Laboratory of molecular bases of embryogenesis

Department of Genomics and Postgenomic Technologies

Head: Andrey Zaraisky, D.Sc, professor

Brain development, regulation of gene expression, transgenic organisms, homeobox genes, regulators of TGF-beta signaling, small GTPases, Zyxin

The Laboratory studies the molecular-genetic mechanisms of early nervous system development and evolution, and also regeneration of big body appendages on the lower vertebrate model.

One of the projects is devoted to monogenic family of homeobox genes Anf in vertebrates (Dev Biol 1992, 152, 373-382; Development 1995, 121, 3839-3847; Gene 1997, 200, 25-34). For the first time it was found that this gene presents exclusively in the vertebrates genomes (including humans) and absents in invertebrates. It was demonstrated that Anf monitors the development of a unique part of the vertebrates brain – the telencephalon – by inhibiting there the expression of genes that normally control development of the posterior parts of the brain (Development 1999, 126, 4513- 4523; Gene 2002, 285, 279.. -286; Development 2004, 131, 2329-2338; Mech Dev (2004) 121, 1425-1441; Dev Biol 2007; 307, 483-497). Known mutations in this gene in mice and humans have the recessive character, but in the homozygous state lead to the serious abnormalities in brain development, ranging from the underdevelopment of the pituitary gland and optic nerve dysplasia and walls of the cerebral hemispheres to the whole lack of these structures. Thus these results allowed us to hypothesized that the appearance of Anf  in vertebrates ancestry could serve as one of the key prerequisites for the final appearance of the telencephalon in evolution (Dev Biol 2007; 307, 483-497). Our recent finding of Anf in the representatives of the most ancient group of modern vertebrates, i.e. in jawless (lampreys), and demonstration that it plays in lamplrey the same function as in other vertebrates, confirm this hypothesis (Sci Rep.. 2016 Dec 23;6:39849)

Also the Laboratory studies the role of genes that were lostg during the vertebrate evolution in the regulation regeneration. We determined that some of the Anf homeobox target genes, namely, the gene of  secreted disulphide isomerase Ag1 and genes of small GTPases Ras-dva1,  present only in the genomes of lower vertebrates, fish and amphibians, but absent in higher vertebrates, reptiles, birds and mammals (Gene Expr Patterns, 2003, 325-30; Development, in 2006, 133, 485-494; Nucleic Acids Res, 2006, 34, 2247-2257; Gene Expr Patterns, 2011, 11, 156-161). Interestingly, we have demonstrated that besides regulation of regeneration, Ag1 and Ras-dva1 regulate another important process – the telencepalon development (Sci Rep, 2013, 3, 1279; Biol Open, 2014, 3, 192-203; Sci Rep, 2015, 5: 8123). Therefore we hypothesized that the disappearance of these and probably some other genes  in vertebrate ancestry  could be a kind of trade of between the reduced regenerative capacity and the opportunity of the progressive development of the telencephalon. Taking in mind this hypothesis, together with our colleagues from the  Institute for  Information Transmission Problems (Prof. A.V. Lyubetsky lab.) we developed bioinformatics program that allows identify genes that have arisen or disappeared at a specified stage of evolution. The functions of some genes found by this program are studying in the Laboratory now.

A study of gene network associated with the Anf gene functioning in the cells of the telencephalon rudiment lead to the discovery of a number of previously unknown genes that play an important role in embryogenesis. For example, we identified and studied regulators of the early brain development – secreted proteins Noggin2 and Noggin4 (Gene Expr Patterns, 2006 6:180-6; Development, 2011, 138, 5345-5356; Int J Dev Biol 2012; 56: 403-6; Sci Rep 1996, 14, 6:23049). In contrast to their commonly known homolog, an inhibitor of the BMP – protein Noggin1 these proteins inhibit the function of the regulator of the posterior regions of the central nervous system –  the secreted protein Wnt8.

Ectopically expressed Noggin2, which inhibits three signaling cascades, BMP, Activin/Nodal and Wnt, is sufficient for the induction of a secondary head on the ventral side of the Xenopus laevis embryo.

In addition, we have developed a number of methods for the study of diffusion and interactions of secreted morphogen proteins in the intercellular space of embryonic tissues (Sci Rep, 2016 6:23049; Biochem Biophys Res Commun, 2015; 468:331-6). For the first time the diffusion coefficients of Noggin2 and 4 and Wnt8 in vivo protein families were measured and the role in their diffusion of the adsorption on the extracellular matrix was demonstrated. Also, we have shown with the mathematical modeling that the adsorption may be an important factor needed to create spatial dynamic structures during embryogenesis (PLoS One. 2017 Feb 7;12(2):e0171212. doi: 10.1371).

