1. Developmental Biology
  2. Evolutionary Biology

Developmental hourglass and heterochronic shifts in fin and limb development

  1. Koh Onimaru  Is a corresponding author
  2. Kaori Tatsumi
  3. Chiharu Tanegashima
  4. Mitsutaka Kadota
  5. Osamu Nishimura
  6. Shigehiro Kuraku  Is a corresponding author
  1. RIKEN Center for Biosystems Dynamics Research, Japan
  2. RIKEN Center for Life Science Technologies, Japan
https://doi.org/10.7554/eLife.62865
Share this article
Cite this article
  1. Koh Onimaru
  2. Kaori Tatsumi
  3. Chiharu Tanegashima
  4. Mitsutaka Kadota
  5. Osamu Nishimura
  6. Shigehiro Kuraku
(2021)
Developmental hourglass and heterochronic shifts in fin and limb development
eLife 10:e62865.
https://doi.org/10.7554/eLife.62865
  2. Download BibTeX
  3. Download .RIS

Abstract

How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls.

Data availability

RNA-seq and ATAC-seq datasets generated during the current study are available in the Gene Expression Omnibus (GEO) repository under accession number GSE136445. Data to reproduce this study are deposited in figshare (https://figshare.com/articles/Onimaru_et_al_Supplementary_Data/9928541; DOI: 10.6084/m9.figshare.9928541). Code for clustering analysis is available at https://github.com/koonimaru/easy_heatmapper.

The following data sets were generated
The following previously published data sets were used
    1. Davis CA
    2. Hitz BC
    3. Sloan CA
    4. Chan ET
    5. Davidson JM
    6. Gabdank I
    7. Hilton JA
    8. Jain K
    9. Baymuradov UK
    10. Narayanan AK
    11. Onate KC
    12. Graham K
    13. Miyasato SR
    14. Dreszer TR
    15. Strattan JS
    16. Jolanki O
    17. Tanaka FY
    18. Cherry JM
    (2018) The Encyclopedia of DNA elements (ENCODE): Data portal update.
    ENCFF478FHR ENCFF955MIX ENCFF210MKE ENCFF431KXE ENCFF275OKU ENCFF426VDN ENCFF002LRT ENCFF576SKK ENCFF592ZRO ENCFF798QON ENCFF336VLY ENCFF407NCE ENCFF572CMB ENCFF695FLH ENCFF130WMA ENCFF224JRS ENCFF337ETV ENCFF535DAV ENCFF540ZEZ ENCFF762LUG ENCFF279LMU ENCFF518FYP ENCFF377YCK ENCFF086MTT ENCFF064NKM ENCFF406EUS ENCFF258GFE ENCFF031SEH ENCFF694SPD ENCFF051GLX ENCFF304CCF ENCFF655OFT ENCFF483MKX ENCFF007HEF ENCFF550NVA ENCFF848NLJ ENCFF929LOH ENCFF382CMV ENCFF360MVK ENCFF159HYY ENCFF618OJP ENCFF329VCX ENCFF341HRL ENCFF894ZND ENCFF702NAP ENCFF109LQF ENCFF146ZCO ENCFF154RTC ENCFF709ZKC ENCFF040SPZ ENCFF912PDM ENCFF141JSP ENCFF985YPA ENCFF064JRU ENCFF774MTJ ENCFF376TIM ENCFF612QXM ENCFF584HRP ENCFF353TSI ENCFF583FIG ENCFF143XEE ENCFF590KVK ENCFF107GOQ ENCFF370RSB ENCFF906UHI ENCFF034BFB ENCFF928FUL ENCFF872PTK ENCFF982ZSW ENCFF454BSG ENCFF035UJZ ENCFF471VWH ENCFF501QKH ENCFF113PQF ENCFF322CQL ENCFF622HGW ENCFF746ASR ENCFF232GHI ENCFF484RFZ ENCFF658OKS ENCFF232PNH ENCFF403VCU ENCFF688KUB ENCFF815LLD ENCFF557YZH ENCFF636YTN ENCFF142IPK ENCFF387ORM ENCFF877QHQ ENCFF877LFX ENCFF994LOF ENCFF398KDL ENCFF618YMO ENCFF598ZGD ENCFF924SYL ENCFF809YXL ENCFF685HFN ENCFF697FTK ENCFF887QYY ENCFF171GOW ENCFF790TWE ENCFF635MWR ENCFF818OKO ENCFF978ZGA ENCFF645HNE ENCFF237MEG ENCFF738MPC ENCFF905ZTZ ENCFF914USA ENCFF417HDL ENCFF105XRN ENCFF302YAI ENCFF502HEW ENCFF978POS ENCFF107SIK ENCFF143SWD ENCFF311YQH ENCFF940KCT.
    https://www.encodeproject.org/

Article and author information

Author details

  1. Koh Onimaru

    Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Japan
    For correspondence
    koh.onimaru@riken.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2428-9510

  2. Kaori Tatsumi

    Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
    Competing interests
    The authors declare that no competing interests exist.

  3. Chiharu Tanegashima

    Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
    Competing interests
    The authors declare that no competing interests exist.

  4. Mitsutaka Kadota

    Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minamimachi,Chuo-ku, Japan
    Competing interests
    The authors declare that no competing interests exist.

