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

Reviewer #1 (Public review):

Summary:

In this manuscript, Weir et al. investigate why the 13-lined ground squirrel (13LGS) retina is unusually rich in cone photoreceptors, the cells responsible for color and daylight vision. Most mammals, including humans, have rod-dominant retinas, making the 13LGS retina both an intriguing evolutionary divergence and a valuable model for uncovering novel mechanisms of cone generation. The developmental programs underlying this adaptation were previously unknown.

Using an integrated approach that combines single-cell RNA sequencing (scRNAseq), scATACseq, and histology, the authors generate a comprehensive atlas of retinal neurogenesis in 13LGS. Notably, comparative analyses with mouse datasets reveal that in 13LGS, cones can arise from late-stage neurogenic progenitors, a striking contrast to mouse and primate retinas, where late progenitors typically generate rods and other late-born cell types but not cones. They further identify a shift in the timing (heterochrony) of expression of several transcription factors. Further, the authors show that these factors act through species-specific regulatory elements. And overall, functional experiments support a role for several of these candidates in cone production.

Strengths:

This study stands out for its rigorous and multi-layered methodology. The combination of transcriptomic, epigenomic, and histological data yields a detailed and coherent view of cone development in 13LGS. Cross-species comparisons are thoughtfully executed, lending strong evolutionary context to the findings. The conclusions are, in general, well supported by the evidence, and the datasets generated represent a substantial resource for the field. The work will be of high value to both evolutionary neurobiology and regenerative medicine, particularly in the design of strategies to replace lost cone photoreceptors in human disease.

Weaknesses:

(1) Overall, the conclusions are strongly supported by the data, but the paper would benefit from additional clarifications. In particular, some of the conclusions could be toned down slightly to reflect that the observed changes in candidate gene function, such as those for Zic3 by itself, are modest and may represent part of a more complex regulatory network.

(2) Additional explanations about the cell composition of the 13LGS retina are needed. The ratios between cone and rod are clearly detailed, but do those lead to changes in other cell types?

(3) Could the lack of a clear trajectory for rod differentiation be just an effect of low cell numbers for this population?

(4) The immunohistochemistry and RNA hybridization experiments shown in Figure S2 would benefit from supporting controls to strengthen their interpretability. While it has to be recognized that performing immunostainings on non-conventional species is not a simple task, negative controls are necessary to establish the baseline background levels, especially in cases where there seems to be labeling around the cells. The text indicates that these experiments are both immunostainings and ISH, but the figure legend only says "immunohistochemistry". Clarifying these points would improve readers' confidence in the data.

(5) Figure S3: The text claims that overexpression of Zic3 alone is sufficient to induce the cone-like photoreceptor precursor cells as well as horizontal cell-like precursors, but this is not clear in Figure S3A nor in any other figure. Similarly, the effects of Pou2f1 overexpression are different in Figure S3A and Figure S3B. In Figure S3B, the effects described (increased presence of cone-like and horizontal-like precursors) are very clear, whereas it is not in Figure S3A. How are these experiments different?

(6) The analyses of Zic3 conditional mutants (Figure S4) reveal an increase in many cone, rod, and pan-photoreceptor genes with only a reduction in some cone genes. Thus, the overall conclusion that Zic3 is essential for cones while repressing rod genes doesn't seem to match this particular dataset.

(7) Throughout the text, the authors used the term "evolved". To substantiate this claim, it would be important to include sequence analyses or to rephrase to a more neutral term that does not imply evolutionary inference.

Reviewer #2 (Public review):

Summary:

This paper aims to elucidate the gene regulatory network governing the development of cone photoreceptors, the light-sensing neurons responsible for high acuity and color vision in humans. The authors provide a comprehensive analysis through stage-matched comparisons of gene expression and chromatin accessibility using scRNA-seq and scATAC-seq from the cone-dominant 13-lined ground squirrel (13LGS) retina and the rod-dominant mouse retina. The abundance of cones in the 13LGS retina arises from a dominant trajectory from late retinal progenitor cells (RPCs) to photoreceptor precursors and then to cones, whereas only a small proportion of rods are generated from these precursors.

