1. Developmental Biology

Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

  1. Kurt Weir
  2. Pin Lyu
  3. Sangeetha Kandoi
  4. Roujin An
  5. Nicole Pannullo
  6. Isabella Palazzo
  7. Jared A Tangeman
  8. Jun Shi
  9. Steven H DeVries
  10. Dana K Merriman
  11. Jiang Qian  Is a corresponding author
  12. Seth Blackshaw  Is a corresponding author
  1. Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, United States
  2. Department of Ophthalmology, Johns Hopkins University School of Medicine, United States
  3. Department of Ophthalmology, Northwestern University Feinberg School of Medicine, United States
  4. Department of Biology, University of Wisconsin Oshkosh, United States
  5. Department of Neurology, Johns Hopkins University School of Medicine, United States
  6. Institute for Cell Engineering, Johns Hopkins University School of Medicine, United States
  7. Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, United States
https://doi.org/10.7554/eLife.108485.3
Share this article
Cite this article
  1. Kurt Weir
  2. Pin Lyu
  3. Sangeetha Kandoi
  4. Roujin An
  5. Nicole Pannullo
  6. Isabella Palazzo
  7. Jared A Tangeman
  8. Jun Shi
  9. Steven H DeVries
  10. Dana K Merriman
  11. Jiang Qian
  12. Seth Blackshaw
(2026)
Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels
eLife 14:RP108485.
https://doi.org/10.7554/eLife.108485.3
  2. Download BibTeX
  3. Download .RIS
6 figures, 1 table and 11 additional files

Figures

Figure 1 with 1 supplement
Download asset Open asset
Overview of the study.

(A) Schematic summary of the study. scRNA- and scATAC-Seq of whole 13LGS retinas were performed at 10 different time points. Major retinal cell types are identified by clustering in both scRNA- and scATAC-Seq datasets. (B) UMAP projections of all 13LGS retinal cells from scRNA- and scATAC-Seq. Each point represents a single cell, with cell type and time point indicated by shading. (C) Cell-specific marker gene expression and accessibility are shown across 11 major retinal cell types. (D) The relative abundances of rods, rod precursors, cones, and cone precursors are different between developing 13LGS and mouse retina.

Figure 1—figure supplement 1
Download asset Open asset
Quality control of scATAC- and scRNA-Seq data.

(A) Transcriptional start site enrichment profiles of scATAC-Seq datasets. Lines are colored by time points. (B) Fragment size distribution of scATAC-Seq datasets. Individual time points are indicated by colored lines. (C) Heatmap showing the Pearson correlation between gene expression and gene accessibility for each retina cell type. (D) Heatmap of cell type-specific genes. (E) Heatmap of cell type-specific peaks. (F) Heatmap of cell type-specific motifs. (G) Examples of transcription factor (TF) footprint profiles for Pou4f2, Crx, Nfix, and Onecut1 in indicated scATAC-Seq cell types. (H) Examples of chromVAR score are shown for Otx2, Pou2f2, Nfix, and Neurod1 using scATAC-Seq datasets. (I) The relative abundance of retinal cell types in scRNA- and scATAC-Seq is different between developing 13LGS and mouse retina.

Figure 2 with 1 supplement
Download asset Open asset
Identification of 13LGS-specific regulatory mechanisms in cone development by integrating late-stage retinal scRNA- and scATAC-Seq data with mouse.

(A) UMAP projections of the integrated scRNA-Seq data from 13LGS and mouse. (B) UMAP projections of the scATAC-Seq data, showing cell types re-annotated based on the integrated scRNA-Seq analysis. (C) Heatmaps displaying eight clusters of genes that are differentially expressed between 13LGS and mouse. Column labels correspond to the five major cell types relevant to photoreceptor development: Late RPCs (late-stage primary retinal progenitor cells), Late NG (late-stage neurogenic progenitor cells), BC/Pho pre (bipolar cell, cone, and rod precursor cells), cone photoreceptors, and rod photoreceptors. (D) Heatmaps showing the chromatin accessibility of positively correlated regulatory elements for each of the eight differentially expressed gene (DEG) clusters. (E) Dot plots depicting the relative number of positively correlated regulatory elements for each conserved gene pair between 13LGS and mouse. Each dot represents a conserved gene pair, with the x-axis indicating the number of regulatory elements in mouse and the y-axis showing the number in 13LGS. Pairwise t-tests were used to compare the number of elements in each species for each gene pair, and the median values are indicated below each plot. (F) Differential motif analysis in five cone development-associated cell types between 13LGS and mouse. (G) Zic3 expression motif accessibility is higher in 13LGS photoreceptor precursors and mature cones than in mouse. (H) Heatmap showing the expression levels of the top 30 cone-promoting genes identified by gene regulatory network (GRN) analysis in 13LGS across retinal progenitor cells (RPCs), neurogenic progenitor cells (N. RPCs), and photoreceptor precursors in both 13LGS and mouse.