  5. Osamu Nishimura

    Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minamimachi,Chuo-ku, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1969-2580

  6. Shigehiro Kuraku

    Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
    For correspondence
    shigehiro.kuraku@riken.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1464-8388

Funding

Japan Society for the Promotion of Science (17K15132)

  • Koh Onimaru

Ministry of Education, Culture, Sports, Science and Technology (N/A)

  • Koh Onimaru
  • Kaori Tatsumi
  • Chiharu Tanegashima
  • Mitsutaka Kadota
  • Osamu Nishimura
  • Shigehiro Kuraku

RIKEN (N/A)

  • Koh Onimaru

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

Ethics

Animal experimentation: Animal experiments were conducted in accordance with the guidelines approved by the Institutional Animal Care and Use Committee (IACUC), RIKEN Kobe Branch, and experiments involving mice were approved by IACUC (K2017-ER032).

Reviewing Editor

  1. Karen E Sears, University of California, Los Angeles, United States

Version history

  1. Received: September 7, 2020
  2. Accepted: February 1, 2021
  3. Accepted Manuscript published: February 9, 2021 (version 1)
  4. Version of Record published: March 4, 2021 (version 2)

Copyright

© 2021, Onimaru 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

  • 2,241
    Page views
  • 360
    Downloads
  • 7
    Citations

Article citation count generated by polling the highest count across the following sources: PubMed Central, Crossref, Scopus.

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. Koh Onimaru
  2. Kaori Tatsumi
  3. Chiharu Tanegashima
  4. Mitsutaka Kadota
  5. Osamu Nishimura
  6. Shigehiro Kuraku
(2021)
Developmental hourglass and heterochronic shifts in fin and limb development
eLife 10:e62865.
https://doi.org/10.7554/eLife.62865

Categories and tags

Research organism

Further reading

    1. Developmental Biology

    Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans

    Taylor N Medwig-Kinney, Brian A Kinney ... David Q Matus
    Research Article

    A growing body of evidence suggests that cell division and basement membrane invasion are mutually exclusive cellular behaviors. How cells switch between proliferative and invasive states is not well understood. Here, we investigated this dichotomy in vivo by examining two cell types in the developing Caenorhabditis elegans somatic gonad that derive from equipotent progenitors, but exhibit distinct cell behaviors: the post-mitotic, invasive anchor cell and the neighboring proliferative, non-invasive ventral uterine (VU) cells. We show that the fates of these cells post-specification are more plastic than previously appreciated and that levels of NHR-67 are important for discriminating between invasive and proliferative behavior. Transcription of NHR-67 is downregulated following post-translational degradation of its direct upstream regulator, HLH-2 (E/Daughterless) in VU cells. In the nuclei of VU cells, residual NHR-67 protein is compartmentalized into discrete punctae that are dynamic over the cell cycle and exhibit liquid-like properties. By screening for proteins that colocalize with NHR-67 punctae, we identified new regulators of uterine cell fate maintenance: homologs of the transcriptional co-repressor Groucho (UNC-37 and LSY-22), as well as the TCF/LEF homolog POP-1. We propose a model in which the association of NHR-67 with the Groucho/TCF complex suppresses the default invasive state in non-invasive cells, which complements transcriptional regulation to add robustness to the proliferative-invasive cellular switch in vivo.

    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Transcription: A hub of activity

    Virginia L Pimmett, Mounia Lagha
    Insight

    Imaging experiments reveal the complex and dynamic nature of the transcriptional hubs associated with Notch signaling.

    1. Cell Biology
    2. Developmental Biology

    Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human

    Simon Schneider, Andjela Kovacevic ... Hubert Schorle
    Research Article

    Cylicins are testis-specific proteins, which are exclusively expressed during spermiogenesis. In mice and humans, two Cylicins, the gonosomal X-linked Cylicin 1 (Cylc1/CYLC1) and the autosomal Cylicin 2 (Cylc2/CYLC2) genes, have been identified. Cylicins are cytoskeletal proteins with an overall positive charge due to lysine-rich repeats. While Cylicins have been localized in the acrosomal region of round spermatids, they resemble a major component of the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. However, the role of Cylicins during spermiogenesis has not yet been investigated. Here, we applied CRISPR/Cas9-mediated gene editing in zygotes to establish Cylc1- and Cylc2-deficient mouse lines as a model to study the function of these proteins. Cylc1 deficiency resulted in male subfertility, whereas Cylc2-/-, Cylc1-/yCylc2+/-, and Cylc1-/yCylc2-/- males were infertile. Phenotypical characterization revealed that loss of Cylicins prevents proper calyx assembly during spermiogenesis. This results in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, and severe structural malformations, ultimately resulting in impaired sperm motility. Furthermore, exome sequencing identified an infertile man with a hemizygous variant in CYLC1 and a heterozygous variant in CYLC2, displaying morphological abnormalities of the sperm including the absence of the acrosome. Thus, our study highlights the relevance and importance of Cylicins for spermiogenic remodeling and male fertility in human and mouse, and provides the basis for further studies on unraveling the complex molecular interactions between perinuclear theca proteins required during spermiogenesis.