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Features & Reviews Editor – Journal of Cell Science

Posted by , on 6 October 2020

Closing Date: 15 March 2021

Journal of Cell Science, published by The Company of Biologists, is seeking enthusiastic and motivated applicants for the role of Features & Reviews Editor.

Joining an experienced and successful team, including Editor-in-Chief Michael Way, this is an exciting opportunity for a talented scientific editor to make a significant contribution to an important journal in the field of cell biology. Journal of Cell Science publishes outstanding primary research articles, reviews and topical comment, and continues to expand its services to authors and readers.

Applicants should have a PhD, and ideally postdoctoral experience, in cell biology or a relevant scientific field, and a broad knowledge of cell biology. The successful candidate will have strong communication, networking and interpersonal skills. We are also looking for enthusiasm, motivation, commitment, and a broad interest in science and the scientific community. Editorial experience is preferable but not essential.

Core responsibilities include:

  • Commissioning, handling peer review and developmental editing of review-type content
  • Maintaining and developing the ‘Cell Scientists to Watch’ interviews section of the journal
  • Writing content for the Research Highlights section of the journal
  • Representation of the journal at local and international conferences and within the wider scientific community
  • Creative involvement in the journal’s development and marketing activities

Additional responsibilities may be available for the right candidate. The Features & Reviews Editor will work alongside both an experienced Executive Editor and Senior Editor. This is a permanent, full-time position, and is based in The Company of Biologists’ attractive modern offices on the outskirts of Cambridge, UK.

The Company of Biologists exists to support biologists and inspire advances in biology. At the heart of what we do are our five specialist journals – Development, Journal of Cell Science, Journal of Experimental Biology, Disease Models & Mechanisms and Biology Open. We take great pride in the quality of the work we publish. We believe that the profits from publishing the hard work of biologists should support scientific discovery and help develop future scientists. Our grants help support societies, meetings and individuals. Our workshops and meetings give the opportunity to network and collaborate.

Applicants should be eligible to work in the UK and are requested to send to recruitment@biologists.com: a CV; a 400-word summary of a recent ground-breaking development in cell biology; and a cover letter explaining their interest in the post. Initial application deadline is 2 November 2020, but we will consider applications on a rolling basis so encourage candidates to apply as soon as possible.

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Community Manager for Microscopy Community Site FocalPlane

Posted by , on 6 October 2020

Closing Date: 15 March 2021

Journal of Cell Science and its publisher The Company of Biologists are seeking to appoint a new Community Manager to run our newly launched microscopy community website, FocalPlane. This is initially offered as a two-year fixed term contract with the expectation that as the project develops the role would become permanent in the future.

Launched in 2020, FocalPlane is a curated and centralised platform for the microscopy community to share news and techniques, discuss issues relevant to the field and read about the latest research and events. We are now looking for an enthusiastic and motivated person with fresh ideas and a willingness to learn to join us to develop and maintain this site.

Core responsibilities of the position include:

  • Creating and commissioning content for FocalPlane, including writing posts and soliciting content from the academic community, societies, companies and other organisations
  • Providing user support and ensuring site functionality on a day-to-day basis
  • Providing creative and practical input into the development of the site
  • Maintaining and developing the site’s presence on social networking sites such as Facebook and Twitter
  • Representing Journal of Cell Science and FocalPlane at international conferences

Essential skills:

  • PhD in a relevant scientific field, ideally with experience of microscopy
  • Willingness to grow and develop knowledge of microscopy
  • Demonstrable ability to write for an online audience and/or produce social media content
  • Clear understanding of the online environment as it applies to scientists
  • Excellent interpersonal and communication skills
  • Strong networking abilities online and in person

Desirable:

  • Experience with additional media (e.g. video or podcasting)
  • Experience with WordPress
  • Contacts within the microscopy community

This is an exciting opportunity to develop a hub for the microscopy community – in a similar vein to the Company’s established community site for developmental biologists, the Node – and to engage with relevant people at all levels: academics, developers, facilities, institutes and companies. The Community Manager will work alongside an experienced in-house team, including the Executive Editor of Journal of Cell Science. Additional responsibilities may be provided for the right candidate.

