This interview first appeared in Development.

Haruhiko Koseki is Director of the Developmental Genetics Research Group at the RIKEN Research Center for Allergy and Immunology in Yokohama, where he studies the epigenetic regulation of Polycomb group genes in development. He recently joined Development as an Editor, and agreed to be interviewed about his research and about science in Japan.

When did you first become interested in developmental biology?

I started university in the school of medicine, and became fascinated with comparative anatomy and embryology. In medical school in Japan, the first 4 years consist of basic classes, and the last 2 years are clinical training. I didn’t enjoy clinical training very much, and decided to move to immunology research instead of becoming a clinician. At that time, the field of immunology was exploding, and the discovery of the rearrangement of immunoglobin genes led to the study of cell differentiation in that field. My PhD research was in immunogenetics, but I discovered that immunology is not really the field to be in to study differentiation or patterning. Because of that, I made the decision to move to developmental biology. I did my postdoc with Rudi Balling in Freiburg (Germany), working on development based on mouse genetics. I really enjoyed life in Freiburg, and during my time there I published my first paper in Development.

How does research in Japan compare with research in Europe?

When I was in Germany, I learned that, in Japan, science is not fundamental science, but it’s science aimed at technology. We’re always asked about the social benefit of our discoveries. That is a natural question to ask, but I think, in Europe, people just appreciate science for the discovery.

Another difference used to be the budget invested into science. Until recently, it was much smaller in Japan compared with Europe or the USA, but in the last few decades this has changed, and at the moment it’s not very different from Europe. But I’m not sure our productivity is at the same level as that of European scientists. I think we’re not very good at sharing resources, infrastructure or ideas. It also seems that Japanese postdocs and students are not interacting much with each other. They’re relatively quiet and shy compared with European students. Traditionally, we’re educated to behave as modestly and quietly as possible. But now we have many foreign students and postdocs, and I think many students are starting to notice that this shy attitude is not ideal to get ahead in science.

What are you currently working on?

I’m mostly studying the epigenetic regulation underlying the maintenance of certain cell types and differentiation. When I did my postdoc in Freiburg, I was investigating how the notochord regulates somite differentiation, but when I got back to Japan in 1994, I realized that field is so competitive. I didn’t want to do similar things to what everyone else was already doing. At that time, my main interest was axial skeletal patterning. In the early 1990s, many people working on mammalian axial patterning were looking at Hox and signalling cascades. In Drosophila, Polycomb was already known to be a very important regulator for anterior/posterior specification, so I decided to work on Polycomb in the mouse. I used the system developed by Andras Nagy in Toronto (Canada) to generate many knockouts for components of mouse Polycomb complexes. Knockouts enabled us to see whether the mammalian Polycomb proteins are doing something important during development, but it’s difficult to address the underlying mechanisms by using developing embryos because of their cellular heterogeneity. To bypass this issue, we’re now focusing on ES cells as a model to study Polycomb function, to find out how various Polycomb complexes cooperate to maintain certain cell types and how their functions are modified when cells differentiate into different states. Now the critical issue is learning how catalytic activities and chromatin binding of Polycomb complexes are regulated during cell cycle progression. Ideally I’d want to get back to real embryos, but for that we need more technical breakthroughs – maybe a new device to image the chromatin status of certain loci in the living embryo, or something like that.

What are some other projects that your research group is working on?

Most of us are working on various aspects of Polycomb function. Polycomb proteins form at least a few multimeric protein complexes, but each component also interacts with many other modules, outside of Polycomb complexes, during differentiation or cell cycle progression, and approximately half of my research group is studying these interactions. For example, work with knockout mice shows that the axial skeleton phenotype of the DNA methyltransferase mutant is very similar to that of the Polycomb knockout. That suggests that there could be a functional and profound interaction between Polycomb and DNA methylation mechanisms, and that’s one of the things we’re investigating. This is a big challenge for us because of its extensive complexity and redundancy.

You also administer the mouse facility at your institute. Who uses this facility?

The mouse facility is shared by the five different institutes that make up the Yokohama RIKEN site. The animal facility is mainly used by the immunologists, but is increasingly also occupied by people from the institutes for human genetics, ‘omics’ sciences and plant sciences. This suggests that mouse genetics is becoming a more general tool to address a wide spectrum of biological and medical questions. Mouse genetics has developed in parallel with immunology, developmental biology and neurosciences, and will be further advanced by collaborating with many other fields of biomedical sciences, as well as other disciplines. It is really exciting to see with my own eyes how things are developing in this field. I am particularly interested to see the upcoming contribution of mouse genetics to the understanding of pathogenic mechanisms underlying various human diseases.

How have you experienced your first few months as a Development Editor?

