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LSD1 regulates the plasmablast transcriptome

ABSTRACT: LSD1 regulates the plasmablast transcriptome

PROVIDER: PRJNA546438 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9202240_1.fastq.gz	Fastqsanger.gz
	SRR9202240_2.fastq.gz	Fastqsanger.gz
	SRR9202250_1.fastq.gz	Fastqsanger.gz
	SRR9202250_2.fastq.gz	Fastqsanger.gz
	SRR9202260_1.fastq.gz	Fastqsanger.gz

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LSD1 regulates the plasmablast transcriptome

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Project description:Transcriptome analysis of LSD1-depleted HepG2 cells revealed that LSD1 regulates the expression of glycolytic and mitochondrial metabolism genes. We found that LSD1 is an important regulator of glycolysis and mitochondrial respiration in hepatoma. We depleted LSD1 in HepG2 human hepatoma cells using two different siRNAs, and then carried out an expression microarray experiment.

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The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation [Affymetrix]

Project description:During brain development, histone-modifying enzymes play an important role by orchestrating transcriptional programs that regulate neuronal maturation. Lysine-Specific Demethylase 1 (LSD1, also named as KDM1A) functions as a transcriptional repressor by removing methyl groups at lysine 4 of histone H3 (H3K4). In neurons, alternative splicing can include an additional exon (exon E8a) within LSD1 transcripts, generating a LSD1+8a neuro-specific isoform. We here report that LSD1+8a isoform does not have the intrinsic ability to demethylate H3K4. LSD1+8a functions as a co-activator on its target genes by removing H3K9 repressive histone marks. We identify the supervillin protein (SVIL) as a LSD1+8a interacting partner and demonstrate that SVIL protein regulates neuronal maturation by controlling LSD1+8a mediated H3K9 demethylation. Thus, our results show that alternative splicing provides a genius mechanism by which LSD1 isoforms can acquire a dual specificity (H3K9 vs H3K4) and therefore differentially control specific gene expression patterns during brain development. In order to find some LSD1+8a regulated genes at differentiated SH-SY5Y cell lines, we infected SH-SY5Y with control or LSD1+8a shRNA, then induced differentiation with RA and BDNF, (Retinoic acid (RA) (Sigma) was added at a final concentration of 10 μM the next day after plating. After 4 days, the cells were washed three times with PBS and incubated with 50 ng/mL of Brain Derived Neural Factor (BDNF) (Millipore) in serum-free medium for 3 days), we extracted RNA from BDNF induced SH-SY5Y cells for expression analysis.Duplicates were included for Affymetrix Human transcriptome version 2 array.

2015-06-05 | E-GEOD-63097 | biostudies-arrayexpress

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