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Homo sapiens

ABSTRACT: ChIP-seq for Nanog in H9 hESC

PROVIDER: PRJNA297768 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2557580_1.fastq.gz	Fastqsanger.gz
	SRR2557580_2.fastq.gz	Fastqsanger.gz
	SRR2557581_1.fastq.gz	Fastqsanger.gz
	SRR2557581_2.fastq.gz	Fastqsanger.gz

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ChIP-seq for Nanog in H9 hESC

Project description:mapping Nanog TF binding sites in H9 hESC

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Project description:In our previous study, we uncovered that OGA significantly elevated in naïve hESC. Therefore, we sought to investigate the effects of O-GlcNAc on hESC and the interconvert of both pluripotent states. Depletion of OGA, which results in global O-GlcNAcylation increased, would impair naïve hESC pluripotency but can promote naïve to primed hESC transition. In addition, we obtained the profiles of O-GlcNAcylated proteins in H9 primed hESC and H9-PXGL hESC via MS based-quantitative proteomics.

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Project description:To assess the effects of SOX9 depletion on active chromatin marks in hESC-derived cranial neural crest cells, we performed genome editing of the H9 hESC lines to tag SOX9 with FKBPV36, V5, and mNeonGreen. Upon differentiating edited hESC to cranial neural crest cells using an established protocol, addition of the degrader molecule dTAGV-1 results in SOX9 depletion. We then profiled the active chromatin mark H3K27ac by ChIP-Seq in undepleted CNCCs or CNCCs in which SOX9 was depleted for 3h or 24h. We also titrated SOX9 to four distinct levels with dTAGV-1 and assessed SOX9 binding by V5 ChIP-seq, as well as TWIST1 and TFAP2A binding by ChIP-seq.

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Crystal structure of Homo sapiens kynureninase.

Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

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Homo sapiens strain:H9 hESC line

Project description:Homo sapiens strain:H9 hESC line Exome

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Homo sapiens whole blood.

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