Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer
- Department of Neurobiology, University of Alabama at Birmingham, United States
- Civitan International Research Center, University of Alabama at Birmingham, United States
Figures
Figure 1 with 1 supplement
Characterization of temporally and functionally distinct activity-dependent gene expression programs in cultured striatal neurons.
(a) Experimental design. DIV11 cultures were depolarized for 1 or 4 hr with 10 mM KCl. Following treatment, RNA-seq libraries were constructed. (b, c) Volcano plots displaying gene expression …
Figure 1—figure supplement 1
Striatal neuron immediate early genes (IEGs) and late response genes (LRGs) are temporally and functionally distinct and are induced by a variety of stimuli.
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Figure 1—figure supplement 1—source data 1
RT-qPCR data.
- https://cdn.elifesciences.org/articles/89993/elife-89993-fig1-figsupp1-data1-v1.xlsx
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Figure 1—figure supplement 1—source data 2
RT-qPCR data.
- https://cdn.elifesciences.org/articles/89993/elife-89993-fig1-figsupp1-data2-v1.xlsx
Figure 2 with 1 supplement
Activity-dependent chromatin remodeling in cultured primary rat striatal neurons.
(a) DIV11 primary rat striatal neurons were treated with 10 mM KCl for 1 or 4 hr. Following treatment, ATAC-seq libraries were prepared. (b, c) Volcano plots displaying differentially accessible …
Figure 2—figure supplement 1
Transcription factor binding and histone modifications in 4 hr differentially accessible regions (DARs), random regions, and vehicle peaks.
Figure 3
Motifs for activity-dependent transcription factors are significantly enriched in 4 hr differentially accessible regions (DARs).
(a, b) Plots showing enrichment of specific transcription factor motifs in vehicle peaks and 4 hr DARs. Motifs with significant adjusted p-values and a percent enrichment greater than 50% are shown …
Figure 4 with 1 supplement
Activity-dependent chromatin remodeling requires protein translation.
(a) Experimental design. DIV11 primary rat striatal neurons were treated with Dimethyl Sulfoxide (DMSO) or anisomycin for 30 min followed by 4 hr of depolarization with 10 mM KCl. (b) Western blot …
Figure 4—figure supplement 1
Enhancers for Fos are open at baseline and do not undergo activity-dependent chromatin remodeling.
Figure 5 with 1 supplement
Transcriptional regulation of Pdyn mRNA.
(a) ATAC-seq tracks at the Pdyn gene locus of embryonic striatal neurons treated with DMSO + Vehicle, DMSO + KCl, or anisomycin + KCl. A differentially accessible region (DAR) 45 kb upstream of the P…
Figure 5—figure supplement 1
Predicted regulators of Pdyn and Scg2 in Drd1-MSNs.
Figure 6
CRISPR-based functional validation of a novel Pdyn enhancer.
(a) Viral strategy for functional validation of putative enhancers using CRISPR interference with dCas9-KRAB-MeCP2 and CRISPR activation with dCas9-VPR. (b) CRISPR sgRNAs (4×) were designed to …
Figure 7 with 1 supplement
Identification and validation of a conserved PDYN enhancer in the human genome.
(a) Experimental design for published RNA- and ATAC-seq datasets from human GABAergic and glutamatergic neurons treated with 55 mM KCl. (b, c) Volcano plots for human GABAergic neurons treated with …
Figure 7—figure supplement 1
Conserved activity-regulated PDYN differentially accessible region (DAR) is selective for GABAergic neurons.
Figure 8
Characterization of the rat Pdyn differentially accessible region (DAR) in the adult nucleus accumbens at single-cell resolution.
(a) Experimental design. (b) Uniform manifold approximation and projection (UMAP) of 10,085 nuclei from adult rat nucleus accumbens (NAc). (c) Genome tracks displaying snATAC-seq data at the Pdyn …
Additional files
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Supplementary file 1
Differential expression testing results for 1 and 4 hr timepoints.
- https://cdn.elifesciences.org/articles/89993/elife-89993-supp1-v1.xlsx
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Supplementary file 2
Molecular function gene ontology (GO) terms for 1 and 4 hr specific differentially expressed genes (DEGs).
- https://cdn.elifesciences.org/articles/89993/elife-89993-supp2-v1.xlsx
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Supplementary file 3
Differential accessibility testing results for 4 h timepoint.
- https://cdn.elifesciences.org/articles/89993/elife-89993-supp3-v1.xlsx
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Supplementary file 4
CRISPR sgRNA and RT-qPCR primer sequences.
- https://cdn.elifesciences.org/articles/89993/elife-89993-supp4-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/89993/elife-89993-mdarchecklist1-v1.pdf