The Company of Biologists exists to support biologists and inspire advances in biology. At the heart of what we do are our five specialist journals – Development, Journal of Cell Science, Journal of Experimental Biology, Disease Models & Mechanisms and Biology Open. All are edited by expert researchers in the field, and all articles are subjected to rigorous peer review. We believe that the profits from publishing the hard work of biologists should support scientific discovery and help develop future scientists. Our grants help support societies, meetings and individuals. Our workshops and meetings give the opportunity to network and collaborate.

Applicants should send a CV along with a covering letter that summarises their relevant experience, and in particular any specific microscopy/image analysis skills, and includes links to any online activities, salary expectations, and details about why they are enthusiastic about this opportunity.

Applications and informal queries should be sent by email to recruitment@biologists.com. We may request written tests in advance of any interview.

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Postdoc position in the genetics of vascular malformations

Posted by , on 6 October 2020

Closing Date: 15 March 2021

The Childs lab studies developmental angiogenesis and vascular stabilization using the zebrafish model. We are looking for an outstanding postdoc to probe the mechanism of genetic vascular malformation development. We are located at the University of Calgary, Canada. Applicants should be within 3 years of their PhD degree and have a demonstrated track record of success in publications. Please send a letter of interest, your CV and the names of 3 potential referees to schilds@ucalgary.ca.

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Butterfly Visual System Development

Posted by , on 6 October 2020

Closing Date: 15 March 2021

 

We seek an outstanding postdoctoral candidate to join the Perry lab at the University of California, San Diego. Our group uses genetic and genomic approaches to study the development and evolution of neural systems. We use the insect visual system as a model to understand how the genome encodes the complexity of the brain and nervous system. We are interested in the mechanisms that generate the exquisite diversity of ways in which animals perceive and interact with the world.

We are specifically seeking independent, passionate, and highly motivated applicants for a postdoctoral position to study the evolution and development of butterfly color vision, with a focus on understanding the specific genetic changes that produce a more complex retinal mosaic. Butterflies have doubled the number of R7 photoreceptors in their retinas, allowing for an increased number of color comparisons (see Perry et al. Nature 2016). We use CRISPR to test gene function directly in developing butterfly retinas. A second part of this project will be aimed at understanding how the brain interprets this additional input and the role of developmental plasticity. A portion of the work will involve using sophisticated genetic tools in Drosophila to understand relevant circuits. A Ph.D. in the biological sciences with at least three years of laboratory research experience in molecular or developmental biology is required. Experience with Drosophila or other genetic model systems is preferred but not required.

This is a renewable two-year position with full benefits, which will be extended as needed upon good performance of the candidate. Salary will be competitive and dependent on the level of experience of the candidate. Applicants should email a CV and a description of research interests to Prof. Perry (mwperry@ucsd.edu), along with contact information for three references. Applications submitted by November 1st, 2020 will receive priority consideration, but the position will remain open until filled. Start date is flexible.

It is an incredibly exciting time to be a developmental biologist as new tools such as CRISPR and single cell sequencing allow us to move beyond model systems in order to ask targeted questions about the mechanisms that adapt animals to their unique environments. Apply and join the adventure!

Note: this is a reposting for a search that was cancelled due to COVID.

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scRNA-seq Biocurator/Ontologist position at FlyBase

Posted by , on 5 October 2020

Closing Date: 15 March 2021

We are seeking to recruit a new member to our team at the University of Cambridge to contribute to the FlyBase Drosophila database (https://flybase.org).

A large and growing community of Drosophila biologists is producing single cell transcriptomic data with potentially high value to the research community. This includes both individual labs and also large-scale community efforts focussed on sharing and annotating single cell RNA sequencing (scRNA-seq) datasets covering the whole fly, such as Fly Cell Atlas (https://flycellatlas.org/).

