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Series GSE244758 Query DataSets for GSE244758
Status Public on Jan 11, 2024
Title The Transcription factor NF-YA is Crucial for Neural Progenitor Maintenance during Brain Development
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.
Overall design E13.5 mouse brain cortices were fixed, lyzed and sonicated. The lysates (input) were subjected to chromatin immunoprecipitation (ChIP) using anti-NF-YC and anti-H3K4me3 antibodies. The DNA libraries of the input and two ChIP samples were generated by Takara ThruPLEX DNA-seq Kit, and sequenced by Illumina NextSeq 2000 using P1 regent (100 cycles).
Contributor(s) Yamanaka T, Nukina N
Citation(s) 38199563
Submission date Oct 05, 2023
Last update date Jan 12, 2024
Contact name Tomoyuki Yamanaka
Organization name Niigata University
Department Brain Research Institute
Lab Department of Neuroscience of Disease
Street address 1-757 Asahimachidori, Chuo-ku
City Niigata
ZIP/Postal code 951-8585
Country Japan
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (3)
GSM7829194 Input
GSM7829195 ChIP_NFYC
GSM7829196 ChIP_H3K4me3
BioProject PRJNA1024510

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Supplementary file Size Download File type/resource
GSE244758_230523-3_S3_uq_peaks.narrowPeak.gz 17.1 Kb (ftp)(http) NARROWPEAK
GSE244758_230523-4_S4_uq_peaks.narrowPeak.gz 517.2 Kb (ftp)(http) NARROWPEAK
GSE244758_RAW.tar 378.8 Mb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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