Strengths:

The paper presents intriguing insights into the gene regulatory network involved in 13LGS cone development. In particular, the authors highlight the expression of cone-promoting transcription factors such as Onecut2, Pou2f1, and Zic3 in late-stage neurogenic progenitors, which may be driven by 13LGS-specific cis-regulatory elements. The authors also characterize candidate cone-promoting genes Zic3 and Mef2C, which have been previously understudied. Overall, I found that the across-species analysis presented by this study is a useful resource for the field.

Weaknesses:

The functional analysis on Zic3 and Mef2C in mice does not convincingly establish that these factors are sufficient or necessary to promote cone photoreceptor specification. Several analyses lack clarity or consistency, and figure labeling and interpretation need improvement.

Reviewer #3 (Public review):

Summary:

The authors perform deep transcriptomic and epigenetic comparisons between mouse and 13-lined ground squirrel (13LGS) to identify mechanisms that drive rod vs cone-rich retina development. Through cross-species analysis, the authors find extended cone generation in 13LGS, gene expression within progenitor/photoreceptor precursor cells consistent with a lengthened cone window, and differential regulatory element usage. Two of the transcription factors, Mef2c and Zic3, were subsequently validated using OE and KO mouse lines to verify the role of these genes in regulating competence to generate cone photoreceptors.

Strengths:

Overall, this is an impactful manuscript with broad implications toward our understanding of retinal development, cell fate specification, and TF network dynamics across evolution and with the potential to influence our future ability to treat vision loss in human patients. The generation of this rich new dataset profiling the transcriptome and epigenome of the 13LGS is a tremendous addition to the field that assuredly will be useful for numerous other investigations and questions of a variety of interests. In this manuscript, the authors use this dataset and compare it to data they previously generated for mouse retinal development to identify 2 new regulators of cone generation and shed insights into their regulation and their integration into the network of regulatory elements within the 13LGS compared to mouse.

Weaknesses:

(1) The authors chose to omit several cell classes from analyses and visualizations that would have added to their interpretations. In particular, I worry that the omission of 13LGS rods, early RPCs, and early NG from Figures 2C, D, and F is notable and would have added to the understanding of gene expression dynamics. In other words, (a) are these genes of interest unique to late RPCs or maintained from early RPCs, and (b) are rod networks suppressed compared to the mouse?

(2) The authors claim that the majority of cones are generated by late RPCs and that this is driven primarily by the enriched enhancer network around cone-promoting genes. With the temporal scRNA/ATACseq data at their disposal, the authors should compare early vs late born cones and RPCs to determine whether the same enhancers and genes are hyperactivated in early RPCs as well as in the 13LGS. This analysis will answer the important question of whether the enhancers activated/evolved to promote all cones, or are only and specifically activated within late RPCs to drive cone genesis at the expense of rods.

(3) The authors repeatedly use the term 'evolved' to describe the increased number of local enhancer elements of genes that increase in expression in 13LGS late RPCs and cones. Evolution can act at multiple levels on the genome and its regulation. The authors should consider analysis of sequence level changes between mouse, 13LGS, and other species to test whether the enhancer sequences claimed to be novel in the 13LGS are, in fact, newly evolved sequence/binding sites or if the binding sites are present in mouse but only used in late RPCs of the 13LGS.

(4) The authors state that 'Enhancer elements in 13LGS are predicted to be directly targeted by a considerably greater number of transcription factors than in mice'. This statement can easily be misread to suggest that all enhancers display this, when in fact, this is only the cone-promoting enhancers of late 13LGS RPCs. In a way, this is not surprising since these genes are largely less expressed in mouse vs 13LGS late RPCs, as shown in Figure 2. The manuscript is written to suggest this mechanism of enhancer number is specific to cone production in the 13LGS- it would help prove this point if the authors asked the opposite question and showed that mouse late RPCs do not have similar increased predicted binding of TFs near rod-promoting genes in C7-8.