The successful applicant will work closely with the Gene Expression Team (https://www.ebi.ac.uk/about/people/irene-papatheodorou) at EMBL-EBI, in particular those members responsible for the Single Cell Expression Atlas (scAtlas) (https://www.ebi.ac.uk/gxa/sc/home), in order to maximise the usefulness of the scRNA-seq data to the community.

Closing date 4th Nov 2020.

More information and application form here: http://www.jobs.cam.ac.uk/job/27175/

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Doctoral positions available at the Graduate School Life Science Munich

Posted by , on 2 October 2020

Closing Date: 15 March 2021

The Graduate School Life Science Munich (LSM) offers an international doctoral programme to motivated and academically qualified next generation researchers at one of Europe’s top Universities. LSM members are internationally recognized for their innovative research approaches and technologies, they are aiming to answer essential questions relevant to basic and applied biological and biochemical research. Within their own research group or in collaboration with a specialized research group on campus, LSM doctorates are given the opportunity to learn and command a variety of techniques. Furthermore, the graduate programme holds various workshops and seminars that strengthen and prepare doctorates for a successful career as scientists.

With over 40 research groups from the Faculty of Biology and the Faculty of Chemistry and Pharmacy of Ludwig Maximilian University (LMU) München, the LSM in its prominent location within the HighTechCampus in Martinsried south of Munich, contributes to the enormous possibilities for support, interdisciplinarity and constant scientific input from the surrounding laboratories. Available research projects cover areas from Cell and Developmental Biology, Epigenetics, Genetics, Microbiology, Molecular Biology, Biochemistry, Evolutionary Biology, Plant Sciences, Pharmacology, and Systematics. https://www.lsm.bio.lmu.de/faculty/index.html

LSM calls for doctoral applications on a yearly basis, open from the 1st of October until the 30th of November 2020. Applicants are selected in a multi-step process through our online portal, thus ensuring openness and fairness throughout the application procedure. Every complete submission is evaluated by the LSM coordinator. Applications will be independently reviewed by several faculty members of the LSM Graduate School. Based on academic qualification, research experience, motivation, scientific background and the letters of recommendation, candidates will be selected to participate in the LSM Interview week. After thorough evaluation through the LSM committee board members, successful candidates will be invited to join the LSM Graduate School. Further information and details about the online application process and the available funded research projects can be found here: https://www.lsm.bio.lmu.de/apply/index.html

Additionally, the DAAD and LSM jointly award 2 full scholarships for doctoral study financed by the DAAD Graduate School Scholarship Programme (GSSP). Further information and details about the online application process and the available DAAD scholarships can be found here: https://www.lsm.bio.lmu.de/daad-lsm-application/index.html

LSM Poster 2020

Contact information:

Graduate School Life Science Munich
Nadine Hamze
Ludwig-Maximilians-University Munich
Faculty of Biology
Grosshadernerstr. 2
82152 Planegg-Martinsried
Germany
Tel: +49 (0) 89 / 2180-74765
E-Mail: info.lsm@bio.lmu.de
Website: http://www.lsm.bio.lmu.de

 

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Development presents… A new developmental biology webinar series

Posted by , on 2 October 2020

Updated 2 October

We’ve had over 400 registrations already! For those attending, this post has been updated with an order of play for the day, and the webinar homepage has also been updated with a How To for Remo, our browser-based conference software – no download needed!


 

 

Development presents… is a new webinar series showcasing the latest developmental biology and stem cell research. The webinars are chaired each month by a different Development Editor, who invites talks from authors of exciting new papers and preprints. First authors are particularly encouraged to present their work – we hope the series will become a forum for supporting early career researchers. As well as presentations and live Q&A sessions, you’ll also get the chance to meet the speakers and fellow participants at interactive virtual tables. For dates and details of future events once confirmed, why not bookmark thenode.biologists.com/devpres

The first webinar of the series will take place on Wednesday 7 October at 16:00 BST and be chaired by Development’s Editor-in-Chief, James Briscoe (Group Leader at the Francis Crick Institute in London), who has has brought together three exciting talks.