It’s a great pleasure, but I’m still getting accustomed to the job, so it’s still taking up a lot of time. This is my first experience as an academic editor, and I learned a lot in the last few months, particularly from reviewers’ comments. Geographically, we’re very isolated in Japan, and not readily exposed to the way science is discussed and evaluated in the USA or Europe. Now, through reviewer comments, I get a look into how people are thinking about papers and how they express their views.

Are there any particular papers that you would really like to see people submit to Development?

Developmental biology is linked to several other fields. For example, imaging is becoming very quantitative and mathematical modelling is now used to describe developmental processes. Unfortunately, genomics is still a bit far from developmental biology, because of the heterogeneity of cells and quantitative limitations of samples. With technical breakthroughs such as chromatin immunoprecipitation, the field of genomics is moving closer to developmental biology, but many genomics researchers don’t consider their work in that context. There might eventually be a lot of genomics studies that are very interesting in terms of developmental biology, but genomics researchers might not think of submitting them to Development. The same is true, for example, for transcriptome and metabolome studies.

What would people be surprised to find out about you?

I have played volleyball since I was a high school student. I didn’t have a lot of opportunity to play when I was in Germany, unfortunately, but except for these 3 years in Freiburg, I have kept playing. I’m now 50, and that’s old in terms of playing volleyball. Ten years ago, I had a fracture on my right ankle and it took almost half a year to recover. Recently, I’m a bit cautious of getting injured. But I still join in competitive games and sometimes go to the other side of Japan for competitions.

(2 votes)

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Here are the highlights from the current issue of Development:

Stem cells get cut loose

During tissue maintenance and regeneration, stem cells (SCs) are mobilised and migrate towards sites of tissue turnover or repair. However, owing to the inaccessible nature of most in vivo SC populations, very little is known about the molecular factors that regulate SC mobilisation. Otto Guedelhoefer and Alejandro Sánchez Alvarado tackle this problem by studying SC mobilisation during tissue homeostasis and regeneration in the planarian flatworm Schmidtea mediterranea (p. 3510). They show that planarian SCs migrate minimally in the absence of wounding; in partially irradiated animals, SCs do not migrate from the areas that were shielded from radiation to populate irradiated areas. Importantly, the researchers report, amputation increases SC dispersal and induces directional recruitment of SCs to sites of tissue repair, suggesting that factors capable of directing SCs are activated upon amputation. These findings highlight that, in planaria, SC depletion alone is not sufficient to trigger SC migration and that loss of tissue integrity is required to promote the directional migration of SCs.

Coupling genome defence to epigenetic reprogramming

DNA methylation plays an important role in gene silencing and repressing transposable elements (TEs). During primordial germ cell (PGC) development, DNA methylation marks are erased during extensive epigenetic reprogramming, so how does this demethylation impact gene expression and TE repression in PGCs? Richard Meehan and co-workers (p. 3623) show that DNA methylation at the promoters of germline-specific genes couples genome-defence mechanisms to epigenetic reprogramming in mouse PGCs. The researchers identify a set of germline-specific genes that are dependent exclusively on promoter DNA methylation for their silencing; their promoters possess specialised chromatin in somatic cells that does not acquire additional repressive histone modifications. This set, they discover, is enriched in genes involved in suppressing TE activity in germ cells, and the expression of these genes is activated during two phases of DNA demethylation in PGCs. These findings suggest that unique reliance on promoter DNA methylation acts as a highly tuned sensor of global DNA demethylation and allows PGCs to be primed to suppress TEs.

Stan points the way in planar polarity

Many epithelial tissues display planar cell polarity (PCP). This phenomenon has been best studied in Drosophila in which most epidermal cells produce hairs at one side that all point in the same direction. The molecular mechanisms underlying PCP establishment remain controversial. Key players are the transmembrane proteins Starry night (Stan; also known as Flamingo), Frizzled (Fz) and Vang Gogh (Vang, also known as Strabismus). Stan, a protocadherin, forms homodimeric bridges between cells. These bridges appear to link Fz and Vang on the abutting distal and proximal faces of adjacent cells, and their resulting asymmetric distributions polarise both cells to point the same way. Now, Struhl, Casal and Lawrence (p. 3665) report the surprising finding that Vang is not essential for cell polarisation. Instead, asymmetric interactions between Stan and Stan/Fz are sufficient to define polarity, and Vang plays an accessory role, probably by enhancing the capacity of Stan to interact with Stan/Fz. These results challenge current models of PCP, although the authors propose an alternative that may reconcile the data.

