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. 2023 Jan 30;51(5):2151–2176. doi: 10.1093/nar/gkad026

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — Pou4f2 and Isl1 bind to RGC-specific enhancers. (A) Activities of Pou4f2-bound enhancers as determined by normalized Tn5 insertion frequencies across different cell states/types at E14.5. (B) Activities of Isl1-bound enhancers across different cell states/types. (C) Activities of enhancers co-bound by at least two of the three transcription factors Atoh7, Pou4f2 and Isl1. G1: Atoh7 + Pou4f2 + Isl1; G2: Atoh7 + Pou4f2; G3: Atoh7 + Isl1; G4: Pou4f2 + Isl1. For (A–C), genomic regions the MACS2 summits ± 1.0 kb were displayed. Color scales represent normalized Tn5 insertion frequencies. Normalized average Tn5 insertion frequencies in the different cell states/types are displayed on top of each heatmap. Pou4f2 summits are used in (C) to generate the heatmap. (D) Motif enrichment analysis by HOMER of Pou4f2-bound enhancers displayed in (A). (E) Motif enrichment analysis by HOMER of Isl1-bound enhancers displayed in (B). (F) A Venn diagram demonstrating the overlaps of genes likely regulated by Atoh7, Pou4f2 and Isl1. (G) Example enhancers bound by Pou4f2 and/or Isl1, with or without Atoh7 binding, and their cell state/type-specific activities at E14.5 as displayed in the genome browser. Note that the activities of all these enhancers were highly RGC specific and significantly reduced in the Atoh7-null early RGCs (Early RGCs MT) as compared to the wild-type early RGCs (early RGCs WT). Genome coordinates (mm10) of the displayed regions and the nearby genes are indicated at the bottom.