 

 

Webinar schedule (all times in GMT+1)

15:55

Remo conference centre opens (accessible via a link sent out on the day to registered participants).

16:00

Welcoming remarks from James Briscoe

16:05

Milica Bulajić (PhD student in Esteban Mazzoni’s lab in NYU)

‘Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns’

16:25

Andrew Economou (now a postdoc with Caroline Hill at the Francis Crick Institute)

‘Networking with Turing: towards high order morphogen models’

16:45

José Blanco-Ameijeiras (PhD student with Elisa Marti at the Institute of Molecular Biology of Barcelona)

‘Cell intercalation driven by SMAD3 underlies secondary neural tube formation’

17:05

Open house – chance to meet the speakers and other participants

18:00

End of event

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Postdoctoral position at The Francis Crick

Posted by , on 2 October 2020

Closing Date: 15 March 2021

A postdoctoral position (fully-funded for 4 years) is available in the laboratory of Dr. Rashmi Priya at the Francis Crick institute. Dr Priya’s laboratory focuses on the mechano-molecular control of organ development during embryogenesis. For a brief overview of the lab, please visit https://www.crick.ac.uk/research/labs/rashmi-priya or get in touch with Dr. Priya.

The Organ Morphodynamics lab is starting at the Francis Crick in January 2021 and will grow to six people over the next 2 years. We have generous core-funding support and access to state-of-the-art facilities and technology platforms including Advanced light microscopy, High throughput sequencing, Bioinformatics and Image analysis help desk. The Francis Crick is a modern, world class biomedical research institute in central London. The Francis Crick and the participating organizations (UCL, Imperial College London and King’s College London) offer a highly inclusive, collaborative and thriving research community with many career development opportunities.

I am especially looking for candidates who are interested in combining interdisciplinary approaches to gain a systemic understanding of organ morphogenesis using a well-suited model system – the developing zebrafish heart. The project will aim to unravel the underlying mechanical, molecular and geometric interactions that transforms a developing heart from a simple epithelium into a highly intricate patterned organ.

The suitable candidate will use advanced microscopic techniques, image analysis, genetic/optical manipulations, biophysical approaches and collaborate with theoreticians to understand how morphological and molecular complexity emerges during heart development. Candidates with a strong background in advanced confocal and/or light sheet imaging, image analysis, zebrafish genetics and a good understanding of the mechanics of tissue morphogenesis and/or heart development are encouraged to apply. The successful candidate should be keen in pursuing collaborative research, should have excellent communication skills and should be a good team player.

For further details about the project and how to apply, please visit the Crick vacancies portal or get in touch – rashmi.priya@crick.ac.uk.

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Forgotten filaments to the fore

Posted by , on 1 October 2020

The cytoskeletal filament network within our cells underpins the functionality of virtually all cellular processes. Apart from conferring a structural framework giving cells their unique shapes, the cytoskeleton also regulates a host of dynamic activities ranging from cell division to migration, transport, and polarization. Understanding how the cytoskeleton orchestrates these events with unique spatial and temporal specificity within a developing organism remains one of the most fascinating questions in the field.

 

During the earliest stages of mammalian life, the cytoskeleton guides the formation of the blastocyst – a cluster of 32- to 64-cells comprising a differentiated outer cell layer known as the trophectoderm that will give rise to placental tissues, and a pluripotent inner cell mass that later forms the foetus itself (White et al., 2018). The early mouse embryo contains all three major cytoskeletal filament classes: actin, microtubules, and intermediate filaments. Interestingly, while many studies have investigated the roles of actin and microtubule filaments in regulating early embryo development, the function of the intermediate filament network during this time has remained entirely unknown. Yet unlike their more well-studied counterparts, intermediate filaments encompass a diverse range of proteins including keratin, vimentin, and desmin that are expressed in unique tissue-specific patterns, and can self-assemble into filaments in the absence of cofactors or nucleators.

