1. Developmental Biology
  2. Neuroscience

Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

  1. Karthik Shekhar  Is a corresponding author
  2. Irene E Whitney
  3. Salwan Butrus
  4. Yi-Rong Peng
  5. Joshua R Sanes  Is a corresponding author
  1. University of California, Berkeley, United States
  2. Harvard University, United States
  3. University of California, Los Angeles, United States
https://doi.org/10.7554/eLife.73809
Share this article
Cite this article
  1. Karthik Shekhar
  2. Irene E Whitney
  3. Salwan Butrus
  4. Yi-Rong Peng
  5. Joshua R Sanes
(2022)
Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
eLife 11:e73809.
https://doi.org/10.7554/eLife.73809
  2. Download BibTeX
  3. Download .RIS

Abstract

The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly-born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC transcriptomic type identity is not specified at mitotic exit, but acquired by gradual, asynchronous restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity emerges. Optimal transport inference identifies groups of RGC precursors with largely non-overlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.

Data availability

Sequencing data has been submitted under GSE185671. Reviewer token : evchicgutpqpnoj.Computational scripts are available at : https://github.com/shekharlab/mouseRGCdev

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Karthik Shekhar

    Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, United States
    For correspondence
    kshekhar@berkeley.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4349-6600

  2. Irene E Whitney

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    Competing interests
    Irene E Whitney, is affiliated with Honeycomb Biotechnologies. The author has no financial interests to declare..

  3. Salwan Butrus

    Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.

  4. Yi-Rong Peng

    Department of Ophthalmology, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.

  5. Joshua R Sanes

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    For correspondence
    sanesj@mcb.harvard.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8926-8836

Funding

National Institutes of Health (R37NS029169)

  • Joshua R Sanes

National Institutes of Health (R01EY022073)

  • Joshua R Sanes

National Institutes of Health (R00EY028625)

  • Karthik Shekhar

National Science Foundation (GRP DGE1752814)

  • Salwan Butrus

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Carol A Mason, Columbia University, United States

Ethics

Animal experimentation: All animal experiments were approved by the Institutional Animal Care and Use Committees (IACUC) at Harvard University. Mice were maintained in pathogen-free facilities under standard housing conditions with continuous access to food and water. Animals used in this study include both males and females. A meta-analysis (not shown) did not show any systematic sex-related effects in either differentially expressed genes or cell-type proportions.

Version history

  1. Received: September 11, 2021
  2. Preprint posted: October 21, 2021 (view preprint)
  3. Accepted: February 21, 2022
  4. Accepted Manuscript published: February 22, 2022 (version 1)
  5. Version of Record published: March 25, 2022 (version 2)

Copyright

© 2022, Shekhar et al.

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

Metrics

  • 2,709
    views
  • 404
    downloads
  • 34
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Karthik Shekhar
  2. Irene E Whitney
  3. Salwan Butrus
  4. Yi-Rong Peng
  5. Joshua R Sanes
(2022)
Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
eLife 11:e73809.
https://doi.org/10.7554/eLife.73809

Share this article

https://doi.org/10.7554/eLife.73809

Categories and tags

Research organism

Further reading

    1. Developmental Biology

    Inhibitory G proteins play multiple roles to polarize sensory hair cell morphogenesis

    Amandine Jarysta, Abigail LD Tadenev ... Basile Tarchini
    Research Article

    Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3, and GNAO proteins, but may also induce unrelated defects. Here, we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner G protein signaling modulator 2 (GPSM2), whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the sub-cellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: (1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and (2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.

    1. Computational and Systems Biology
    2. Developmental Biology

    A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

    Gang Xue, Xiaoyi Zhang ... Zhiyuan Li
    Research Article

    Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.

    1. Developmental Biology
    2. Evolutionary Biology

    The rapidly evolving X-linked MIR-506 family fine-tunes spermatogenesis to enhance sperm competition

    Zhuqing Wang, Yue Wang ... Wei Yan
    Research Article

    Despite rapid evolution across eutherian mammals, the X-linked MIR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (SLITRK2 and FMR1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked MIR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernible defects, but simultaneous ablation of five clusters containing 19 members of the MIR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility, and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked MIR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the MIR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.