Figure 2—figure supplement 1
Download asset Open asset
Transcription factors that show heterochronic gene expression and co-expression with Otx2 show sustained expression in 13LGS retinas.

Fluorescent in situ hybridization showing co-expression of (A) Pou2f1 and Otx2 or (B) Zic3, Rxrg, and Otx2 in P1, P5, P10, and P24 retinas. Insets show higher power images of highlighted areas. (C) Zic3, Rxrg, and Otx2 fluorescent in situ hybridization from P24 with matched (C’) negative controls. (D) Pou2f1 and Otx2 fluorescent in situ hybridization from P24 with matched (D’) negative controls. (E) Quantification of the fraction of Otx2-positive cells in the outer neuroblastic layer (P1, P5) and ONL (P10, P24) that also express Zic3. (F) Immunohistochemical analysis of Mef2c and Otx2 expression in P1, P5, P10, and P24 retinas. (G) Mef2c and Otx2 immunohistochemistry from P24 with matched (G’) negative controls. Negative controls for fluorescent in situ hybridization omit the probe and for immunohistochemistry omit primary antibodies. Scale bars, 10 µm (S2A–F), 50 µm (S2G), and 5 µm (inset). Cell counts in E were analyzed using one-way ANOVA analysis with Sidak multiple comparisons test and 95% confidence interval. **p < 0.01, ****p < 0.0001, and ns = non-significant. N = 3 independent experiments. DAPI, 4′,6-diamidino-2-phenylindole; NbONL, neuroblastic outer nuclear layer; ONL, outer nuclear layer; INL, inner nuclear layer. Arrowheads indicate cells co-expressing indicated markers.

Figure 3 with 2 supplements
Download asset Open asset
Zic3 is necessary for normal mouse cone development and sufficient to promote cone gene expression.

(A) Diagram of overexpression strategy used to test effects of ZIC3 overexpression. (B) Heatmap of log2 fold change in expression between cone-like precursors and rods separated by condition for select genes, scaled by gene. (C) Upset plot of significant differentially expressed genes shared between conditions. (D) Diagram of retinal progenitor cell-specific conditional loss of function analysis of Zic3. (E) Immunohistochemistry showing GFP and Arr3 expression in P14 wild type (WT) and Zic3lox/lox (Zic3 cKO) mouse retinas. Scale bars, 20 µm. (F) Box plot of the number of cones per micron along the retinal slice (n = 11 WT, 10 Zic3 cKO). p-values calculated by Wilcoxon rank-sum test. P0, postnatal day 0; P5, postnatal day 5; P14, postnatal day 14; FACS, fluorescence-activated cell sorting; scRNA-Seq, single-cell RNA sequencing; ONL, outer nuclear layer; INL, inner nuclear layer; DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein; OE, overexpression; log2FC, log2 fold change; DEG, differentially expressed gene; WT, wild type; cKO, conditional knockout.

Figure 3—figure supplement 1
Download asset Open asset
ZIC3 overexpression promotes the formation of cone-like photoreceptor precursor cells.

(A) UMAP representation of P5 mouse retinal explants from four conditions: electroporated with a plasmid expressing GFP alone (Empty), GFP in a bicistronic transcript with ZIC3 (ZIC3) or POU2F1 (POU2F1), or both the ZIC3 and POU2F1 plasmids (ZIC3 + POU2F1) (n = 1901 cells Empty, 1578 cells ZIC3, 904 cells POU2F1, 2111 cells ZIC3 + POU2F1), split by condition. Each point represents a single cell and is colored by cell type as determined by clustering and marker gene expression. (B) UMAP representation of P5 mouse retinal explants from four conditions: electroporated with a plasmid expressing GFP alone (Empty), GFP in a bicistronic transcript with POU2F1 (POU2F1) or Onecut1 (Onecut1), or both the ZIC3 and POU2F1 plasmids (ZIC3 + POU2F1) (n = 4313 cells Empty, 6287 cells POU2F1, 4455 cells Onecut1, 2476 cells ZIC3 + POU2F1), split by condition. Each point represents a single cell and is colored by cell type as determined by clustering and marker gene expression. (C) Heatmap of log2 fold change in expression between cone-like precursors and rods separated by condition for select genes, scaled by gene. (D) Upset plot of significant differentially expressed genes shared between conditions. RPC, retinal progenitor cell; N. RPC, neurogenic retinal progenitor cells; HC, horizontal cell; BC, bipolar cell; AC, amacrine cell; log2FC, log2 fold change; DEG, differentially expressed gene.

