Figure 4. Chromatin accessibility of cell types in the CNS.

(A) Schematic of CNS lineage progression indicating cell types examined in this study. (B) Example profiles resulting from Dam expression in the CNS. Genomic region encompassing Wnt2 and bruchpilot genes is shown. Multiple open chromatin regions are dynamic across development. Y-axes = reads per million (rpm). (C) Clustering of differentially accessible regions in CNS lineages indicates two major groupings in which chromatin is most accessible in either stem cells or mature neurons. (D) Motif analysis using these sequences results in identification of expected motifs (e.g. ase E-box motif in stem cell accessible loci), as well as novel motifs. Most highly enriched motifs for each cluster shown. All motifs E-values < 1 × 10⁻⁵. (E) log2 enrichment scores for selected GO terms in individual cell types. Clear trends can be seen as development progresses. (NSC, GMC, L3 neuron, adult neuron - from left to right). (i) GO terms are either enriched in stem cells becoming less significant as the lineage progresses or (ii) vice versa.

Figure 4—figure supplement 1. Chromatin accessibility in neural cell types demonstrating dynamic accessibility of R71C09 enhancer region - used to define GMC/immature neuron populations in this study.

(A) A clear peak can be identified within the R71C09 sequence which shows greatest accessibility in the GMCs and youngest populations of neurons in the lineage (arrow). (B) Schematic indicating cell types assayed in this study with GAL4 diver lines used to drive Dam expression. (C) Expression pattern of R71C09-GAL4/UAS-GFP in the larval CNS. GFP is most strongly detected in cells adjacent to the neuroblast (Dpn - Red). These cells include presumptive GMCs (Dpn negative, Elav negative), and immature neurons (Elav - Blue).

Figure 4—figure supplement 2. Example loci showing dynamic chromatin accessibility in neuronal cell-types.

Regions of open chromatin are enriched in progenitor cell types for (A) deadpan (dpn) (B) Cyclin E (CycE) (C) asense (ase), and (D) prospero (pros); whilst peaks of greater accessibility are apparent in differentiated neurons at the (E) neuronal Synaptobrevin (nSyb), and (F) Dopamine 1-like receptor 1 (Dop1R1) loci.

Figure 4—figure supplement 3. Top enriched motifs identified in regions of enhanced chromatin accessibility in neuronal cell types.

Top five enrched motifs are shown for each group, unless fewer than five total enriched motifs were identified. Predicted transcription factors binding to observed motifs are shown if detected.

Figure 4—figure supplement 4. Further motifs enriched in cell types of the nervous system.

Further examination of sub-clusters reveals novel motifs enriched in different cell types of neurogenesis. The ase-like motif (CAGCNG) described in Figure 4D is enriched specifically in the NSC-specific cluster but not for regions that are accessible in both NSC and GMCs/neurons.

Figure 4—figure supplement 5. Top enriched GO terms for cell types of the CNS.