the enzymatically inactive mutant, rescues the differentiation defects of Usp16-/- ESCs. Therefore, this study identifies Usp16 and H2A deubiquitination as critical regulators of ESC gene expression and differentiation. Examination of binding pattern of H2A deubiquitinase Usp16 and ubH2A in mouse embryonic stem cells and embroid bodies

2014-05-02 | E-GEOD-52899 | biostudies-arrayexpress

AP-MS analysis of human RIOK1 and USP16

Project description:To discover novel factors involved in the final steps of 40S ribosomal subunit biogenesis in human cells, we isolated late cytoplasmic 40S subunit precursors by affinity purification (AP) of the assembly factor RIOK1. Subsequent analysis of their composition by mass spectrometry (MS) led to identification of the deubiquitinase USP16. AP-MS of USP16 confirms that it is a component of late cytoplasmic pre-40S particles and we further show that USP16 possesses a new, ribosome-associated function.

2020-03-04 | PXD016458 | Pride

Genome-wide maps of Usp16, ubH2A and gene expression profiles in wild type and Usp16 knock out mouse embryonic stem cells (ESCs) and embryoid bodies (EBs)

2014-05-02 | GSE52899 | GEO

Usp16

Project description:Usp16

| PRJNA265376 | ENA

Analysis of gene deletion induced changes in the transcriptome of human macrophage-like cells

Project description:To study the effect of genes that interface inflammatory and metabolic signaling, CRISPR/Cas9 has been used to delete CD5L and RORA in THP-1 human monocytic cell line. Cells transduced with sgRNAs targeting Renilla luciferase gene were used as controls. Deletion and control lines were differentiated with PMA and allowed to rest for 24 hours prior to isolation of total RNA.

2018-12-17 | E-MTAB-7295 | biostudies-arrayexpress

Usp16 WT and KO RNA-Seq ckit and sca1 positive cells

Project description:RNA-seq in wt and Usp16 deleted HSC/P

2015-12-30 | GSE62824 | GEO

Usp16 deletion-induced gene expression in MEFs

Project description:To determine the molecular signaling pathways responsible for USP16 regulation of cell growth, RNA sequencing was conducted on MEFs with or without Usp16 deletion

2021-07-20 | GSE160485 | GEO

ChIP-seq of CSF-1R in THP-1 cell lines deleted for EGR1 gene by CRISPR-Cas9 and ChIP-seq of CSF-1R in 2 CMML patients

Project description:CSF-1R is recruited on EGR1 motifs in monocytes where it colocalizes with EGR1. To address if EGR1 required for CSF-1R recruitment on chromatin, THP-1 monocytic cell line has been deleted for EGR1 by CRISPR-Cas9 approach. 3 clones were generated by single cell cloning and CSF-1R localization on chromatin was compared to two unmodified THP-1 clones by ChIP-sequencing. Since the read number was strongly decreased in the EGR1-deleted clones, the three clones were pooled for the comparison with wild-type clones. ChIPseq of CSF-1R (Nter Antibody) in monocytes of two CMML patients (CMML2130 and CMML2609)

2019-03-28 | E-MTAB-7756 | biostudies-arrayexpress

USP16 knockdown-induced gene expression in NCI-H23 cells

Project description:To determine the molecular signaling pathways responsible for USP16 regulation of cell growth, RNA sequencing was conducted on NCI-H23 cells with or without USP16 knockdown

2021-07-20 | GSE160388 | GEO

USP16-mediated Histone H2A Lysine-119 Deubiquitination during Oocyte Maturation is a Prerequisite for Zygotic Genome Activation

Project description:Maternal-to-zygotic transition (MZT) is the first and key step in the control of animal development and is intimately related to changes of chromatin structure and histone modifications. Mono-ubiquitination of histone H2A at lysine-119 (H2AK119ub1), an important epigenetic modification in regulating chromatin configuration and function, is primarily catalyzed by polycomb repressive complex 1 (PRC1) and contributes to resistance to transcriptional reprogramming in mouse embryos. In this study, the genome-wide dynamic distribution of H2AK119ub1 during MZT in mice was investigated by chromosome immunoprecipitation and sequencing. The results indicated that H2AK119ub1 accumulated in fully grown oocytes, enriched at the transcriptional start sequences (TSSs) of maternal genes, but was promptly removed after meiotic resumption, particularly at the TSSs of early zygotic genes, by a previously unidentified mechanism. Genetic evidences indicated that ubiquitin-specific peptidase 16 (USP16) is the major deubiquitinase of H2AK119ub1 in mouse oocytes. Conditional knockout of Usp16 in oocytes did not impair their survival, growth, andor meiotic maturation. However, oocytes lacking USP16 were unable to undergo zygotic genome activation or gain developmental competence after fertilization, due to high levels of H2AK119ub1 deposition on the zygotic genomes. Taken together, this study indicates that H2AK119ub1 is erased during oocyte maturation by an USP16-dependent mechanism, which ensures zygotic genome reprogramming and transcriptional activation of essential early zygotic genes.

2022-06-05 | GSE154412 | GEO

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