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ChIP-seq on Zfp961 GFP flox/flox mESCs to verify Zfp961 binding capacity at PBS-Lys elements.

ABSTRACT: We performed ChIP-seq assay with anti-GFP antibodies on Zfp961-GFPflox/flox ESCs.We found PBS-Lys-containing endogenous virus K subgroup repeats (ERV-K) were significantly enriched in the strong peak regions (40%, 165 out of 413), compared to their abundance in the mouse genome (~5%), suggesting Zfp961 binding preference towards ERV-K regions. And Zfp961 has a PBS-Lys motif. We performed H3K9me3 ChIP on Zfp961 WT or KO mESCs. We found that Zfp961 recruits H3k9me3 modification at ERVKs, and H3K9me3 level showed a moderate decrease upon Zfp961 deletion.

ORGANISM(S): Mus musculus

PROVIDER: GSE156599 | GEO | 2022/02/10

REPOSITORIES: GEO

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Project description:In order to elucidate transcriptional and metabolic networks associated with Lys metabolism, we utilized developing seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism. This seed-specific metabolic perturbation stimulated Lys accumulation starting from the initiation of storage reserve accumulation. Our results revealed that the response of seed metabolism to the inducible alteration of Lys metabolism was relatively minor, however, that which was observable operated in a modular manner. They also demonstrated that Lys metabolism is strongly associated with the operation of the TCA cycle, whilst largely disconnected from other metabolic networks. In contrast, the inducible alteration of Lys metabolism was strongly associated with gene networks, stimulating the expression of hundreds of genes controlling anabolic processes that are associated with plant performance and vigor, whilst suppressing a small number of genes associated with plant stress interactions. The most pronounced effect of the developmentally-inducible alteration of Lys metabolism was an induction of expression of a large set of genes encoding ribosomal proteins as well as genes encoding translation initiation and elongation factors, all of which are associated with protein synthesis. With respect to metabolic regulation, the inducible alteration of Lys metabolism was primarily associated with altered expression of genes belonging to networks of amino acids and sugar metabolism. The combined data are discussed within the context of network interactions both between and within metabolic and transcriptional control systems. Experiment Overall Design: Arabidopsis thaliana (WS) seeds of the WT and KD genotype (Zhu and Galili, 2003)were germinated on soil and grown in the greenhouse (23oC). Flowers were marked and at given time intervals following flowering (14DAF to Dry ). Maturing siliques were collected, then seeds were dissected from siliques . Mature seeds were collected at the end of the desiccation period and stored at 4ºC. Two repeats were collected from each time point. Three to five thousands seeds were harvested for each extraction.

Dataset Information

ChIP-seq on Zfp961 GFP flox/flox mESCs to verify Zfp961 binding capacity at PBS-Lys elements.

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