Journal: bioRxiv
Article Title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels
doi: 10.1101/2025.04.25.650540
Figure Lengend Snippet: Conserved TFs bind to species-specific enhancers to promote Cone specification in 13LGS. ( A ) Schematic illustrating annotation of cis-regulatory elements in RPCs and Photoreceptor Precursors by integration of scATAC-Seq and CUT&RUN 13LGS and mouse datasets. ( B ) Heatmaps show annotated accessible regulatory elements in both 13LGS and mouse. Promoters, activated enhancers (AEs), and poised enhancers (PEs) which are associated with histone markers associated with genes in clusters C2 and C3, which are selectively active in 13LGS RPCs and/or photoreceptor precursors. Shading indicates CUT&TAG signal for the corresponding histone modification within 2kb of the scATAC-Seq peak center. Bar plots displaying the number of each category of regulatory element in each species that are conserved or species-specific. ( C ) Dot plots showing the enrichment of binding sites for Otx2 and Neurod1, TFs which are broadly expressed in both neurogenic RPC and rod and cone precursors, which are enriched in both evolutionarily-conserved cis-regulatory elements in both species. ( D ) Bar plots showing the number of evolutionarily-conversed and species-specific enhancers per TSS in four cone-promoting genes between 13LGS and mouse. (E) The gene regulatory networks regulating Thrb expression in 13LGS and mouse late N. RPCs. ( F ) An example of a Thrb-related regulon and its corresponding scATACseq and CUT&RUN tracks. The arrow indicates the consistent regulatory relationships between GRNs prediction and experimental validations. ( G ) The epigenetic model of cone specification in 13LGS and mouse.
Article Snippet: Then 0.5 µg of the following antibodies were added to each respective reaction: IgG control (EpiCypher, 13-0042), H3K4me1 (EpiCypher, 13-0057), H3K4me3 (EpiCypher, 13-0041), H3K27ac (EpiCypher, 13-0059), H3K27me3 (EpiCypher, 13-0055), NeuroD1 (Cell Signaling, 62953), Otx2 (R&D Systems, BAF1979), or Otx2 (Atlas Antibodies, HPA000633).
Techniques: Modification, Binding Assay, Expressing
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