Predicting embryonic axes

In many animals, the polarised transport of maternal factors by the microtubule cytoskeleton is required for setting up embryonic axes. Now, Karuna Sampath and colleagues show that microtubules at the vegetal cortex of early zebrafish embryos are dynamically remodelled and predict the future embryonic axis (p. 3644). Using live imaging, they find that two transient populations of microtubules – perpendicular bundles and parallel arrays – are detected exclusively at the vegetal cortex of fertilised embryos before the first cell division. The perpendicular bundles, which are likely to transport maternal factors via the yolk to the blastoderm, extend from the vegetal cortex and orient along the animal-vegetal axis. The parallel arrays form autonomously even in the absence of sperm entry and fertilisation. Importantly, the asymmetric orientation of parallel arrays shortly after fertilisation predicts where the zebrafish dorsal structures will form. Finally, the authors provide in vivo evidence for cortical rotation-like movements of cytoplasmic granules, similar to those occurring in Xenopus, suggesting that such movements might be more common in development than previously thought.

Potassium channels and patterning

Mutations that disrupt the function of the inwardly rectifying Kir2.1 potassium channel cause developmental defects in both humans and mice, but the mechanisms underlying these abnormalities remain unclear. Now, on p. 3653, Emily Bates and co-workers show that disruption of a homologous Drosophila potassium channel, Irk2, causes developmental defects by modulating signalling of Decapentaplegic (Dpp), a bone morphogenetic protein (BMP) homologue. The authors find that compromised Irk2 function causes wing patterning defects similar to those observed when Dpp signalling is disrupted. The phenotypes of Irk2 mutant flies are enhanced by reducing Dpp function. Importantly, the researchers demonstrate that aberrant Irk2 function leads to a decrease in Dpp signalling within the wing: phosphorylation of Mad (a downstream effector of Dpp signalling) and the expression of spalt (a transcriptional target of Dpp) are decreased in Irk2 mutant wing discs. Collectively, these findings identify a novel mechanism by which potassium channels act during development and suggest that BMP pathways might somehow sense alterations in membrane potential.

Insights into the origins of HSCs

In mice, haematopoietic stem cells (HSCs) are first found in the dorsal aorta of early embryos shortly after 10.5 days post coitus (dpc) and in the foetal liver at 11 dpc. However, multipotent haematopoietic progenitors can also be detected in the dorsal aorta from 9 dpc. Do these cells contribute to adult haematopoiesis? Here, Ana Cumano and co-workers address this question by characterising this population of cells (p. 3521). The researchers show that multipotent progenitors detected in the dorsal aorta at 9 dpc, which they term immature HSCs (imHSCs), are endowed with long-term reconstitution capacity. Furthermore, they report, these cells are capable of evolving into HSCs under appropriate culture conditions and are able to colonise the mouse foetal liver. Of note, the early colonisation of the foetal liver by imHSCs precedes that of HSCs. Moreover, organ culture experiments suggest that, in the liver environment, imHSCs are able to mature into HSCs, thus identifying a novel stage in HSC development.

Plus…

An interview with Haruhiko Koseki

Primer: Epithelial-mesenchymal transitions: insights from development

Review: Tooth shape formation and tooth renewal: evolving with the same signals

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A detailed view of mice and fish

Michael Wong wrote about the 3D mouse embryo atlas he has worked on. The high-resolution atlas of an E15.5 mouse embryo allows for easier phenotyping of mutant strains, which can then be compared to the wildtype.

“If you have two groups of mouse embryos, one wild-type and one mutant, with a single gene knockout, how do you find out what’s different about them? How do you get clues to the function of the knocked out gene and its role in mouse embryo development? The most intuitive answer would be to look at the two groups of mouse embryos with a microscope and see if you can find any gross differences in morphology in the mutant group. You could hypothesize that the organ or structure that shows an aberration in comparison with the wild-type group is an area where that particular gene function is important and carry on with more focused phenotyping assays from there. This is the exact premise of our recent paper in Development.”

Mice were not the only animals that we’ve looked at in high-resolution detail. A recent paper in JCB described “virtual nanoscopy”, a method to collate multiple EM images to create a detailed map of a zebrafish embryo.

Gene rearrangement

Kalin Narov introduced us to recent work on gene rearrangement in the lamprey.

“…according to the authors, it is the first known example of a genome rearrangement of such scale in vertebrates, which makes it especially important for better understanding the evolution and mechanisms of vertebrate gene regulation.”

Conferences:

The Santa Cruz Developmental Biology Meeting took place earlier this month, and Katherine Brown wrote a summary for the Node.

Last month, at the SDB meeting, we continued our chain of poster winner interviews, as BSDB poster award winner Stephen Fleenor interviewed SDB poster award winner John Young.

