Close

Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis

Erin Jarvis Alberstat, Kevin Chung, Dennis A Sun, Shagnik Ray, Nipam H. Patel

Posted on: 14 April 2022

Preprint posted on 27 March 2022

and

Distinct regulation of Hox genes by Polycomb Group genes in a crustacean

Dennis A Sun, Yuri Takahashi, Rebecca J Chang, Nipam H Patel

Posted on:

Preprint posted on 28 March 2022

A double feature on crustacean Hox regulation

Selected by Olivia Tidswell

Background

Hox genes act as master regulators of anterior-to-posterior (AP) axial identity in nearly all animals. Precise spatial and temporal regulation of these genes during embryogenesis is crucial for establishing a normal body plan. The regulation of Hox genes is tightly linked to their genomic organisation; they tend to be clustered in the genome, and the order of Hox genes in a cluster mirrors their order of expression along the AP axis (a phenomenon known as “spatial collinearity”). .

Hox gene regulation has perhaps been best characterised in the animal in which Hox genes were first discovered, Drosophila.  In Drosophila, Hox gene expression boundaries are initially established by genes of the segmentation cascade. They are then reinforced and maintained by Polycomb group (PcG) and Trithorax group (TrxG) genes, which introduce and maintain chromatin modifications, and by cross-regulation between Hox genes. Whether these phases of regulation are representative of the arthropods in general, or are specific to some insects (including Drosophila), remains unclear.

The two preprints I have chosen to highlight here reveal aspects of Hox gene regulation in a non-insect arthropod, the amphipod crustacean Parhyale hawaiensis. Like other crustaceans, Parhyale sports one pair of appendages per segment – this makes it quick and easy to spot homeotic phenotypes using appendage morphology as a readout. The first preprint, by Alberstat et al., focuses on cross-regulation between Hox genes, while the second preprint by Sun et al. focuses on the regulation of Hox genes by PcG and TrxG chromatin modifying enzymes. Both preprints hail from Nipam Patel’s lab, and use a combination of CRISPR/Cas9 mutagenesis and in situ hybridisation to infer regulatory interactions.

Key Findings

Preprint 1 – Posterior prevalence and the Hox code

The first preprint, by Alberstat et al., focuses primarily on cross-regulation of the posterior Hox genes, Ultrabithorax (Ubx), abdominal-A (abd-A) and Abdominal-B (Abd-B). These genes are encoded and expressed at the posterior of the Hox cluster and embryo, respectively. In Drosophila, these genes display a property known as posterior prevalence; posterior genes are phenotypically dominant to more anterior genes. This dominance can emerge through transcriptional or post-transcriptional suppression. By knocking down each of the posterior Hox genes individually and in combination with each other, Alberstat et al. revealed that the situation in Paryhale is a little more complex.

Some Parhyale Hox genes do interact in a manner consistent with the posterior prevalence model. The authors found that Ubx is transcriptionally repressed by the most posterior gene of the cluster, Abd-B, and that Ubx is functionally repressed by its posterior neighbour, abd-A, although this is repression is not at the transcriptional or translational level. They also showed that Ubx, abd-A and Abd-B are all capable of repressing the more anterior Hox gene Sex combs reduced (Scr). However, abd-A does not appear to be repressed transcriptionally or otherwise by any of the other posterior Hox genes. In fact, it is co-expressed with its posterior neighbour, Abd-B, in the swimming appendages, where the two genes act co-operatively to specify appendage identity. Furthermore, abd-A seems to have a dose-dependent effect on appendage identity, with different levels of expression generating different appendage types.

In summary, cross-regulation between Hox genes appears to be essential for normal axial patterning in Parhyale, but does not entirely align with a simple posterior prevalence model.  The authors suggest that Parhyale utilises a “Hox code” to pattern its appendages, wherein both the dosage and combination of Hox genes present determine appendage fate. If conserved more broadly amongst the crustaceans, this model might help to explain the huge diversity of appendage types in this lineage.

 

Figure 1. The combinations and dosages of Hox genes proposed to code for each appendage type in Parhyale. Adapted from Figure 9B in the preprint by Alberstat et al.