 

We initially approached this question by consulting the literature: in 1980, the first papers were published identifying keratins as the first and only cytoplasmic intermediate filaments expressed in the early mouse embryo (Jackson et al.,1980; Paulin et al., 1980). Although there are over 50 keratin subtypes, the predominant ones in the early embryo are K8 and K18, the same subtypes that are characteristic of simple epithelia in mature tissues. A number of studies subsequently investigated keratin expression patterns during these early developmental stages, establishing their restricted localization in trophectoderm cells of the blastocyst and complete absence within the inner cell mass (Chisholm and Houliston, 1987; Duprey et al., 1985; Oshima et al., 1983). Yet their expression prior to blastocyst formation was never firmly established, owing to conflicting findings and differing methodologies. Combined with the fact that keratin knockout embryos survived preimplantation development (Baribault et al., 1993, 1994; Magin et al., 1998) and that the few early studies perturbing keratin functions reported no significant embryo phenotypes (Emerson, 1988), interest in keratin filaments during early embryo development gradually waned around the turn of the millennium.

 

Relooking at keratin filaments in the early mouse embryo almost three decades later offered us surprising insights. Although keratins are most well-known for their structural role in hair, skin, and nails, more recent studies have found that keratins within epithelial tissues also have diverse non-structural roles, including cell polarization, apoptosis, and cell cycle regulation (Kirfel et al., 2003; Pan et al., 2013). Armed with this knowledge and the foundation laid by earlier studies, we thus explored whether keratins in the early embryo – with their unique expression pattern in the outer epithelial layer (trophectoderm) of the blastocyst – could play specific structural or non-structural roles during embryo development like other epithelial keratins.

 

To investigate keratin functions, we established a combination of immunofluorescence and live-embryo imaging techniques that enabled us to explore keratin patterns with high spatial resolution and evaluate their dynamic changes during development. Apart from these technical improvements offered by newer microscopy tools, we also went beyond the early keratin studies by establishing knockdown and overexpression methods to manipulate keratin filaments within the living embryo, providing a valuable model for assessing keratin functions.

 

In our paper, we report some of the first functions for keratin filaments in the early mouse embryo. We find that keratin filaments act as asymmetrically inherited fate determinants that specify the first trophectoderm cells of the early embryo. Unlike actin and microtubule filaments that dramatically reorganize during cell division, keratins are stably retained within the apical region of the mitotic cell, during the first divisions that segregate cells into inner and outer positions at the 8- to 16-cell stage (Fig. 1). This apical retention of keratins biases their asymmetric inheritance by the outer forming daughter cell (Fig. 2). Apical keratin localization is further mediated by the F-actin-rich apical domain,without which keratin filaments become homogenously distributed throughout the cell, and no longer segregate unequally between the forming daughter cells. This underscores the importance of keratin-actin interactions in guiding keratin filament dynamics and functions during embryonic development.

 

Fig. 1. Keratin filaments (labelled by K8 immunofluorescence) are stably retained in both interphase and mitotic cells of the embryo. In contrast, both the apical enrichment of actin (labelled by Phalloidin-Rhodamine) and the microtubule network (labelled by alpha-tubulin immunofluorescence) throughout the cytoplasm are lost when cells enter mitosis.

Fig. 2. Live embryo imaging reveals that keratin filaments (labelled by K18-Emerald) are asymmetrically inherited by outer daughter cells, during the cell divisions segregating inner and outer cells of the embryo.

 

How do keratins go on to function as fate determinants? Following their asymmetric inheritance by outer cells of the embryo, we find that keratins promote apical polarization and levels of downstream members of the Hippo pathway including Amot and nuclear Yap. This in turn drives the expression of Cdx2, one of the key transcription factors specifying trophectoderm fate in the early embryo. Conversely, outer cells that did not inherit keratin filaments or those with keratin knockdown fail to establish these trophectoderm features, instead displaying levels of Cdx2 comparable to inner cells of the embryo.