Also on the Node:

– We’re going to make author biographies public on the Node. Make sure to check that yours is up to date!

– The culture medium used for preimplantation cultures in IVF labs may have long-term effects on development.

– Several new jobs have been posted on the site.

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This rather lengthy summary describes a fascinating progress in the field of GRN modeling; it is a review of the article “Predictive computation of genomic logic processing functions in embryonic development”, which appeared few days ago in PNAS.

Gene regulatory networks (GRNs) are complex systems of interacting genes that deploy in both space and time and are the main regulatory logic behind the specification of cell fates during embryogenesis (Li et Davidson, 2009). Gene networks can be derived for any developmental process or structure and, in simple terms, consist of nodes (the genes themselves) connected by lines, which represent the causal relationships between the different genes. More or less, the GRNs unfold in time in a hierarchical mode where the products of earlier genes serve as regulatory factors (inputs), controlling the expression (output) of downstream targets. Provided that sufficiently detailed knowledge about the gene expression pattern and interactions for a given process is available, a computational model of the respective GRN can be constructed. The main objective of constructing a GRN model is to be able to causally explain each regulatory event in the system and, most importantly, to be able to predict the outcomes of experimental perturbations.

One of the the most complete, if not the best for any developmental process to date, is the GRN behind endomesoderm specification in the embryo of a sea urchin with the lovely name Strongylocentrotus purpuratus, famous for being the favorite model organism in Eric H. Davidson’s lab. Eric’s lab has been instrumental in establishing the endomesoderm network, which currenty contains some 50 genes, and their recent article describes the generation of a Boolean computational model, which beautifully and correctly reconstructs the spatiotemporal expression pattern of the interacting genes and allows for predictions to be made about the effects of changes in the system (Peter et al, 2012).

The computational model has been created by the incorporation of several sources of data: observations on the expression patterns of regulatory genes in space and time and results from trans and cis perturbation experiments. There are four spatial domains in the sea urchin embryo, based on differential gene expression, concerned with the endomesoderm specification -skeletogenic and non-skeletogenic mesoderm, and anterior and the future posterior endoderm. The data was used to construct an abstract representation of the interactions using Boolean logic. At the core of the model are the vector equations – one for every gene in the model. Each equation captures all inputs that sum at a respective node and give its output in Boolean terms, 1 – “on” or 0 – “off”. Understandably, the inputs are the outputs of other genes in the system and the relevant maternal inputs provide the initial triggers – the starting regulatory state.

A strong feature of the model is the incorporation of several other characteristics of the developing embryo, like the notion of intercellular signalling, embryonic geometry (which is the relative position of the four spatial domains in the embryo) and real-time kinetics of gene expression. Including such parametres in the model is important for the configuration of the spatial domains relative to each other changes with time and the kinetics of target gene transcription is a function of the temporal expression features of its regulators (like kinetics of RNA and protein synthesis and turnover). As for the latter, an earlier investigation by the same group has revealed a rather surprising phenomenon, that the step time (this is the “interval between activation of a given regulatory gene and the activation of an immediate downstream target…”) is rather uniform for most genes operating during early sea urchin development, and is approximately 3 hours. This characteristic was included in the model.

The usefulness of the computational model was first revealed by testing its ability to reproduce the regulatory state (the sum of all known regulatory genes expressed at a particular time interval) for each domain. Remarkably, there was a perfect match between the experimentally observed and computed patterns of expression of 33 genes, with only two exceptions – the bm1/2/4 and wnt8 genes. For these genes, the model resulted into a novel expression domain or prolonged expression, respectively, which is most likely due to the lack of knowledge about additional inputs operating in the embryo. Second, the incorporation of a uniform time step in the model successfully reproduced the observed dynamics of spatial gene expression, which is rather surprising, and further supports the idea that the regulatory genes of the S. purpuratus embryo operate with similar kinetics. Curiously, when the model was run with a different step time ( of 4 hours instead) the result was a catastrophic discrepancy in the expression kinetics of many genes.

The next task, and a most daunting one, was to challenge the model’s explanatory power by manually changing selected initial parameters (“removing” or “expressing ectopically” selected genes) and comparing the computational results with data derived from previous experimental perturbations of those same genes. For instance, in one of the settings the authors extinguished delta expression from the skeletogenic mesoderm, which in the model resulted in the loss of gatae and gcm  expression in the non-skeletogenic mesoderm and the ectopic expression of V2 endoderm genes, like blimpb1, foxa and hox11/13b. So far so good – this was exactly in agreement with the experimental observations. However, the real predictive power of the model was revealed when the expression of additional genes appeared perturbed, genes that have not yet been tested experimentally! For example, the GRN model predicted that the absence of delta affects not only gatae and gcm, but also genex and j(suh). It would be interesting to experimentally investigate the expression profile of the latter two genes in embryos injected with delta morpholinos, to check whether their patterns conform to the model’s predictions. If they do, then “Hail The Model!”; if they do not, it would simply mean that there exist regulatory inputs beyond our current knowledge.