Preprint 2 – Polycomb in Parhyale

In the second preprint, by Sun et al., the authors focus on the role of Polycomb Group (PcG) and Trithorax Group (TrxG) genes in regulating Parhyale Hox genes. They found that the genome of Parhyale contains homologs of all core PcG and TrxG genes known in Drosophila. As observed in other animals, knocking out PcG genes generated homeotic transformations and misexpression of Hox genes. They also observed a number of non-homeotic defects in limb patterning, cuticle deposition, and plate formation, suggesting that PcG genes play pleiotropic roles in Parhyale development. Surprisingly, TrxG knockouts did not display any homeotic transformations. It may be that TrxG genes play a more subtle role in regulating Hox gene expression in Parhyale than in Drosophila.

Sun et al. also demonstrate that the interactions between individual PcG and Hox genes are highly gene- and tissue-dependent in Parhyale. Knocking out different PcG genes resulted in different degrees of de-repression for different Hox genes, in a tissue-specific manner. For example, the PcG gene Sce seems to repress Ubx strongly in the nervous system and appendages; abd-A weakly in the nervous system, but not appendages; and Abd-B strongly in the nervous system and very weakly in the appendages. The timing of de-repression also varies between Hox genes – for example, Ubx is initially expressed normally in PcG knockouts, and only subsequently becomes ectopically expressed, while ectopic expression of Abd-B is observed at the same time as the wild-type domain is established.

In summary, Sun et al. show that PcG, but not necessarily TrxG, genes are required for Hox regulation in Parhyale. However, the interactions between PcG and Hox genes are not one-size fits all, and depend on the individual PcG gene and Hox gene in question, and the tissue where they are expressed.

Why I think these two preprints are important

Our understanding of Hox gene regulation is dominated by research from a very small number of model organisms – in particular, Drosophila and mice. By developing detailed models of Hox gene regulation in other organisms, we can make inferences about how it has evolved over time and how this influences axial patterning.

Based on these preprints, it seems likely that the three broad phases of Hox gene regulation identified in Drosophila – PcG-independent anterior boundary establishment, PcG-dependent boundary maintenance, and Hox cross regulation – are conserved in Parhyale, and were a common feature of the ancestor of insects and crustaceans. However, both preprints highlight complexities in regulation that might help Parhyale to fine tune its Hox gene expression and generate its diverse complement of appendages.

Tags: crustacean, hox, hox regulation, parhyale, polycomb, trithorax

doi: https://doi.org/10.1242/prelights.31822

(2 votes)

Author's response

Nipam Patel shared about Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis

Your triple Hox knockouts are really fantastic! Are there efforts underway to do similar analyses for the anterior Hox genes? If so, which interactions are you most intrigued to investigate?

We would like to extend these studies, with double and triple knockouts combined with Hox gene expression analysis, to the more anterior Hox genes, particularly to further refine the functions and interactions of Scr, Antp, and Ubx.  One challenge is that these more anterior appendages are more difficult to image and analyze due to their small size and position tucked into the head.

You note that abd-A has been also found to act co-operatively with Ubx and Abd-B to specify regional identity in other arthropod species. Do you think that abd-A shows an unusual propensity for co-operating with other Hox genes to specify identity, and why might this be?

abd-A does seem to hold the key to several interesting transformations during evolution.  It appears that both changes in abd-A’s expression domain, and “escape” from posterior prevalence, have been key to several transitions in arthropod body plans, and may also be key to the origin of early insects without abdominal limbs.  We are quite interested in pursuing many of the unique properties of abd-A in Parhyale and other arthropods to understand its special role.

and

Dennis Sun shared about Distinct regulation of Hox genes by Polycomb Group genes in a crustacean

In your preprint, you reveal that different Parhyale PcG proteins have varying levels of repressive ability depending on the tissue they are expressed in and the Hox gene they are targeting. Do you think that this level of specificity is likely to be unique to crustaceans, or more generally representative of arthropods? In particular, to what extent to Drosophila PcG genes seem to act in a tissue- or Hox gene-specific manner?

