Dataset Information

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

ABSTRACT: To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance across postnatal stages of neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated, and verified, using H3K27ac ChIP-seq, reporter gene assays and CRISPR-mediated activation, that many of these regions function as neuronal enhancers. Motif discovery in differentially accessible chromatin regions suggested a previously unknown role for the Zic family of transcription factors in CGN maturation. We confirmed the association of Zic with these elements by ChIP-seq and found, using knockdown, that Zic1 and Zic2 are required for coordinating mature neuronal gene expression patterns. Together, our data reveal chromatin dynamics at thousands of gene regulatory elements that facilitate the gene expression patterns necessary for neuronal differentiation and function.

SUBMITTER: Frank CL

PROVIDER: S-EPMC4414887 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

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Publications

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

Frank Christopher L CL Liu Fang F Wijayatunge Ranjula R Song Lingyun L Biegler Matthew T MT Yang Marty G MG Vockley Christopher M CM Safi Alexias A Gersbach Charles A CA Crawford Gregory E GE West Anne E AE

Nature neuroscience 20150406 5

To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance across postnatal stages of neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated, and verified, using H3K27ac ChIP-seq, reporter g ...[more]

PMID: 25849986

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Project description: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.

Dataset Information

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

Publications

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.

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