In a final and rather challenging test, the authors computationally mimicked an experiment from the classic days of transplantation studies by Hoerstadius, when donor skeletogenic micromeres were transplanted on the animal pole of a host embryo, which resulted in a complete second gut and associated mesodermal tissues. In modern terms, this implies that the donor micromeres were sufficient to induce the downstream GRN required for endomesoderm development. However, in their model the authors computationally endowed the animal pole cells (which normally do not form skeletogenic micromeres) with maternal factors sufficient to induce the micromere cell fate. Then, remarkably, the surrounding cells formed three successive spatial domains – ring 1, 2 and 3, which expressed the regulatory states of the mesoderm, veg1 and veg2 endoderm, respectively, precisely mimicking the experimental results.

In conclusion, this study demonstrates the great predictive importance of GRN modeling but also its usefulness for further in silico evaluation of current GRNs structure and discovery of knowledge gaps, or lacunae, as described by the authors. One type of lacunae appear as discrepancies between what is observed and what is computationally generated but, as this study reveals, their frequency is low. In fact, what seems as a rare “failure” of the model could potentially guide future investigations.

References:

Peter IS, Faure E and Davidson EH, Predictive computation of genomic logic processing functions in embryonic development, PNAS Early Edition, Aug 27^th 2012

Li E and Davidson EH, Building developmental gene regulatory networks, Birth Defects Research (Part C) 87:123–130, 2009

(1 votes)

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When you click on an author’s name on a Node post, you are currently shown a page with all of the posts by that author. You can try it on this post.

In a few weeks, this is going to change! We will soon have profile pages for everyone who has written (or will write) on the Node. The profile page will list biography information that you can edit yourself. We’ve created a page that describes how to do that.

If you currently have a post anywhere on the Node, whether it’s a job ad or a two-year-old conference report, I recommend checking what you have filled out in your profile, because it will soon be public!

We have a few other changes in the works for the Node, and we hope to have the redesign up in the third week of September. If you can find a minute to update your profile before September 13, that would be very helpful.

You can always edit your profile later, but please just be aware that in a few weeks the biography section from your profile will become public.

The information page clearly describes what part of your profile will become public, and how to edit it.

If you have any questions, let us know via email, or leave a comment below.

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To celebrate our 25th Anniversary (see here for some memories of the last quarter century of the journal), and to look forward to the next 25 years, Development is hosting a one day symposium in Cambridge on October 25th 2012. We’ve got a great line-up of speakers, and we’ll also be holding a panel discussion on the future of the field. We hope some of you will be able to join us for this exciting event!

Here are the details:

Development: Past, Present and Future

One-day Symposium

October 25th 2012

Magdelene College, Cambridge, UK

Join us for a special one-day symposium featuring talks from members of Development’s editorial board past and present, and concluding with a panel discussion on the future of developmental biology.

Speakers:

Kenneth Chien     Magdalena Götz     Peter Lawrence

Thomas Lecuit     Mike Levine     Olivier Pourquié     Jim Smith

To register, please go to

http://www.biologists.com/dev_symposium_2012.html

Here’s the poster for the meeting

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The Wellcome Trust-Medical Research Council Stem Cell Institute provides outstanding scientists with the opportunity to undertake ground-breaking research into the fundamental properties of mammalian stem cells.

The Institute offers a comprehensive flow cytometry service to its members. The facility comprises MoFlo and FACSAria l cell sorters, Cyan and LSR-Fortessa analysers, and associated flow cytometry equipment.

The role will encompass:

Heading a team of two people providing high quality cell sorting and analysis services for various research projects.
Future proofing the flow facility in the Stem Cell Institute, and manage the operation, upkeep and development of equipment.
Recruitment, training and line management of second member core facility staff.
Provide training, advice and guidance to researchers in the theory and practice of flow cytometry.

The ideal candidate will have all of the following:

A proven ability to design flow experiments and to analyse and interpret data.
Be computer literate and technically innovative.
Excellent communication and interpersonal skills in this service-focused environment
Excellent organisational and interpersonal skills.
Extensive expertise in multiparameter flow cytometry.
Experience in a multi-user flow cytometry service will be an advantage.

The successful applicant will be able to demonstrate leadership qualities and the ability to work well within an academic research setting.

This appointment is subject to a health assessment.