Also we have studied during the early development of the central nervous system the role of the cytoskeletal protein Zyxin. This protein is able to binding with Anf homeodomain protein as well as with the effector of Shh signaling cascade – Gli1 transcription factor, inhibiting their  activity (Dev Dyn, 2008, 237, 736-749; Dev Biol, 2013, 380, 37-48). The findings are important because they demonstrate for the first time a link between one of the cytoskeletal regulatory proteins that control cells morphogenetic movements and mechanical tensions in the developing embryo and an important signaling pathway, that regulates cell differentiation during early development of the central nervous system.  Now we studying the role of Zyxin in regulation of other pathways and also the role of mechanical tensions in gene expression during embryogenesis (Genesis. 2017 Feb 25. doi: 10.1002/dvg.23026)

The Laboratory is also working on testing the possibility of using genetically encoded fluorescent reporters and sensors for studying various processes in early embryogenesis and regeneration (Nat Biotechnol, 1999, 17, 969-973; Science, 2000, 290: 1478-1479; Nat Biotechnol, 2003 , 21: 191-194; Nat Methods, 2007, 4, 741-746; Nat Methods, 2010, 7, 827-829; Nat Commun, 13, 2012; 3:1204). In particular, for the first time the possibility of using fluorescent proteins from coral polyps for in vivo monitoring of cells in Xenopus embryos was demonstrated (Nat Biotechnol, 1999, 17, 969-973).

Aquarium room, in which frogs and tadpoles of some transgenic lines, as well as adult frogs expressing fluorescent proteins under the control of promoters of various genes are kept.

The Laboratory collaborates with other laboratories of the Institute, as well as with the Department of Biophysics of the Moscow State University, the Department of Embryology of the Moscow State University, the Center "Bioengineering" RAS, the Belozersky Institute of Physico-Chemical Biology of the Moscow State University, the Institute for Information Transmission Problems RAS, Kurchatov Institute, Massachusetts Institute of Technology (USA), the University of Virginia (USA).

The Laboratory was founded in 2005 by a group of the same name released in 1995 from the Laboratory of structure and function of human genes.

  • Study the molecular genetic mechanisms of early development and evolution of the nervous system.
  • Study and modeling of the morphogens diffusion in the embryonic tissues.
  • Study of the processes of the large body appendages regeneration on lower vertebrate models.
  • Creating and maintaining lines of transgenic Xenopus frogs, expressing genetically encoded fluorescent reporters and sensors.
  • Anf/Hesx1 homeobox gene was identified for the first time in different vertebrates, including human. It was shown that this gene present only in vertebrates. The hypothesis of the role of Anf/Hesx1 as the primary factor that initiated emergency of the telencephalon in vertebrates was proposed.
  • It is found that some of the target genes of Anf homeobox gene (Ag1, Ras-dva1)  present only in the genomes of lower vertebrates, fish and amphibians, but absent in higher vertebrates, reptiles, birds and mammals. It was shown that in lower vertebrates these genes are involved both in regulation of the telencephalic development  and the body appendages regeneration. It was hypothesized that disappearance of these and probably some other genes  in vertebrate ancestry  could be a kind of trade of between the reduced regenerative capacity and the opportunity of the progressive development of the telencephalon.
  • Early brain development regulators – secreted proteins and Noggin2 Noggin4 – were identified and studied.
  • A number of methods for the studing of diffusion and interactions of secreted morphogens in the intercellular space of embryonic tissues were developed. By these methods, diffusivities of some morphogens were measured in vivo.
  • For the first time the role of Zyxin cytoskeletal protein in the early embryonic development was studied. In particular, it was shown that Zyxin  is able to binding with Anf homeodomain protein and with the effector of Shh signaling cascade – the transcription factor Gli1 and inhibit their activity.
  • The technology of two-color reporter vector, significantly increases the efficiency of the functional analysis of the promoter, with the ability to compare the expression of two potential deletion mutants studied gene promoter in the same transgenic embryos was developed (Development, 2004, 131, 2329-2338).
  • Using genetically encoded SypHer2 pH-indicator on the tadpole Xenopus model was discovered a previously unknown effect – the rapid acidification of the cells cytoplasm near the site of the tail amputation (Biochim Biophys Acta, 2015 1850:2318-28). This effect is one of the first reactions of the organism to amputation, and may be important for subsequent regeneration.
Andrey Zaraisky, D.Sc, professorHead of
Andrey Bayramov, Ph.D.s. r.
Fedor Eroshkin, Ph.D.s. r.
Natal'ja Martynova, Ph.D.s. r.
Galina Ermakovar.
Anastasiya Ivanovar.
Alexey Nesterenkor.
Maria Tereshina, Ph.D.r.
Daria Korotkovaj. r. f.
Evgeny Orlovj. r.
Alexandr Borodulin, Ph.D.PhD
Olga Aver'yanovasen. eng.
Marina Serebryakovaeng.+7(495)336-86-11

All publications (show selected)


Andrey Zaraisky

New mechanism of regulation of the embryonic cells stem status

In collaboration with Department of metabolism and redox biology

Researchers from the Laboratory of Molecular Bases of Embryogenesis IBCh RAS, in technical cooperation with colleagues from the Department of Metabolism and Redox Biology IBCh RAS, the Laboratory of Genomics and Epigenomics of Vertebrates in the Federal Center "Fundamentals of Biotechnology" RAS, as well as with colleagues from the Cell Motility Group of the Institute of Protein Research RAS, discovered a previously unknown mechanism of the regulation of the activity of genes that determine the pluripotent status of the embryonic stem cells. This mechanism is based on the ability of the cytoskeletal protein Zyxin to displace mRNA of pluripotency genes from complexes with the mRNA-stabilizing protein Ybx1, which accelerates the degradation of these mRNAs. The authors suggest that this mechanism helps to coordinate the processes of morphogenesis and cell differentiation in embryogenesis.