Figure 3—figure supplement 2
Download asset Open asset
Zic3 is required for normal patterns of gene expression in cones and Müller glia.

(A) Immunohistochemistry showing GFP and Nr2e3 expression in P14 wild type (WT) and Zic3lox/lox (Zic3 cKO) mouse retinas. (B) Box plot of the number of rods per square micron along the retinal slice (n = 12 WT, 10 Zic3 cKO). (C) Immunohistochemistry showing GFP and LHX1 expression in P14 WT and Zic3 cKO mouse retinas. Orange arrows indicate horizontal cell nuclei and yellow arrows indicate mouse-on-mouse vascular staining. (D) Box plot of the number of horizontal cells per micron along the retinal slice (n = 3 WT, 2 Zic3 cKO). (E) UMAP representation of P14 WT and Zic3 cKO mouse retinas (n = 6174 cells (N = 4) WT, 7562 cells (N = 4) Zic3), split by genotype. Each point represents a single cell and is colored by cell type as determined by clustering and marker gene expression. Heatmaps of expression in (F) Cones and (G) Müller glia for select genes for WT and Zic3 cKO retinas, scaled by gene. Scale bars, 10 µm. p-value calculated by Wilcoxon rank-sum test. DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein; ONL, outer nuclear layer; INL, inner nuclear layer; HC, horizontal cell; AC/HC, amacrine cells/horizontal cell; RGC, retinal ganglion cell; BC, bipolar cell; MG, Müller glia.

Figure 4 with 2 supplements
Download asset Open asset
Mef2c is sufficient to promote cone-specific gene expression and repress rod-specific gene expression in mouse.

(A) Diagram of overexpression strategy used to test effects of MEF2C overexpression. (B) UMAP representation of P8 mouse retinal explants electroporated with a plasmid expressing GFP alone (Empty) or GFP in a bicistronic transcript with human MEF2C (MEF2C) (n = 7445 cell Empty, 11,949 cells MEF2C). Each point represents a single cell and is colored by cell type as determined by clustering and marker gene expression. (C) Heatmap of expression for select genes for cones, cone-like photoreceptor precursors, rod photoreceptor precursors, and rods in cells overexpressing MEF2C, scaled by gene. (D) Immunohistochemistry showing GFP and GNAT2 expression in P8 mouse retinas from Empty and MEF2C conditions. Scale bars, 50 µm. (E) Box plot of the number of Gnat2+, GFP+ cells divided by the total number of GFP+ cells (n = 8 for both conditions). p-values calculated by Wilcoxon rank-sum test. P0, postnatal day 0; P8, postnatal day 8; FACS, fluorescence-activated cell sorting; scRNA-Seq, single-cell RNA sequencing; ONL, outer nuclear layer; INL, inner nuclear layer; DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein; OE, overexpression.

Figure 4—figure supplement 1
Download asset Open asset
Mef2c overexpression does not obviously impact non-cone cell type proportions.

Immunohistochemistry showing GFP and (A) Nrl, (B) Otx2, (C) Sox9, or (D) Tfap2a expression in P8 mouse retinal explants electroporated with a plasmid expressing GFP alone (Empty) or GFP in a bicistronic transcript with MEF2C (MEF2C). Scale bars, 50 µm. DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein; ONL, outer nuclear layer; INL, inner nuclear layer.

Figure 4—figure supplement 2
Download asset Open asset
Mef2c loss of function does not affect cone cell production or survival.