Whether an outcome is satisfactory will be determined by the University.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK. CLOSING DATE: 21st September 2012 at 12.00pm INTERVIEW DATE: Week beginning 8th October 2012

If you have not been invited for interview by the 1st October 2012, you have not been successful on this occasion.

Applications must be made via our online applications site on:

http://www.stemcells.cam.ac.uk/careers-study/vacancies/

We do not accept applications by post or email except in exceptional circumstances.

Please note that you cannot amend your application once you have submitted it, so please ensure that you upload all the correct documents the first time.

Application Forms:

All applications MUST include the following:

-Cover letter
-CV
-The relevant CHRIS form (Parts 1 & 2 ONLY).

If you do not wish to submit the Equal Opportunities data, please upload a blank form to the applications site.

Contact:

If you have any questions, please email cscrjobs@cscr.cam.ac.uk

This appointment is subject to a health assessment.

Whether an outcome is satisfactory will be determined by the University.

The University values diversity and is committed to equality of opportunity.

The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

Quote reference: PS00519

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The purpose of this summary is to present to “The Node” readers a recent update to the story which, in my opinion, is a quite interesting example of the phenomenon of programmed genome rearrangement (PGR) that occurs in the lamprey Petromyzon marinus.

Programmed genome rearrangement describes the regulated structural changes in the genome, which result in the generation of new coding sequences, changes in the control of genome functions and gene expression etc, within ontogeny (not to be confused with similar structural changes on the phylogenetic level). Although on a smaller scale, a form of PGR also occurs during the formation of the T- and B-cell progenitors in mammals, the V(D)J somatic recombination system, which generates the diversity of forms of the Ig- and T-cell receptors.

The PGR in P. marinus occurs during embryonic development and results in the differential deletion of hundreds of millions of base pairs specifically in the genomes of the somatic lineages, as contrasted to the germline. In effect, the germline retains sequences that are deleted in the soma. Of course, this is not the first known case in the Metazoan clade (it has been previously described in sciarid dipterans, nematodes, copepods, etc (see references in the articles cited below)) but according to the authors, it is the first known example of a genome rearrangement of such scale in vertebrates, which makes it especially important for better understanding the evolution and mechanisms of vertebrate gene regulation. Speculatively, lampreys eliminate particular sequences from the somatic tissues’ genomes, which are otherwise important for the complex meiotic rearrangements and pluripotency regulation in the germline, because misregulation of such sequences in the soma may lead to disruptions in genome integrity and defects in cell commitment/differentiation (e.g., tumorigenesis). However, DNA breaks are also visible at later stages of development, which suggests that further rearrangements probably do occur, possibly in a tissue-specific mode (as suggested by variation in the DNA content measured by flow cytometry), which may potentially lead not only to loss of function, but also to the assembly of new sequences (regulatory, coding, etc), that facilitate the differential development of the somatic lineages.

In the newer of the studies, the authors used a customized oligonucleotide microarray that targeted all available germline sequences and a small fraction of the somatic sequences. This revealed that nearly 13% of the screened germline sequences were deleted in the soma and that five of the promising candidate sequences were expressed in the juvenile and adult testes. A large fraction of the somatically deleted sequences are single-copy and protein-coding DNA, which argues against a predominant deletion of repeats. Intriguingly, the authors do not rule out the possibility that whole chromosome elimination may also contribute. Genes presented in the deleted regions include: APOBEC-1, cancer/testis antigen 68, WNT7A/B, SPOPL etc, which in other vertebrates have known roles in cell fate maintenance, proliferation and oncogenesis. Interestingly, some of the genes indentified in the germ-line specific fraction have homologs in other vertebrates where they are not known to function in germline development. I could easily hypothesize that those genes were recruited for germline functions during lamprey evolution or, alternatively, they were germline-specific in ancestral vertebrates but they were later deployed in somatic functions with concomitant loss of germline function. Or it simply means that our knowledge about vertebrate germline function genes is imperfect!

Despite this important differences in genome biology between lampreys and gnathostomes (as we know them), there are many fundamental similarities in embryonic development and gene content. It is expected that some of the factors involved in the lamprey’s PGR will have homologs in gnathostomes. I am curious whether these homologs perform similar functions in jawed vertebrates? Do such PGR mechanisms of a similar scale (excluding the V(D)J system) occur in gnathostomes as well?

From a broader view, these observations suggest that lampreys use an additional strategy for gene regulation as compared to the rest of vertebrates. However, it is important to note that similar PGRs also occur in hagfish (Myxini (please, see the references)). One is prompted to ask: “What is the extent of this process in Myxini? Do their PGRs specifically occur in the soma versus the germline, as in lampreys?” Considering the fact that both lampreys and hagfish use PGRs, it is legitimate to suggest that this strategy of gene regulation was an ancestral system for the early vertebrates, and that the evolution of a gene regulation system predominantly based on epigenetic modification of chromatin was a later invention. However, this is a pure speculation.

