Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

Abstract

The proneural transcription factor Ascl1 coordinates gene expression in both proliferating and differentiating progenitors along the neuronal lineage. Here, we used a cellular model of neurogenesis to investigate how Ascl1 interacts with the chromatin landscape to regulate gene expression when promoting neuronal differentiation. We find that Ascl1 binding occurs mostly at distal enhancers and is associated with activation of gene transcription. Surprisingly, the accessibility of Ascl1 to its binding sites in neural stem/progenitor cells remains largely unchanged throughout their differentiation, as Ascl1 targets regions of both readily accessible and closed chromatin in proliferating cells. Moreover, binding of Ascl1 often precedes an increase in chromatin accessibility and the appearance of new regions of open chromatin, associated with de novo gene expression during differentiation. Our results reveal a function of Ascl1 in promoting chromatin accessibility during neurogenesis, linking the chromatin landscape at Ascl1 target regions with the temporal progression of its transcriptional program.

Graphical abstract

Figure 1

A Cellular Model of Neurogenesis Driven by Ascl1 (A) Cellular localization of Ascl1-ERT2 in NS5 cells before and 30 min after the addition of tamoxifen, as assessed by immunostaining against HA-tag (green). White arrowheads mark cytoplasmic expression in the absence of tamoxifen. Cell nuclei are labeled with DAPI (blue). Scale bar represents 30 μm. (B) Quantification of total Ascl1 protein levels in E14.4 ventral telencephalic progenitors (left) or NS5 Ascl1-ERT2 cells (right). Histograms show absolute fluorescence intensity after normalization (see Experimental Procedures for details). (C) State of differentiation of NS5 Ascl1-ERT2 cells in the presence or absence of tamoxifen 3 days after induction of differentiation, as assessed by the expression of the neuronal marker TUJ1 (red). Cell nuclei are labeled with DAPI (blue). Scale bar represents 200 μm. (D) Expression of Gad65/67 (red) in NS5 Ascl1-ERT2 cells 4 days after induction of differentiation. Cell nuclei are labeled with DAPI (blue). Scale bar represents 200 μm. (E) Electrophysiological properties of GFP-labeled neurons generated from NS5 Ascl1-ERT2 cells 14 days upon induction of differentiation. Representative responses of two neurons to step-current injection at a holding potential of −70mV in current-clamp mode. Note the brief burst of action potentials on top of a prolonged calcium spike following depolarization (red traces) and the rebound burst following release from hyperpolarization (black trace). Scale bar represents 200 μm. (F) Experiment design for the transcriptome analysis and the resulting number of deregulated genes determined at different time points after induction of differentiation (fold change > 1.2, p < 10⁻³). (G) Enrichment of Gene Ontology biological process terms among genes deregulated during neuronal differentiation. Total number of genes associated with each term is in brackets. See also Figure S1.

Figure 2

Genome-wide Mapping of Ascl1 Binding Sites in Differentiating NS Cells (A) Location of Ascl1 BEs respective to various genomic features. (B) Location of Ascl1 BEs in relation to the closest annotated TSS. (C) Chromatin state in differentiating NS cells, at Ascl1 bound regions in the vicinity of Fbxw7, Olig2, and Dll3 genes. (D) Heat maps of chromatin states for H3K27ac and H3K4me1 within ±2 kb of Ascl1-ERT2 peak summits in proliferating or differentiating NS cells (before and 24 hr after the addition of tamoxifen, respectively). (E) DNA motif enrichment for Ascl1 E-box within a 20-bp region centered at Ascl1 peak summits (R, enrichment over local genomic background; S, motif score). See also Figure S2.

Figure 3

Ascl1 Functions as a Transcriptional Activator at a Genome-wide Level (A) Cumulative fraction of Ascl1 BEs considered regulatory by association with upregulated or downregulated genes following a nearest gene annotation. The dashed line marks the most stringent cutoff (p < 10⁻²⁵) for peak enrichment and defines a list of BEs with the highest regulatory potential (n = 8,624, 2.5 times over control). (B) Heat map displaying the cumulative fraction of deregulated genes 12 hr after induction of differentiation that is directly regulated by Ascl1 (up, top left panel; down, bottom left panel). Transcripts are divided in equal bins of decreasing expression fold change and plotted against Ascl1 BEs (bin = 166) with increasing p value. Control: 100 sets of random BEs (right, mean value shown). (C) Heat maps displaying the cumulative fraction of upregulated genes at 4, 12, 24, and 50 hr after induction of differentiation, defined as in (B). (D) Association of Ascl1 BEs to each gene cluster. The red (activation) or blue (repression) bar represents the number of high-confidence Ascl1 BEs (p < 10⁻²⁵) annotated to genes belonging to each cluster and is juxtaposed to the distribution of Ascl1 binding annotations, which can be found in 1,000 different random clusters of genes. Test data represented as box with median of test and first and third quartiles; whiskers, ±1.5 × innerquartile range (IQR). See also Figures S3–S5.