(A) Diagram of conditional knockout strategy used to test for the necessity of Mef2c for normal cone development. (B) Immunohistochemistry showing GFP and Arr3 expression in P14 wild type (WT) and Chx10-Cre;Mef2clox/lox (Mef2c cKO) mouse retinas. Scale bars, 50 µm. (C) Box plot of the number of ARR3+, GFP+ cells divided by the total number of GFP+ cells (n = 4). p-value calculated by Wilcoxon rank-sum test. WT, wildtype; cKO, conditional knockout; DAPI, 4′,6-diamidino-2-phenylindole; GFP, green fluorescent protein; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer.

Figure 5 with 3 supplements
Download asset Open asset
Conserved transcription factors (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 2 kb 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 photoreceptor precursors, which are enriched in both conserved cis-regulatory elements in both species. (D) Bar plots showing the number of conserved and species-specific enhancers per transcription start site (TSS) in four cone-promoting genes between 13LGS and mouse. (E) The gene regulatory networks (GRNs) regulating Thrb expression in 13LGS and mouse late N. RPCs. (F) An example of a Thrb-related regulon and its corresponding scATAC-Seq and CUT&RUN tracks. The arrow indicates the consistent regulatory relationships between GRN prediction and experimental validations. (G) The epigenetic model of cone specification in 13LGS and mouse.

Figure 5—figure supplement 1
Download asset Open asset
Transcriptional regulatory networks controlling Thrb expression are more complex in 13LGS than mouse at all developmental stages.

Thrb is regulated by more extensive gene regulatory networks in 13LGS than mouse. Gene regulatory networks directing Thrb expression in (A) 13LGS photoreceptor precursors, (B) mouse photoreceptor precursors, (C) 13LGS cones, and (D) mouse cones.

Figure 5—figure supplement 2
Download asset Open asset
Zic3 is regulated by more extensive gene regulatory networks in 13LGS than mouse at all developmental stages.

(A) Gene regulatory networks controlling Zic3 expression in 13LGS late-stage neurogenic RPCs, photoreceptor precursors, and cones. (B) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in 13LGS. (C) Example of Zic3-related regulons and their corresponding scATAC-Seq and CUT&RUN tracks in mouse.

Figure 5—figure supplement 3
Download asset Open asset
Transcriptional regulatory networks controlling cone-specific gene expression in 13LGS increase in connectivity and complexity as differentiation proceeds.

Cell type-specific 13LGS gene regulatory networks with cone-promoting transcription factors (TFs) in (A) late-stage neurogenic retinal progenitor cells (late N. RPCs), (B) photoreceptor precursors, and (C) cones.

Author response image 1
Download asset Open asset
Relative expression levels of cone-promoting genes and accessibility of enhancer elements associated with these genes in early- and late-stage RPCs and cone precursors.