Whatever the case is, I imagine that there exist specific DNA sequences that recruit the recombineering machinery (RM) to those regions destined for deletion. Then, it should be of importance that these sequences are occupied by the RM in the particular somatic lineages only and not in the germline. This could be achieved by any of the mechanisms that regulate the function of other regulatory sequences, like enhancers for instance, and may include control of sequence accessibility via epigenetic modification on the chromatin. In addition, tissue-specific expression of the RM components could also be a factor.

Future exploration of the PGR phenomenon will surely provide better understanding of the mechanisms that regulate genome stability, with important implications for cancer biology as well.

References:

Genetic consequences of programmed genome rearrangement, Current Biology, August 21 2012

http://www.cell.com/current-biology/retrieve/pii/S0960982212006732

Programmed loss of millions of base pairs from a vertebrate genome, PNAS, July 7 2009

http://www.pnas.org/content/106/27/11212.long

(5 votes)

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Here are the highlights from the current issue of Development:

Retinoic acid’s developmental role illuminated

The role of all-trans retinoic acid (RA) in hindbrain development and other developmental processes is usually studied by blocking endogenous RA synthesis and then continuously supplying exogenous RA by soaking embryos in all-trans RA or by implanting RA-soaked beads. Now, on p. 3355, David Bensimon and colleagues use photo-isomerisation of 13-cis RA to all-trans RA and vice versa to manipulate RA activity spatiotemporally in zebrafish embryos. In embryos in which all-trans RA synthesis is impaired, they report, brief incubation in all-trans RA or in 13-cis RA followed by UV illumination before the bud stage rescues hindbrain development. By contrast, rescue is impaired in embryos treated with all-trans RA and then exposed to UV light. Notably, activation of all-trans RA via photo-isomerisation of 13-cis RA at the end of gastrulation in head, but not tail, precursor cells rescues hindbrain development. These results suggest that all-trans RA is sequestered in embryos during normal development. Furthermore, they illustrate how RA activity can be spatiotemporally controlled in developing zebrafish embryos.

Branching out studies of dendritic patterning

The dendritic arbours of neurons in the central nervous system have highly diverse morphologies that determine neuronal connectivity and, consequently, brain function. But how is dendritic architecture sculpted during development? On p. 3442, Kazuto Fujishima, Mineko Kengaku and co-workers investigate this question by combining computer simulations and time-lapse imaging of cultured mouse cerebellar Purkinje cells. The researchers show that the characteristic Purkinje cell space-filling dendritic arbour of non-overlapping branchlets is shaped by several reproducible dynamic processes, including constant tip elongation, stochastic terminal branching and retraction triggered by contacts between growing dendrites. This last process, they report, is regulated by protein kinase D signalling. Their computer simulation of dendrite branch dynamics, which incorporates their experimental measurements, reproduces dendritic development in live Purkinje cells and confirms the important contribution that dendritic retraction makes to the formation of the Purkinje cell dendritic arbour. Further development of this two-pronged approach, suggest the researchers, will help to clarify the fundamental mechanisms of dendrite patterning in the developing brain.

Pancreatic development keeps its Sox on

All mature pancreatic cell types arise from a pool of organ-specific multipotent progenitor cells. Cell-intrinsic and cell-extrinsic cues promote the proliferation and cell fate commitment of these progenitor cells but what integrates these cues during pancreatic morphogenesis? Maike Sander and co-workers now report that the transcription factor Sox9 forms the centrepiece of a gene regulatory network that controls pancreatic development (see p. 3363). Pancreatic progenitor-specific ablation of Sox9 during early mouse pancreatic development, they report, leads to cell-autonomous loss of fibroblast growth factor receptor 2b (Fgfr2b), which is required to transduce mesenchymal Fgf10 signals. In turn, Fgf10 is required to maintain progenitor expression of Sox9 and Fgfr2b. Perturbation of this Sox9/Fgfr2b/Fgf10 feed-forward expression loop results in pancreas-to-liver fate conversion. Given that Fgf signalling is necessary for pancreatic progenitor cell proliferation, the researchers propose that a Sox9/Fgf feed-forward loop coordinately controls organ fate commitment and progenitor cell expansion in the developing pancreas, a finding that may advance efforts to generate insulin-producing cells for therapeutic use.

