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. 2023 Jul 25;12:e85093. doi: 10.7554/eLife.85093

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© 2023, Isoe, Nakamura et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 6. — (A) Enrichment of known transcription factor binding motifs in open chromatin region (OCR) clusters are shown as dot plots. Size and color of circles indicate -log₁₀(p-value) and percent target, respectively. Circle was plotted only if -log₁₀(p-value) is higher than 100. (B) Result of de novo motif finding analysis. Top 3 of the enriched motifs in OCR C6 and 7 and candidate transcription factors that have similar binding motifs are shown. (C) Expression of candidate transcription factors in Dd, the pallium except Dd (D), and the subpallium (V) analyzed by RNA-sequencing (n = 2 replicate). (D) Expression pattern of the candidate transcription factors in the telencephalon visualized by in situ hybridization (ISH). Orange triangles indicate the position of Dd2p. (E) Medaka OCR C6 motif enrichment in human brain region-specific OCRs. Existence of each medaka C6 motif was examined around human brain ATAC-seq peaks, and the motif density was calculated. HC: hippocampus; MDT: medial dorsal thalamus; NCX: neocortex; PVC: primary visual cortex; ST: striatum. Darker blue shades indicate higher correlation. (F) Relative expression levels of Dd2-preferentially expressed genes (809 genes) in the mouse brain. We examined the expression of Dd2-preferentially expressed genes across 12 regions in the mouse brain (isocortex. OLF: olfactory areas; HPF: hippocampal formation; CTXsp: cortical subplate; STR: striatum; PAL: pallidum; TH: thalamus; HY: hypothalamus; MB: midbrain; P: pons; MY: medulla; CB: cerebellum). The gene expression levels were from the ISH data of Allen Brain Atlas (https://mouse.brain-map.org/).

Figure 6—figure supplement 1. — (A) Enrichment of known transcription factor binding motifs in open chromatin region (OCR) clusters are shown as dot plots. Size and color of circles indicate -log₁₀(p-value) and percent target, respectively. Circle was plotted only if -log₁₀(p-value) is higher than 100. (B) Result of de novo motif finding analysis. Top 3 of the enriched motifs in OCR C6 and 7 and candidate transcription factors that have similar binding motifs are shown. (C) Expression of candidate transcription factors in Dd, the pallium except Dd (D), and the subpallium (V) analyzed by RNA-sequencing (n = 2 replicate). (D) Expression pattern of the candidate transcription factors in the telencephalon visualized by in situ hybridization (ISH). Orange triangles indicate the position of Dd2p. (E) Medaka OCR C6 motif enrichment in human brain region-specific OCRs. Existence of each medaka C6 motif was examined around human brain ATAC-seq peaks, and the motif density was calculated. HC: hippocampus; MDT: medial dorsal thalamus; NCX: neocortex; PVC: primary visual cortex; ST: striatum. Darker blue shades indicate higher correlation. (F) Relative expression levels of Dd2-preferentially expressed genes (809 genes) in the mouse brain. We examined the expression of Dd2-preferentially expressed genes across 12 regions in the mouse brain (isocortex. OLF: olfactory areas; HPF: hippocampal formation; CTXsp: cortical subplate; STR: striatum; PAL: pallidum; TH: thalamus; HY: hypothalamus; MB: midbrain; P: pons; MY: medulla; CB: cerebellum). The gene expression levels were from the ISH data of Allen Brain Atlas (https://mouse.brain-map.org/).