Tables

Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Antibodyrabbit anti-Arr3 polyclonalMilliporeNo. AB152821:200 dilution
Antibodyrabbit anti-Gnat2 polyclonalInvitrogenPA5-1195581:200 dilution
Antibodychicken anti-GFP polyclonalInvitrogenA102621:400 dilution
Antibodymouse anti-Nr2e3 monoclonalR&D SystemsPP-H7223-001:200 dilution
Antibodygoat anti-Nrl polyclonalR&D SystemsAF29451:200 dilution
Antibodygoat anti-Otx2 polyclonalR&D SystemsAF19791:400 dilution
Antibodyrabbit anti-Sox9 polyclonalMilliporeAB55351:400 dilution
Antibodymouse anti-Tfap2a monoclonalDSHBCat# 3b5, RRID:AB_5280841:400 dilution
Antibodymouse anti-Lhx1 monoclonalDHSBCat# 4F2/concentrate1:400 dilution
Antibodygoat anti-Otx2 polyclonalR&D SystemsBAF19791:200 dilution
Antibodyrabbit anti-Mef2c polyclonalAtlas AntibodiesHPA0055331:200 dilution
Antibodydonkey anti-mouse Alexa Fluor Plus 647 polyclonalThermo Fisher ScientificA-110551:250 dilution
Antibodydonkey anti-rabbit Alexa Fluor 488 polyclonalThermo Fisher ScientificA-212061:250 dilution
Antibodydonkey anti-goat IgG Alexa Fluor 555 polyclonalThermo Fisher ScientificA-214321:250 dilution
AntibodyCF633 donkey anti-rabbit polyclonalSigmaSAB4600132-50UL1:250 dilution
Antibodygoat anti-chicken Alexa Fluor 488 polyclonalInvitrogenA-110391:250 dilution
Antibodydonkey anti-mouse Alexa Fluor 568 polyclonalInvitrogenA100371:250 dilution
AntibodyCUTANA IgG Negative Control Antibody for CUT&RUN and CUT&TagEpiCypher13-00420.5 µg/reaction
AntibodyH3K4me1 Antibody, SNAP-Certified for CUT&RUN and CUT&TagEpiCypher13-00570.5 µg/reaction
AntibodyH3K4me3 Antibody, SNAP-Certified for CUT&RUNEpiCypher13-00410.41 µg/reaction
AntibodyH3K27ac Antibody, SNAP-Certified for CUT&RUN and CUT&TagEpiCypher13-00590.5 µg/reaction
AntibodyH3K27me3 Antibody, SNAP-Certified for CUT&RUN and CUT&TagEpiCypher13-00550.5 µg/reaction
AntibodyNeuroD1 (E3E4F) Rabbit mAbCell Signaling629530.5 µg/reaction
Antibodyrabbit Anti-OTX2 Antibody polyclonalAtlas AntibodiesHPA0006330.5 µg/reaction
AntibodyAnti-Histone H3 (tri methyl K9) antibody – ChIP GradeAbcamab88980.5 µg/reaction
Biological sample13LGS retinal samplesThis studyN/AAnimal colony in De Vries and Merriman labs
Commercial assay/kitChromium Next GEM Single Cell 3′ Kit v3.110X GenomicsPN-1000268
Commercial assay/kitDual Index Kit TT Set A10X GenomicsPN-1000215
Commercial assay/kitChromium Next GEM Single Cell ATAC Reagent Kits v1.110X GenomicsPN-1000175
Commercial assay/kitSingle Index Kit N, Set A10X GenomicsPN-1000212
Commercial assay/kit3′ CellPlex Kit Set A10X GenomicsPN-1000261
Commercial assay/kitDual Index Kit NN Set A10X GenomicsPN-1000243
Commercial assay/kitCUTANA ChIC/CUT&RUN KitEpicypher14-1048
Commercial assay/kitCUTANA CUT&RUN Library Prep KitEpiCypher14-1001
Commercial assay/kitNEBNext Ultra II DNA Library Prep Kit for IlluminaNEBE7645S
Commercial assay/kitNEBNext Multiplex Oligos for IlluminaNEBE7395S
OtherMouse retinal development scRNA-seq dataClark et al., 2019GEO: GSE118614
OtherMouse retinal development scATAC-seq dataLyu et al., 2021GEO: GSE181251
Other13LGS retinal development scRNA-seq, scATAC-seq data
13LGS and Mouse Cut&Run data
Mouse Zic3, Pou2f1, Onecut1, Mef2c overexpression and Zic3 cKO scRNA-seq data		This studyGEO: GSE295358
Other13LGS genome GCF_016881025.1_HiC_Itri_2Rhie et al., 2021https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/881/025/GCF_016881025.1_HiC_Itri_2/
Genetic reagentMus musculus: Zic3+/lox: B6;129-Zic3tm2.1Jwb/JThe Jackson LabRRID:IMSR_JAX:023162Jiang et al., 2013
Genetic reagentMus musculus: Mef2c+/lox: Mef2ctm1Jjs/JThe Jackson LabRRID:IMSR_JAX:025556Vong et al., 2005
Genetic reagentMus musculus: Chx10Cre-GFPThe Jackson LabRRID:IMSR_MGI:3051137Rowan and Cepko, 2004
Recombinant DNA reagentZIC3 Gateway Ultimate Human ORF CloneThermo Fisher ScientificNM_003413 (coding sequence only)
Recombinant DNA reagentPOU2F1 Gateway Ultimate Human ORF CloneThermo Fisher ScientificXM_011509654 (coding sequence only)
Recombinant DNA reagentOnecut1 Mouse ORF CloneThis studyNM_008262 (coding sequence only)Available upon request
Recombinant DNA reagentMEF2C Gateway Ultimate Human ORF CloneThermo Fisher ScientificNM_002397 (coding sequence only)
Recombinant DNA reagentPlasmid: pCAGIG IRES-GFPAddgene plasmid #11159N/AMatsuda and Cepko, 2004
Recombinant DNA reagentPlasmid: pCAGIG-GW-IRES-GFPVenkataraman et al., 2018N/AAvailable upon request
Software, algorithmCellRanger Pipeline (version 3.1.0)10X Genomicshttps://www.10xgenomics.com/support/software
Software, algorithmCellRanger Multi Pipeline (version 6.0)10X Genomicshttps://www.10xgenomics.com/support/software
Software, algorithmCellRanger Aggr Pipeline (version 3.1.0)10X Genomicshttps://www.10xgenomics.com/support/software
Software, algorithmCellRanger ATAC pipeline (version 1.2.0)10X Genomicshttps://www.10xgenomics.com/support/software
Software, algorithmSeurat (version 4.0.4)Hao et al., 2021https://satijalab.org/seurat/articles/install_v5.html
Software, algorithmSignac (version 1.4.0)Stuart et al., 2021https://satijalab.org/signac
Software, algorithmcutadapt (version 3.5)Martin, 2011https://cutadapt.readthedocs.io/en/stable/
Software, algorithmTrim Galore (version 0.6.4_dev)Krueger et al., 2023https://github.com/FelixKrueger/TrimGalore
RRID:SCR_011847
Software, algorithmBowtie2Langmead and Salzberg, 2012; Langmead et al., 2026https://github.com/BenLangmead/bowtie2;
RRID:SCR_016368
Software, algorithmSAMtools (version 1.12)Danecek et al., 2021https://www.htslib.org
Software, algorithmUMI-toolsSmith et al., 2017https://umi-tools.readthedocs.io/en/latest/index.html
Software, algorithmdeepTools (version 3.5.1)Ramírez et al., 2016https://deeptools.readthedocs.io/en/latest/
Software, algorithmmacs2Zhang et al., 2008https://pypi.org/project/MACS2/
Software, algorithmArchRGranja et al., 2021https://www.archrproject.com
Software, algorithmChromVARSchep et al., 2017https://greenleaflab.github.io/chromVAR/
Software, algorithmImageJSchindelin et al., 2012https://imagej.net/ij/

