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Chromatin profiling in HT22 hippocampal cells

ABSTRACT: Chromatin profiling in HT22 hippocampal cells

PROVIDER: PRJNA521221 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8539805_1.fastq.gz	Fastqsanger.gz
	SRR8539805_2.fastq.gz	Fastqsanger.gz
	SRR8539806_1.fastq.gz	Fastqsanger.gz
	SRR8539806_2.fastq.gz	Fastqsanger.gz
	SRR8539807_1.fastq.gz	Fastqsanger.gz

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Chromatin Immunoprecipitation analysis of mouse hippocampal neuron HT22 cells

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Project description:Krüppel-like factors (KLFs) play key roles in nervous system development and function. Several KLFs are known to promote, and then maintain neural cell differentiation. Our previous work focused on the actions of KLF9 in mouse hippocampal neurons. Here we investigated genomic targets and functions of KLF9’s paralog KLF13, with the goal of understanding how these two closely related transcription factors influence hippocampal cell function, proliferation, survival and regeneration. We engineered the adult mouse hippocampus-derived cell line HT22 to control Klf13 expression with doxycycline. We also generated HT22 Klf13 knock out cells, and we analyzed primary hippocampal cells from wild type and Klf13-/- mice. RNA sequencing showed that KLF13, like KLF9, acts predominantly as a transcriptional repressor in hippocampal neurons and can regulate other Klf genes. Pathway analysis revealed that genes regulated by KLF13 are involved in cell cycle, cell survival, cytoarchitecture regulation, among others. Chromatin-streptavidin sequencing conducted on chromatin isolated from HT22 cells expressing biotinylated KLF13 identified 9506 genomic targets; 79% were located 1 kilobase upstream of transcription start sites. Transfection-reporter assays confirmed that KLF13 can directly regulate transcriptional activity of its target genes. Comparison of the target genes of KLF9 and KLF13 found that they share some functions that were likely present in their common ancestor, but have also acquired distinct functions during evolution. Flow cytometry showed that KLF13 promotes cell cycle progression, and it protects cells from glutamate-induced excitotoxic damage. Taken together, our findings establish novel roles and molecular mechanisms for KLF13 actions in mammalian hippocampal neurons.

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