 

At later stages, in line with the established role of keratins in conferring structural support to epithelial tissues, the dense keratin network in the trophectoderm is also important for supporting blastocyst morphogenesis. Keratin knockdown reveals that without this filamentous network, embryos display defective apical and junctional morphologies suggestive of weakened tension, as well as reduced cellular stiffness. Thus, keratins in the embryo regulate both morphogenesis and fate specification to promote blastocyst formation and the specification of the first cell lineages in development.

 

Finally, our study also led us to uncover a surprising pattern of keratin expression during preimplantation development: Keratins assemble a dense filament network extending throughout all cells of the blastocyst trophectoderm, but instead display a salt-and-pepper pattern during earlier stages (Fig. 3). In both the mouse and human embryo, the first filaments form in a subset of cells of the 8- to 16-cell embryo, and the proportion of keratin-assembling cells increases over time. Importantly, the heterogenous keratin expression stands in stark contrast to actin filaments and microtubules, which both do not differ significantly in expression from cell to cell. This initial heterogenous expression of keratins at the 8-cell stage can be further attributed to cell-cell differences in the levels of the BAF chromatin remodelling complex within the 4-cell embryo, with manipulations of BAF levels sufficient to trigger changes in keratin expression patterns.

 

Fig. 3. Keratin filaments are heterogeneously expressed in the early embryo, beginning first in a subset of cells of the 8- to 16-cell mouse and human embryo. By the blastocyst stage, all trophectoderm cells are covered with a dense keratin filament network, but inner cells remain devoid of filaments.

 

Together, these findings connect cellular heterogeneities within the early embryo to fate specification pathways at later stages via the regulation of keratin expression. Although keratins have long been utilized as markers of the trophectoderm, our work further identifies keratins as regulators of trophectoderm fate, elucidating one of the first functions for these filaments during early development. With keratins once again placed in the spotlight and more experimental tools at our disposal, our understanding of keratins in the early mammalian embryo is set to expand in the years to come.

 

Lim, H.Y.G. et al. Keratins are asymmetrically inherited fate determinants in the mammalian embryo. Nature 585, 404–409 (2020). doi: 10.1038/s41586-020-2647-4.

 

References

Baribault, H., Price, J., Miyai, K., and Oshima, R.G. (1993). Mid-gestational lethality in mice lacking keratin 8. Genes & Development 7, 1191–1202.

Baribault, H., Penner, J., Iozzo, R.V., and Wilson-Heiner, M. (1994). Colorectal hyperplasia and inflammation in keratin 8-deficient FVB/N mice. Genes & Development 8, 2964–2973.

Chisholm, J.C., and Houliston, E. (1987). Cytokeratin filament assembly in the preimplantation mouse embryo. Development 101, 565–582.

Duprey, P., Morello, D., Vasseur, M., Babinet, C., Condamine, H., Brulet, P., and Jacob, F. (1985). Expression of the cytokeratin endo A gene during early mouse embryogenesis. Proceedings of the National Academy of Sciences of the United States of America 82, 8535–8539.

Emerson, J.A. (1988). Disruption of the cytokeratin filament network in the preimplantation mouse embryo. Development 104, 219–234.

Jackson, B.W., Grund, C., Schmid, E., Bürki, K., Franke, W.W., and Illmensee, K. (1980). Formation of Cytoskeletal Elements During Mouse Embryogenesis: Intermediate Filaments of the Cytokeratin Type and Desmosomes in Preimplantation Embryos. Differentiation 17, 161–179.

Kirfel, J., Magin, T.M., and REICHELT, J. (2003). Keratins: a structural scaffold with emerging functions. Cellular and Molecular Life Sciences (CMLS) 60, 56–71.