Additional files

Supplementary file 1

List of cell type-specific patterns of differential gene expression, chromatin accessibility, and motif enrichment in accessible chromatin for 13LGS.

Counts for each cell type in each scRNA- and scATAC-Seq library are also shown.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp1-v1.zip
Supplementary file 2

Genes differentially expressed in S- and M-cones in 13LGS.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp2-v1.xlsx
Supplementary file 3

Related to Figure 2, gene ortholog pairs for 13LGS and mouse used in this analysis.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp3-v1.xlsx
Supplementary file 4

Related to Figure 2, genes and accessible transcription factor motifs showing differential activity between 13LGS and mouse in late-stage progenitors and differentiating photoreceptors.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp4-v1.zip
Supplementary file 5

Related to Figure 2, top cone-promoting transcription factors active in 13LGS.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp5-v1.xlsx
Supplementary file 6

Related to Figure 2, list of genes differentially expressed following overexpression of ZIC3, Onecut1, POU2F1, and ZIC3+POU2F1 as detected by scRNA-Seq and proportions of major cell types observed in each sample.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp6-v1.xlsx
Supplementary file 7

Related to Figure 3, a list of genes differentially expressed in Chx10-Cre;Zic3lox/lox retina and proportions of major cell types observed in each sample.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp7-v1.xlsx
Supplementary file 8

Related to Figure 4, list of genes differentially expressed following overexpression of MEF2C and proportions of major cell types observed in each sample.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp8-v1.xlsx
Supplementary file 9

Related to Figure 5, cis-regulatory elements inferred by scATAC-Seq and CUT&TAG for genes in clusters 2 and 3 in 13LGS and mouse.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp9-v1.xlsx
Supplementary file 10

Related to Figure 5, active and poised enhancers associated with Mef2c, Rxrg, Thrb, and Zic3 in 13LGS and mouse.

https://cdn.elifesciences.org/articles/108485/elife-108485-supp10-v1.xlsx
MDAR checklist
https://cdn.elifesciences.org/articles/108485/elife-108485-mdarchecklist1-v1.pdf

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Kurt Weir
  2. Pin Lyu
  3. Sangeetha Kandoi
  4. Roujin An
  5. Nicole Pannullo
  6. Isabella Palazzo
  7. Jared A Tangeman
  8. Jun Shi
  9. Steven H DeVries
  10. Dana K Merriman
  11. Jiang Qian
  12. Seth Blackshaw
(2026)
Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels
eLife 14:RP108485.
https://doi.org/10.7554/eLife.108485.3