Figure 5

Application of sci-ATAC-seq to npas4l embryos reveals unexpected cell-type-specific regulation

(A) Representative images of npas4l wild-type/heterozygous and homozygous mutants at 24 hpf exhibiting fli1a:GFP expression.

(B) UMAP representation of the cell-Topic matrix from cisTopic on 8,976 cells, 3,769 homozygous npas4l mutants, and 5,207 siblings. Percentages represent the proportion of mutant cells relative to all mutant and sibling cells per density cluster.

(C) Summary chromatin accessibility from aggregated cells for each cluster (pseudo-bulks) at the npas4l locus. Three cell-type-specific peaks of accessibility are highlighted as putative enhancers enh1, enh2a, and enh2b ∼8–10 kb from the npas4l TSS.

(D) Motif detection in the enh1, enh2a, enh2b sequences with JASPAR motifs.⁶⁹ Motif scanning at the specific enhancer was with FIMO⁷⁰ and the 20 highest enriched motif sequences are displayed, collapsed per family. Bold black represents a core sequence match shared across the whole family, and gray represents less frequent variations of the motif sequence.

(E) Per-cell distribution of accessibility at putative npas4l enhancer enh1 (highlighted in C), represented in UMAP space.

(F) Per-cell distribution of accessibility at putative npas4l enhancer enh2a and enh2b (highlighted in C), represented in UMAP space.

(G) Enh1E1b:GFP expression at 24 hpf. (i, ii) Single plain optical cross-section through the axial vessels.

Scale bars: 200 μm (A and G), 20 μm (i), 10 μm (ii). DA, dorsal aorta, PCV, posterior cardinal vein.