The discovery of four genes of the Noggin family in lampreys is consistent with the hypothesis of two rounds of genomic duplications in vertebrate ancestors

Researchers from the Laboratory of Molecular Bases of Embryogenesis, in the co-operation with a colleague from the Severtsov Institute of Ecology and Evolution, described for the first time four genes of the Noggin family in the oldest representatives of vertebrates - lampreys, and compared their structure, expression and some functional features with those of the known genes of this family in other vertebrates. The Noggin genes encode secreted factors that regulate many important processes in embryogenesis. As a result, it was concluded that the entire set of the data obtained is in the best agreement with the hypothesis of two successive rounds of duplications of the ancestral genome of invertebrates that occurred at the earliest stage of vertebrate evolution, i.e. about 550 millions years ago, in Paleozoic Era.

Novel modulator of FGF and ADP signaling, c-Answer, regulates regeneration and brain development in the cold-blooded animals, but lacks in the warm-blooded, including human.

Earlier the hypothesis was proposed in the laboratory of the Molecular Bases of Embryogenesis (IBCH RUS) that the loss in warm-blooded animals of the ability to regenerate limbs and, as a compensation, the progressive development of the brain may be associated with the loss of some genes by the warm-blooded ancestors. Now we developed a new bioinformatics method which allows one to reveal genes that appeared or disappeared at a certain stage of evolution. Using this method, a previously unknown modulator of FGF and ADP signaling, the transmembrane protein c-Answer was revealed, which stimulates regeneration and affects brain development in cold-blooded animals, but has disappeared in warm-blooded animals, including humans. The effectiveness of the new bioinformatics method was also confirmed by finding genes specific only for short-lived mammals.


  1. Rubanov LI, Zaraisky AG, Shilovsky GA, Seliverstov AV, Zverkov OA, Lyubetsky VA (2019). Screening for mouse genes lost in mammals with long lifespans. BioData Min 12 (1), 20
  2. Korotkova DD, Lyubetsky VA, Ivanova AS, Rubanov LI, Seliverstov AV, Zverkov OA, Martynova NY, Nesterenko AM, Tereshina MB, Peshkin L, Zaraisky AG (2019). Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration. Cell Rep 29 (4), 1027–1040.e6

Ras-dva small GTPases lost during evolution of amniotes regulate regeneration in anamniotes

Anamniotes — fishes and amphibians — have an amazing ability to regenerate organs. For example, limbs, tail, heart, eyes and brain. Unfortunately, in the course of evolution, amniotes — reptiles, birds, and mammals — lost their ability to efficient regeneration. We assumed that the loss of regenerative capacity is associated with the loss of some genes responsible for the formation of the wound blastema - a group of actively dividing dedifferentiated cells that guarantee regeneration. In confirmation of this, we showed that amniotes lacks the genes of small GTPases of Ras-dva family, which are responsible for the formation of the regeneration blastema in fish and amphibians, and, consequently, for one of the mechanisms of regeneration.

The discovery and study of the function of the homeobox gene Anf / Hesx1 in lampreys confirms its key role in the appearance of the telencephalon in vertebrates

An important feature of vertebrates, including humans, is the presence of a unique part of the forebrain, called the telencephalon, which has no homologs in invertebrates. Previously, we discovered a  monogenic class of homeobox genes Anf / Hesx1, which is also  absent in all invertebrates but plays a key role in regulation of the telencephalon development  in vertebrates. However, until recently, the Anf / Hesx1 gene was not found in the most ancient group of vertebrate - in jawless fishes (extant lampreys and myxins), while the telencephalon in these animals was described and their genomes were sequenced. Now we have shown for the first time that Anf / Hesx1 is still present in lampreys, in which it also regulate development of the telencephalon. The obtained data confirm the hypothesis, which we have formulated earlier, that the emergence of the telencephalon in evolution was associated with the appearance of the homeobox gene Anf / Hesx1.

The secreted factor Ag1 missing in higher vertebrates regulates fins regeneration in Danio rerio.

Using the model of the Danio rerio caudal fin regeneration, it is established that the secreted protein Ag1 is required for regeneration. It is shown that the caudal amputation induces rapid activation of the expression of Ag1 in cells of the wound epithelium. However, inhibition of the Ag1 mRNA translation causes a retardation of the regeneration. The results of this work are important because Ag1 presents in genomes of only the lower, well regenerating vertebrates, including fish and amphibians, but not in higher vertebrates, which cannot effectively regenerate limbs. The data obtained indicate that a reduction of the regeneration capabilities in higher vertebrates, including humans, could be attributed to the disappearance of some genes important for regeneration, in particular, Ag1.