Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity
- Department of Neurosciences, Case Western Reserve University, United States
Figures
Figure 1 with 1 supplement
Unique distal enhancers and super-enhancers define the Pet1 lineage.
(a) Principal component analysis (PCA) reveals the unique accessible chromatin landscape of Pet1 neurons. Dots of the same color represent biological replicates. (b) Bar plot showing percentage of …
Figure 1—figure supplement 1
ATAC-seq quality control and analysis.
(a) FACS plots of collecting Yfp-positive neurons (Pet1 neurons) collected from dissociated E14.5 mouse hindbrain cells using forward vs. side-scattered light gating followed by removal of cell …
Figure 2 with 2 supplements
Heterogeneity in chromatin accessibility and transcriptomes reveals transcriptional programs determining Pet1 neuron subtype identities.
(a) Venn diagram showing overlap of single-cell Pet1 neuron TACs vs. bulk ATAC-seq TACs. (b) Genome browser view of Pet1 locus showing high concordance between the pseudobulk scATAC-seq and bulk …
Figure 2—figure supplement 1
Identification of Pet1 neuron subtype-specific TACs.
(a) scATAC-seq quality metrics showing the distribution of percent of reads in peaks, number of fragments, transcriptional start site enrichment, blacklist ratio, and nucleosome signal per cell. (b) …
Figure 2—figure supplement 2
Pet1 neuron subtype-specific TF activity, expression, and accessibility.
(a) Transposase accessible chromatins (TACs) associated with Lmx1b. Loops represent statistically significant TAC-gene association. Loop height represents the p-value of TAC-gene correlation. (b) …
Figure 3 with 1 supplement
Gene regulatory dynamics in maturing Pet1 neurons.
(a) PCA showing the distribution of Pet1 neuron ATAC-seq data over two principal components. (b) Distribution of chromatin states that exhibit gain (green), loss (red), or no change (blue) in …
Figure 3—figure supplement 1
Dynamic developmental remodeling of distal cis-regulatory elements.
(a) ATAC-seq quality metrics showing the distribution of total reads (left) and usable reads after filtering for mapping quality and PCR duplicates (right) for each developmental time point. (b) …
Figure 4 with 1 supplement
Pet1 reorganizes postmitotic chromatin accessibility.
(a) PCA showing the distribution of ATAC-seq data for wildtype and Pet1-/- Pet1-lineage neurons (Pet1-/- neurons) over two principal components. (b) In vivo Pet1 footprints derived from Tn5 …
Figure 4—figure supplement 1
Related to Figures 4 and 5: Pet1 is required for chromatin accessibility at Pet1 neuron-specific TACs.
(a) Motif enrichment within Pet1 neuron-specific TACs using the Bioconductor package monaLisa. Similar motif hits are combined and assigned to their closest match of a TF class or family. (b) …
Figure 5
Sustained Pet1 input is required for chromatin accessibility.
(a) Top: Volcano plot showing the differential chromatin accessibility of TACs between Pet1-cKO and wildtype Pet1 neurons, with fold change cutoff of 2-fold and significance cutoff of FDR < 0.01 (in …
Figure 6 with 1 supplement
Lmx1b co-regulates chromatin accessibility with Pet1 at 5-HT neurotransmission genes but has broader impact on accessibility landscape.
(a) PCA showing the distribution of wildtype, Pet1-/-, Pet1-cKO, Lmx1b-cKO, and DKO neuron ATAC-seq data over two principal components. (b) Comparison of in vivo Lmx1b footprints over representative …
Figure 6—figure supplement 1
Pet1 and Lmx1b control the global landscape of TF binding sites.
(a) Distribution of gene features for E14.5 Pet1 and Lmx1b CUT&RUN peaks using either ‘stringent’ or ‘relaxed’ peak calling parameters (Meers et al., 2019).(b) Top: overlap of Pet1 and Lmx1b CUT&RUN …
Figure 7 with 1 supplement
Loss of Pet1 and Lmx1b alters chromatin accessibility at synaptic gene enhancers and disrupts 5-HT neuron connectivity.
(a) GO analysis of all Pet1- and/or Lmx1b-maintained TACs identified from E14.5 DKO ATAC-seq datasets, depicted as volcano plot of enrichment (x-axis) vs. FDR statistical significance (y-axis), …
Figure 7—figure supplement 1
Pet1 and Lmx1b control chromatin access to synapse and axon gene linked TACs.
(a) Top gene ontology terms for the differentially accessible TACs in Pet1-cKO (top), Lmx1b-cKO (middle), and DKO Pet1 neurons (bottom) ranked by fold enrichment. (b) Left: volcano plot for E17.5 …
Author response image 1
Additional files
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Transparent reporting form
- https://cdn.elifesciences.org/articles/75970/elife-75970-transrepform1-v2.docx
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Source data 1
TAC-gene predictions.
- https://cdn.elifesciences.org/articles/75970/elife-75970-data1-v2.csv