COP1 sheds light on root development

Although the roots of most plant species are not directly exposed to light, root growth is controlled by light and integrated with the growth of above-ground organs. Here (p. 3402), Teva Vernoux, Jian Xu and colleagues uncover a novel long-distance mechanism by which light signals through the master photomorphogenesis repressor COP1 to coordinate root and shoot development in Arabidopsis. The authors show that, in the shoot, COP1 regulates shoot-to-root transport of auxin by controlling transcription of the auxin efflux carrier gene PIN-FORMED1 (PIN1). In addition, they report, COP1 regulates auxin transport and cell proliferation in the root apical meristem by modulating the intracellular distribution of PIN1 and PIN2 in the root, thereby ensuring rapid and precise tuning of root growth to the light environment. Together, these results identify auxin as a long-distance signal in light-regulated plant development and show how spatially separated control mechanisms can converge on a single signalling system to coordinate development at the whole plant level.

Pten-less neuroblasts stop en route

Neuronal precursors in the subventricular zone (SVZ) of the adult rodent brain differentiate into neuroblasts and migrate through the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into interneurons. Diverse extracellular cues control neuroblast migration but what are the intracellular pathways that respond to these cues? On p. 3422, Suzanne Baker and colleagues identify a role for Pten, a negative regulator of phosphoinositide 3-kinase (PI3K) signalling, in mouse neuroblast development. The PI3K-Akt-mTorc1 pathway is inactivated in migrating neuroblasts in the SVZ and RMS, they report, but activated when the cells reach the olfactory bulb. Postnatal deletion of Pten, they show, causes aberrant activation of PI3K-Akt-mTorc1 signalling, premature termination of neuroblast migration, neuroblast differentiation and enlargement of the SVZ and RMS. Notably, live imaging of slice cultures shows that, although some Pten-null neuroblasts lack directional migration and have a non-polarised morphology, others migrate normally towards the olfactory bulb. Thus, the researchers suggest, the neuroblast migration defect associated with Pten loss is secondary to precocious neuroblast differentiation.

Haploid ESCs: a future in the germline

Parthenogenetic haploid embryonic stems cells (ESCs), which have recently been established through chemical activation of unfertilised mouse cells, give rise to a wide range of differentiated cell types in embryos and in vitro. But can they contribute to the germline, which is the defining hallmark of mouse diploid ESCs? Here (p. 3301), Martin Leeb, Anton Wutz and co-workers show that parthenogenetic haploid mouse ESCs have a robust germline potential and that transgenic mouse strains can be produced from genetically modified haploid ESCs. Differentiation of haploid ESCs in chimeric embryos, they report, correlates with the acquisition of a diploid karyotype by the ESCs through endoreduplication. By contrast, haploid ESCs induced to differentiate to an extra-embryonic fate by expression of the transcription factor Gata6 retain their haploid content. Parthenogenetic haploid mouse ESCs, the researchers conclude, are authentic pluripotent ESCs that can, potentially, be used to elucidate new details about developmental pathways through extension of genetic screens and manipulations directly into mouse models.

Plus…

Left-right patterning: conserved and divergent mechanisms

This Development At a Glance poster by Nakamura and Hamada summarizes the common and divergent mechanisms by which LR asymmetry is established in vertebrates.

Review: Principles and roles of mRNA localization in animal development

Intracellular targeting of mRNAs, which has long been recognised as a means to produce proteins locally, has recently emerged as a mechanism used to polarise various cell types. Here, Florence Besse and colleagues review the regulation and functions of RNA localisation during animal development. See Review on p. 3263

Review: Partitioning the heart: mechanisms of cardiac septation and valve development

On p. 3277, Zhou, Chang, and colleagues review the morphogenetic events and genetic networks that regulate spatiotemporal interactions between the cells that partition the heart.

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Let’s take a very close look at the inside of a fish!

A recent paper in the Journal of Cell Biology describes a technique for generating large, composite, images from electron microscopy data. Frank Faas, Raimond Ravelli, and colleagues at the Leiden University Medical Center developed a method to computationally collect and align EM images. In the data viewer accompanying the paper, they show a large section of a zebrafish embryo, 5 days post-fertilisation, which is comprised of 26,434 individual images! The total size of the composite image is 921,600 pixels by 380,928 pixels. (For reference, the screenshots below are 500 pixels wide.)

In these screenshots you can see the overall fish in the bottom right, with the red area indicating where the larger, detailed, view is located. These are two different magnifications of the (edge of the) eye. In the bottom image you can also see the edge of the composite image, and appreciate how many individual images there are, and how well they connect.

To find out more about the method, and its practical applications, read the full paper and editorial at JCB.

Faas FG, Avramut MC, M van den Berg B, Mommaas AM, Koster AJ, & Ravelli RB (2012). Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps. The Journal of cell biology, 198 (3), 457-69 PMID: 22869601

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