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Series GSE58258 Query DataSets for GSE58258
Status Public on Jun 05, 2015
Title The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design Examination of 2 different LSD1 isoforms LSD1 and LSD1+8a, LSD1+8a's cofactor SVIL, H3K9me2 in SH-SY5Y cells infected with control or LSD1+8a shRNA during neuronal maturation induced with BNDF at Day0(B0) and Day3(B3).ChIP-seq datas were generated by deep sequencer Hiseq2500.
Contributor(s) Shi Y, Laurent B, Ruitu L
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Submission date Jun 05, 2014
Last update date May 15, 2019
Contact name Ruitu Lyu
Organization name Institutes of Biomedical Sciences Fudan University
Lab Epigenetics lab
Street address 138 Yixueyuan Road Xuhui District
City Shanghai
ZIP/Postal code 200030
Country China
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (23)
GSM1542251 Sample_H3K9me2_Input_shLSD18a_B0_I18
GSM1542252 Sample_H3K9me2_Input_shLSD18a_B3_I20
GSM1542253 Sample_H3K9me2_Input_SH-SY5Y_B0_I17
This SubSeries is part of SuperSeries:
GSE63153 The LSD1/KDM1A neuro-specific isoform regulates neuronal differentiation through H3K9 demethylation
BioProject PRJNA251753
SRA SRP042983

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58258_RAW.tar 1.8 Gb (http)(custom) TAR (of BEDGRAPH)
GSE58258_Sample_LSD18a_SH-SY5Y_B3_vs_Input_peaks.txt.gz 65.5 Kb (ftp)(http) TXT
GSE58258_Sample_LSD1_SH-SY5Y_B0_vs_Input_peaks.txt.gz 316.8 Kb (ftp)(http) TXT
GSE58258_Sample_LSD1_SH-SY5Y_B3_vs_Input_peaks.txt.gz 401.8 Kb (ftp)(http) TXT
GSE58258_Sample_LSD1_shLSD18a_B0_vs_Input_peaks.txt.gz 193.6 Kb (ftp)(http) TXT
GSE58258_Sample_SVIL_SH-SY5Y_B3_vs_Input_peaks.txt.gz 27.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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