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Series GSE211309 Query DataSets for GSE211309
Status Public on Mar 01, 2023
Title Bioinformatic Investigation of the Zic1/2 binding reveals novel co-factors in Zic-mediated gene regulation in the cerebellum
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The family of Zic transcription factors (TFs) are required for cerebellar development, and their binding is highly enriched at developmentally regulated enhancers active in cerebellar granule neurons at the progenitor stage around postnatal day 7 (P7) and the mature adult stage at P60 in the mouse cerebellum. Interestingly, Zic1/2 ChIP-seq data reveal that the Zics change their binding profile over time. To characterize these differences in Zic targeting between early and late cerebellar maturation, we compared the sequence underlying Zic Peaks, their relationship with active chromatin and gene expression at P7 and P60. From this we found Zic peaks tend to be large and bind open-active chromatin. Strikingly, Zic peaks shift from binding at promoter proximal regions at P7 to distal enhancer regions at P60. We hypothesize that other TFs collaborate with the Zic TFs to change their binding targets and affect their regulatory activity. A multi-tiered approach was used to predict TF binding at those Zic ChIP sites. We assessed motif enrichment (HOMER) and in-vivo TF binding profiles (BART) to determine putative TFs collaborating with Zic to drive this regulation. We then validated the presence of the predicted TFs in granule neurons using gene expression. This workflow identified known and novel distinct collaborators of Zic between early and late development. Early collaborates of Zic includes bHLH factors and chromatin remodelers whereas late collaborators of Zic are activity regulated TFs which are markers of synaptic maturation. To identify Zic’s developmental gene targets in cerebellar maturation, we used H3K4me3 PLAC-seq data, which captures promoter-enhancer loops from the adult mouse cerebellum and Hi-C data from the young mouse cerebellum to map genes to Zic bound enhancers. This revealed Zic as a transcriptional activator of late developmental genes in the cerebellum. Using this same approach with in vitro Zic KD, we were able to identify Zic dependent developmental gene targets which have functions in axonogenesis, axon guidance, and ion channel signaling, which are integral in proper maturation of a neuron. These integrated analyses reveal how Zic and other TFs regulate temporal expression of CGN developmental genes and provides information that will enhance our understanding of the molecular mechanisms that regulate the mode of TF function at enhancers.
 
Overall design Zic1/2 CUT&RUN-seq performed on cerebellar granule neurons harvested after 1, 3, 5 and 7 days in vitro. (n=3 biological replicates)
 
Contributor(s) Minto M, Sotelo-Fonseca J, Ramesh V, West AE
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Submission date Aug 15, 2022
Last update date Mar 04, 2023
Contact name Anne E West
E-mail(s) west@neuro.duke.edu
Organization name Duke University
Department Neurobiology
Lab West Lab
Street address 311 Research Dr
City Durham
State/province NC
ZIP/Postal code 27705
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM6465772 CGN, DIV1, Zic, CUT&RUN, Rep 1
GSM6465773 CGN, DIV1, Zic, CUT&RUN, Rep 2
GSM6465774 CGN, DIV1, Zic, CUT&RUN, Rep 3
Relations
BioProject PRJNA869747

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE211309_RAW.tar 15.1 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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