Magin, T.M., Schröder, R., Leitgeb, S., Wanninger, F., Zatloukal, K., Grund, C., and Melton, D.W. (1998). Lessons from Keratin 18 Knockout Mice: Formation of Novel Keratin Filaments, Secondary Loss of Keratin 7 and Accumulation of Liver-specific Keratin 8-Positive Aggregates. J Cell Biol 140, 1441–1451.

Oshima, R.G., Howe, W.E., Klier, G., Adamson, E.D., and Shevinsky, L.H. (1983). Intermediate Filament Protein Synthesis in Preimplantation Murine Embryos. Developmental Biology 99, 447– 455.

Pan, X., Hobbs, R.P., and Coulombe, P.A. (2013). The expanding significance of keratin intermediate filaments in normal and diseased epithelia. Current Opinion in Cell Biology 25, 47–56.

Paulin, D., Babinet, C., Weber, K., and Osborn, M. (1980). Antibodies as probes of cellular differentiation and cytoskeletal organization in the mouse blastocyst. Experimental Cell Research 130, 297–304.

White, M.D., Zenker, J., Bissiere, S., and Plachta, N. (2018). Instructions for Assembling the Early Mammalian Embryo. Developmental Cell 45, 667–679.

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The long road to understanding homeobox genes in the nervous system

Posted by , on 1 October 2020

Following the initial discovery of the homeobox in the 1980s in invertebrates and then vertebrates, it became quickly clear that homeobox genes come in two flavors – that of the Antennapedia-like HOX cluster genes and that of the many more non-clustered genes with diverse sequence and expression features (Gehring, 1998). One theme that became evident through expression and mutant analysis in a variety of organisms was the selective expression and function of homeobox genes within the nervous system (Gehring, 1998).

When I started to look for postdoctoral positions in the early 1990s, I was particularly intrigued by mutant phenotypes of several fly and worm homeobox genes (Blochlinger et al., 1988; Doe et al., 1988; Finney and Ruvkun, 1990; Way and Chalfie, 1988), but also by the work of the late Tom Jessell, who proposed a LIM homeobox code in the vertebrate spinal cord (Tsuchida et al., 1994). The simplicity and well-characterized nature of the C. elegans nervous system, as well as its genetic amenability was very appealing to me and, in 1996, I decided to join Gary Ruvkun’s lab. Gary’s lab had not only characterized one of the first C. elegans homeobox genes, unc-86 (Finney and Ruvkun, 1990; Finney et al., 1988); Thomas Bügrlin in Gary’s lab had also used library screening with degenerate probes, a method that now, in the post-genome era, seems quite archaic, to discover the abundance of homeobox genes in this simple organism (Burglin et al., 1989).

In Gary’s lab, I set out to study the expression and function of the LIM homeobox subfamily, which were discovered initially by Marty Chalfie (Way and Chalfie, 1988) and implicated further in neuronal identity specification by Tom Jessell’s lab (Tsuchida et al., 1994). Using emerging GFP reporter technology (Chalfie et al., 1994) and mutant analysis, I determined what turned out to be mostly incomplete expression patterns (owing to the shortcomings of “classic” reporter genes which often just contained fractions of their surrounding gene regulatory regions) and mutant phenotypes that could only be very superficially analyzed (owing to a shortage of markers that allowed for a more in-depth analysis of mutant phenotypes)(Hobert et al., 1998; Hobert et al., 1997; Hobert et al., 1999).

