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Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

ABSTRACT: We examined the chromatin occupancy of ZNF410 by conducting CUT&RUN. We used an HA antibody to probe for epitope tagged ZNF410 in HUDEP-2 cells. We used a ZNF410 antibody to probe for endogenous ZNF410 in HUDEP-2 cells, human CD34+ hematopoietic stem and progenitor cell (HSPC) derived erythroid precursors and mouse erythroleukemia (MEL) cells.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE166221 | GEO | 2021/02/05

REPOSITORIES: GEO

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Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

Project description:Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

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Gene expression profiling of HUDEP-2 cells edited with either ZNF410 targeting or control sgRNA

Project description:RNA sequencing was performed of HUDEP-2 cells edited at either ZNF410 or AAVS1 (control locus) to measure gene expression changes due to loss of ZNF410 expression. CHD4 was the most significantly downregulated gene upon ZNF410 editing. We observed that ZNF410 binds to DNA upstream of the CHD4 gene. To test the requirement of ZNF410 binding for CHD4 expression we generated a HUDEP-2 clone in which this region of ZNF410 binding was deleted (CHD4 6.7 kb element deletion clone). We performed RNA-seq of CHD4 6.7 kb element deleted HUDEP-2 cells after either ZNF410 or AAVS1 (control locus) editing and only observed 2 differentially expressed genes after ZNF410 editing in CHD4 6.7 kb element deletion cells, consistent with our results that nearly all gene expression changes found after ZNF410 editing are due to changes in CHD4 expression.

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shRNA profiling of mouse erythroleukemia (MEL) cells and their corresponding G9a knock downs reveals a dual role for the methyltransferase G9a in the maintenance of beta-globin gene expression

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