The original work on Drosophila Polycomb genes showed that there were differences in the effects of individual Polycomb genes on the expression of each Hox gene, although the precise differences in tissue or Hox specificity seem to have only been lightly investigated. We now have more advanced techniques for visualizing gene expression at higher resolution, such as reporter lines or fluorescent in situ hybridization. It would be great to revisit the Hox misexpression phenotypes of PcG mutations in Drosophila and to explore their function in other genetically tractable insects such as Tribolium. I think such studies would likely reveal that insect PcG genes also have tissue- and Hox-specific mechanisms. It’s likely that this specificity is ancestral to pancrustaceans and understanding the ancestral mechanisms of this specificity could provide insight into the evolution of the insect Hox cluster.

Significantly, your findings suggest that PcG genes are not required for the initial establishment of Hox gene boundaries, as is the case in insects. In insects, this phase of regulation is instead driven by segmentation genes, most prominently the gap genes – none of which appear to be expressed at the right time for this role in Parhyale. Do you have any theories as to which genes might be responsible for establishing early Hox boundaries in Parhyale?

We have some preliminary data that a few Parhyale orthologs of some gap genes play a role in segmentation and Hox regulation. We expect that those genes, as well as other genes found to have gap gene-like activity in non-Drosophila insects (such as nubbin in Tribolium), would be good candidates for the factors involved in the PcG-independent boundary formation in Parhyale. As Parhyale is quite phylogenetically distant from insects, it would also be important to identify candidates in a more unbiased fashion, such as by using single-cell or spatial sequencing of early developmental stages to identify regionally-expressed factors that might contribute to this pre-PcG phase of Hox regulation. Identifying such factors would also provide useful insights into how the Hox regulatory mechanisms of insects and crustaceans may have diverged.

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the developmental biology category:

Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation

Marianne Basso, Alexia Mahuzier, Syed Kaabir Ali, et al.

Selected by 30 October 2024

Ryan Harrison

Developmental Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Axis reset is rate limiting for onset of whole-body regenerative abilities during planarian development

Clare L.T. Booth, Brian C. Stevens, Clover A. Stubbert, et al.

Selected by 10 October 2024

Isabella Cisneros

Developmental Biology

Also in the evolutionary biology category:

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

Nikolai Hecker , Niklas Kempynck , David Mauduit, et al.

Selected by 02 July 2024

Rodrigo Senovilla-Ganzo

Bioinformatics

Modular control of time and space during vertebrate axis segmentation

Ali Seleit, Ian Brettell, Tomas Fitzgerald, et al.

AND

Natural genetic variation quantitatively regulates heart rate and dimension

Jakob Gierten, Bettina Welz, Tomas Fitzgerald, et al.

Selected by 24 June 2024

Girish Kale, Jennifer Ann Black

Developmental Biology

Fetal brain response to maternal inflammation requires microglia

Bridget Elaine LaMonica Ostrem, Nuria Dominguez Iturza, Jeffrey Stogsdill, et al.

Selected by 24 April 2024

Manuel Lessi

Neuroscience

Also in the genetics category:

Intracellular diffusion in the cytoplasm increases with cell size in fission yeast

Catherine Tan, Michael C. Lanz, Matthew Swaffer, et al.

Selected by 18 October 2024

Leeba Ann Chacko, Sameer Thukral

Cell Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA

Brett T. Wisniewski, Laura L. Lackner

Selected by 30 August 2024

Leeba Ann Chacko

Cell Biology

preLists in the developmental biology category:

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

GfE/ DSDB meeting 2024

This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.

 



List by Joyce Yu

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Society for Developmental Biology 79th Annual Meeting

Preprints at SDB 2020

 



List by Irepan Salvador-Martinez, Martin Estermann

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EDBC Alicante 2019

Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.

 



List by Sergio Menchero et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.

 



List by Alexa Sadier

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the evolutionary biology category:

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

EMBO | EMBL Symposium: The organism and its environment

This preList contains preprints discussed during the 'EMBO | EMBL Symposium: The organism and its environment', organised at EMBL Heidelberg, Germany (May 2023).

 



List by Girish Kale

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

COVID-19 / SARS-CoV-2 preprints

List of important preprints dealing with the ongoing coronavirus outbreak. See http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic

 



List by Dey Lab, Zhang-He Goh

1

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.

 



List by Alexa Sadier

Also in the genetics category:

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar
Close