After starting my own lab at Columbia University in 1999, a string of students and postdocs (Zeynep Altun, Adam Wenick, Ephraim Tsalik, Feifan Zhang, Pat Gordon, Vincent Bertrand, Maria Doitsidou, Nuria Flames, Rich Poole, Paschalis Kratsios, Marie Gendrel, Esther Serrano-Saiz, Laura Pereira, among others) continued to work on a small number of specific homeobox genes, digging much deeper into what these genes did in the nervous system. One theme that continued to emerge throughout this analysis was that not only the classic unc-86 and mec-3 genes, studied in impressive depth by Marty Chalfie over the years (Chalfie, 1995), but other homeobox genes as well had a remarkably broad effect on the differentiation of specific neuron types. Rather than regulating only some subset of specific identity features in a neuron, several homeobox genes fulfilled a “master regulatory” role in controlling most, if not all, known identity features of a neuron, through direct initiation and maintenance of terminal differentiation gene batteries. This led me to propose the concept of “terminal selectors” of neuronal identity, a term extended from the Drosophila field where “selector genes” were coined as genes that act earlier in development to specify the identity of developing fields and tissues (Hobert, 2016).

This trajectory finally led to the work of Molly Reilly, a graduate student in my lab, who recently set out to achieve the ambitious goal of describing the expression patterns of the entire homeobox gene family across the entire C. elegans nervous system (Reilly et al., 2020). This tremendous leap forward was, as so often is the case, enabled by novel technology. First, gene expression patterns, or even better, protein expression patterns, can now be much more reliably identified by not just extracting some arbitrary small regulatory region adjacent to your gene of interests to drive a reporter gene. Rather, bacterial recombineering technology enables the reporter tagging of genes in the context of very large genomic intervals containing many genes up- and downstream of the gene of interest (Tursun et al., 2009). Moreover, CRISPR/Cas9 technology even allowed for reporter tagging of an entire locus in the endogenous context (Dickinson et al., 2013). But even with good reagents at hand, identifying sites of expression of a reporter gene across the entire nervous system has traditionally not been a small feat because neurons in C. elegans are tightly packed and their position can be locally variable. Here is where Eviatar Yemini, a postdoc in my lab, came in to solve the long-standing problem of neuronal cell identification. Using multiple distinct fluorophores (excluding GFP), Eviatar built a multicolor landmark strain, NeuroPAL, which unlike Brainbow-style technology, assigned neurons a strictly deterministic color code (Yemini et al., 2019). Crossing NeuroPAL with a GFP reporter strain enables unambiguous identification for the sites of gene expression, anywhere in the nervous system (Figure 1).

 

Figure 1: Examples of homeobox reporter gene expression patterns. The NeuroPAL transgene (left panel) was crosses to these reporters to unambiguously identify sites of homeobox gene expressions. Images courtesy of Molly Reilly and Ev Yemini.

 

Molly exploited these technological advances to (a) tag all but one of the 102 homeobox genes of C. elegans with a fluorescent reporter and (b) identify their sites of expression throughout the entire nervous system. What she found was something I could barely have dreamed of when starting my postdoc in Gary’s lab: Most of the conserved homeobox genes are not only sparsely expressed throughout the nervous system of the worm, but each of the 118 different neuron classes displayed a unique combination of homeobox genes (Figure 2).

 

Figure 2: Homeobox codes. Shown are all the homeobox gene expression patterns that contribute to neuron class specific expression. Homeobox genes are on top, neuron classes on the left. Reproduced from Reilly et al., 2020.

 

Homeobox genes are thus a comprehensive “descriptor” of neuronal diversity throughout an entire nervous system – a homeobox code for all neurons! Furthermore, the mapping of these homeobox genes led another graduate student, Cyril Cros, to find that neurons previously not known to express or require a homeobox gene, do indeed also require a homeobox gene for their identity specification (Reilly et al., 2020).

This is not the end of the road. The lab remains motivated to test whether indeed every single C. elegans neurons not only expresses, but requires a homeobox gene for their identity specification. Moreover, it remains little explored to what extent we can reprogram the identity of neurons by respecifying their homeobox codes. I am looking forward to see whether work in other systems with more complex brains will also uncover the broad employment of homeobox codes. Recent transcriptome analysis in restricted parts of the flies and mice CNS indeed provides tantalizing hints for similar specificity and selectivity of homeobox gene expression in more complex nervous systems (Allen et al., 2020; Davis et al., 2020; Sugino et al., 2019).

 

 

References

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