Figure 4

Ascl1 Accessibility to Its Target Sites Remains Similar throughout Differentiation (A) Visual representation of ChIP-seq profiles at t = 30 min (blue) and t = 18 hr (red) in a large genomic region centered on Dll3 gene. (B) Comparison of Ascl1 BEs at t = 30 min and t = 18 hr (p < 10⁻¹⁰) by cumulative bins of increasing p value (bin = 1,007). The proportion of sites bound by Ascl1 in both conditions (overlapping peaks) is calculated in relation to the condition with the lowest number of BEs. Dashed lines represent higher confidence lists defined by p < 10⁻¹⁸, analyzed in (C). (C) Density plot of Ascl1 ChIP-seq reads mapping to the genomic regions surrounding the summit of Ascl1 BEs. The signal intensity represents the Ascl1 ChIP-seq normalized tag count in the 4kb region surrounding the summit of each overlapping (top) and nonoverlapping peak at t = 30 min (blue) and t = 18 hr (red).

Figure 5

Characterization of Changes in Chromatin Accessibility during Differentiation of NS Cells (A) Number of DHSs in proliferating NS cells and 24 hr upon Ascl1-mediated differentiation. (B) FAIRE-PCR validation of differentiation-induced DHSs. Bars show fold enrichment of genomic DNA obtained from NS cells 24 hr after induction over cells prior to addition of tamoxifen. Data are represented as mean ± SD. (C) Differentiation-induced DHSs are significantly associated with clusters of activated genes (left) and not with clusters of repressed genes (right). Red bars, total number of DHSs annotated to each set of genes; boxplots, distribution of DHSs associations with 1,000 random sets of genes. Test data are represented as box with median of test and first and third quartiles; whiskers, ±1.5 × IQR. (D) Activated genes associated with differentiation-induced DHSs have low or no expression in proliferating cells. Gene expression levels in proliferating cells are significantly lower (p < 10⁻¹¹, Wilcoxon test) for activated genes associated with induced DHSs (right) than for activated genes with no such association (left). Red bar, level of expression of NeuroD4 gene. Data distribution represented as box with median and first and third quartiles; whiskers, ±1.5 × IQR; notches, ±1.58 × IQR/n^1/2). (E) Frequency of motif occurrence at high occupancy sites found within differentiation-induced DHSs by Digital Genomic Footprinting (overrepresentation ratio indicated between brackets). (F) Comparison of Ascl1 BEs at t = 30 min (left) or t = 18 hr (right) with the DNase-seq profile. Color shows the proportion of Ascl1 BEs by cumulative bins of increasing p value (bin = 1,842), which fall within regions of open chromatin (DHSs) in proliferating (top) or differentiating (bottom) NS cells.

Figure 6

Ascl1 Binds Closed Chromatin and Promotes Chromatin Accessibility (A) Visual representation of ChIP-seq and DNase-seq enrichment profiles in the vicinity of various Ascl1 targets. Examples are shown of differentiation-induced and constant DHSs localized at Ascl1 binding sites (green and red arrows, respectively) and DHSs with no apparent association with Ascl1 binding (blue arrows). (B) Induction of expression of genes upon Ascl1-induced differentiation as quantified by real-time PCR. Data are represented as mean ± SD. (C) FAIRE-PCR validation of differentiation-induced DHSs at Ascl1 binding sites (green arrows in A). Bars show quantification of genomic DNA obtained from proliferating and differentiating NS cells (before and 24 hr after induction, respectively). Data are represented as mean ± SD. (D) DNase-seq signal profile at genome-wide Ascl1 BEs at t = 30 min (top left) or restricted to BEs falling within differentiation-induced DHSs (top right). Profile determined as the median read count of DNase-seq reads mapped to the 4-kb regions centered at the peak summits in proliferating (blue) and differentiating cells (red). (Bottom) Corresponding fold change for the median profiles. (E) Ascl1 BEs located at differentiation-induced DHSs are significantly associated with clusters of activated genes (left) and not with clusters of repressed genes (right). Red bars, total number of Ascl1 BEs annotated to each set of genes; boxplots, distribution of Ascl1 BEs associations with 1,000 random sets of genes. Test data represented as box with median of test and first and third quartiles; whiskers, ±1.5 × IQR. See also Figure S6. (F) In vivo binding of Ascl1 to the NeuroD4 regulatory region assessed by ChIP-PCR using chromatin extracted from mouse ventral telencephalon. Data are represented as mean ± SD. (G) Chromatin structure analysis by FAIRE-PCR of NeuroD4 and Dll1 regulatory regions bound by Ascl1, in mouse ventral telencephalon. Data are represented as mean ± SD.