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The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes

ABSTRACT: The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes

PROVIDER: PRJNA603329 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10970170_1.fastq.gz	Fastqsanger.gz
	SRR10970170_2.fastq.gz	Fastqsanger.gz
	SRR10970171_1.fastq.gz	Fastqsanger.gz
	SRR10970171_2.fastq.gz	Fastqsanger.gz
	SRR10970172_1.fastq.gz	Fastqsanger.gz

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The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes

Project description:Epigenetic regulation is important for establishing lineage-specific gene expression during early development. Although signaling pathways have been well-studied for regulation of trophectoderm reprogramming, epigenetic regulation of trophectodermal genes with histone modification dynamics have been poorly understood. Here, we identify that plant homeodomain finger protein 6 (PHF6) is a key epigenetic regulator for activation of trophectodermal genes using RNA-sequencing and ChIP assays. PHF6 acts as an E3 ubiquitin ligase for ubiquitination of H2BK120 (H2BK120ub) via its extended plant homeodomain 1 (PHD1), while the extended PHD2 of PHF6 recognizes acetylation of H2BK12 (H2BK12Ac). Intriguingly, the recognition of H2BK12Ac by PHF6 is important for exerting its E3 ubiquitin ligase activity for H2BK120ub. Together, our data provide evidence that PHF6 is crucial for epigenetic regulation of trophectodermal gene expression by linking H2BK12Ac to H2BK120ub modification.

2020-07-13 | GSE144298 | GEO

The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes.

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BRCT phosphoprotein recognition, but not E3 ligase activity, is essential for BRCA1 tumor suppression

Project description:It has been recognized that BRCA1, in the form of the BRCA1/BARD1 heterodimer, acting as an ubiquitin E3 ligase offered a possible mechanism to explain its pleiotrophic nature of BRCA1 activity. Our observation that mice lacking BRCA1 enzymatic activity are viable apart from male sterility was unexpected. Our results suggest that the E3 ligase activity of BRCA1 is largely dispensable for normal development and is not essential for all BRCA1 functions. Thus, many of the known and unknown functions of BRCA1 are likely to be mediated independent of its ability to catalyze ubiquitination. The genome copy number patterns were studied on the mice tumors that lacks E3 ubiqitin ligase activity of BRCA1 and were compared to copy number profile of mice lacking p53 and both brca1 and p53. Array CGH was performed using Agilent mouse CGH microarray 244K kit. Genomic DNA isolated from tumor tissue and its corresponding mouse tail were labelled with two different dyes and hybridized simultaneously on to microarray slides to perform comparitive genomic hybridization.

2011-08-25 | E-GEOD-31673 | biostudies-arrayexpress

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation

Project description:MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that down-regulate target RNAs, including messenger RNAs from most human genes. Within each complex, the miRNA pairs to target RNAs, and AGO provides effector function while also protecting the miRNA from cellular nucleases. Although much is known about miRNA-directed gene regulation, less is known about how miRNAs themselves are regulated. One pathway that regulates miRNAs involves unusual targets called ‘trigger’ RNAs, which reverse the canonical regulatory logic and instead down-regulate miRNAs. This target-directed miRNA degradation (TDMD) is thought to require a cullin–RING E3 ligase because it depends on the cullin protein CUL3 and other ubiquitylation components, including the BC-box protein ZSWIM8. ZSWIM8 is required for murine perinatal viability and for destabilization of most short-lived miRNAs, which suggests biological importance of TDMD. Here, biochemical and cellular assays establish AGO binding and polyubiquitylation by the ZSWIM8–CUL3 E3 ligase as the key regulatory steps of TDMD, and thereby define a unique cullin–RING E3 ligase class. Cryogenic electron microscopy analyses show ZSWIM8 recognizing distinct AGO and RNA conformations shaped by pairing of the miRNA to the trigger. Specificity of AGO ubiquitylation is established through generalizable RNA–RNA, RNA–protein and protein–protein interactions. The substrate features recognized by the E3 ligase do not conform to a conventional degron but instead establish a two-RNA-factor authentication mechanism for specifying a protein ubiquitylation substrate.

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UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer

Project description:UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer

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UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [RNA-Seq]

Project description:Plant Homeo Domain (PHD) is a versatile chromatin reader/effector module which recognizes methylated, acetylated or unmodified histone substrates and regulates cellular gene expression programs. Although PHD domains shows selective epigenetic recognition of methylated, acetylated and unmodified histone substrates, there has been no previous report on its catalytic function regulating malignant transformation of cells. Here we report that PHD finger of UBR7 (Ubiquitin Protein Ligase E3 Component N-Recognin 7 (Putative)), in isolation or in context of full length protein, harbors E3 ubiquitin ligase activity towards monoubiquitination of histone H2B at lysine 120 . Knockdown of UBR7 in MCF10a and breast cancer cells decreased H2BK120ub both at the global levels and on specific genes. Conversely, overexpression of wild type, but not catalytic mutant, rescued H2BK120ub levels. Low UBR7 expression was associated with basal-like and triple negative breast cancers as well as showed poor expression in metastatic tumors. Consistently, UBR7 loss resulted in invasion properties, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 reduced cell growth, invasion and tumor growth in mouse fat pad. Mechanistically, UBR7 reduced H2BK120ub gene body of cell-adhesion related genes as well as gene expression including on CDH4 gene. Importantly, rebuilding CDH4 levels rescued invasion phenotypes seen in UBR7-low cells. Collectively, our results establish that UBR7 PHD has novel H2B ubiquitin ligase activity and it suppresses tumor growth in basal-like breast cancers.

2019-02-08 | GSE93758 | GEO

UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [ChIP-Seq]

2019-02-08 | GSE93757 | GEO

BRCT phosphoprotein recognition, but not E3 ligase activity, is essential for BRCA1 tumor suppression

2011-08-26 | GSE31673 | GEO

The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation

Project description:The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation

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Regulation of metablism by mitochondrial MUL1 E3 ubiquitin ligase

Project description:Regulation of metablism by mitochondrial MUL1 E3 ubiquitin ligase

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