Patrick Lemaire

Institute of Biological Sciences, French National Centre for Scientific Research · Centre de Recherches de Biologie cellulaire de Montpellier (CRBM), France

Protein kinases (PKs) and protein phosphatases (PPs) regulate the phosphorylation of proteins that are involved in a variety of biological processes. To study such biological processes systematically, it is important to know the whole repertoire of PKs and PPs encoded in a genome. In the present study, we surveyed the genome of an ascidian (Ciona r...

Gastrulation is the first major morphogenetic event during ascidian embryogenesis. Ascidian gastrulation begins with the invagination of the endodermal progenitors, a two-step process driven by individual cell shape changes of endoderm cells. During the first step, endoderm cells constrict apically, thereby flattening the vegetal side of the embryo...

Gastrulation is a near universal developmental process of animal embryogenesis, during which dramatic morphogenetic events take place: the mesodermal and endodermal tissues are internalized, the ectoderm spreads to cover the embryo surface, and the animal body plan and germ layers are established. Morphogenesis during gastrulation has long been con...

Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin net...

The larvacean Oikopleura dioica is a planktonic chordate, and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of five days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established...

Cell-cell contacts specify cell fate Ascidians, or sea squirts, are marine invertebrate filter feeders with highly reproducible cellular events and invariant embryonic cell lineages. Guignard et al. studied the ascidian embryo to address the determinants of this cellular reproducibility. They introduce computational methods for the robust and autom...

Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to...

ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates...

Developing biological structures are highly complex systems, within which shape dynamics at different places is tightly coordinated. One key process at play during development is the regulation of cell division orientation. In this work, through a reformulation of cell division in terms of its energetic cost, we propose that oriented cell division...

Transcription factors (TFs) control gene transcription, binding to specific DNA motifs located in cis-regulatory elements across the genome. The identification of TF-binding motifs is thus an important aspect to understand the role of TFs in gene regulation. SELEX, Systematic Evolution of Ligands by EXponential enrichment, is an efficient in vitro...

Powerful novel imaging and image-processing methods are revolutionizing many fields of biology, at scales ranging from the molecule to the functional organ. To support this big-data revolution, we develop a concept of generic web-based morphodynamic browser to interactively visualize complex image datasets, with applications in research and educati...

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evo...

The ascidian neural plate consists of a defined number of identifiable cells organized in a grid of rows and columns, representing a useful model to investigate the molecular mechanisms controlling neural patterning in chordates. Distinct anterior brain lineages are specified via unique combinatorial inputs of signalling pathways with Nodal and Del...

Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin net...

In 1994, Lewis Wolpert wondered “Will the egg be computable? That is given a total description of the fertilized egg – the total DNA sequence and the location of all proteins and RNA – could one predict how the embryo will develop?”. In this review, we discuss what computing the embryo entails and explore how advanced imaging, single-cell genomics...

Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evo...

Background: Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolu...

Asexual propagation and whole body regeneration are forms of non-embryonic development (NED) widespread across animal phyla and central in life history and evolutionary diversification of metazoans. Whereas it is challenging to reconstruct the gains or losses of NED at large phylogenetic scale, comparative studies could benefit from being conducted...

Background Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutio...

ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigen...

Background miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi h...

Only a minority of the many genomic clusters of transcription factor binding motifs (TFBM) act as transcriptional enhancers. To identify determinants of enhancer activity, we randomized the spacer sequences separating the ETS and GATA sites of the early neural enhancer of the tunicate Ciona intestinalis Otx gene. We show that spacer sequence random...

Canalization of developmental processes ensures the reproducibility and robustness of embryogenesis within each species. In its extreme form, found in ascidians, early embryonic cell lineages are invariant between embryos within and between species, despite rapid genomic divergence. To resolve this paradox, we used live light-sheet imaging to quant...

Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Ove...

How can the study of tunicates help up us to better understand evolution?

Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Ove...

Most developmental biologists equate tunicates to the sessile ascidians, including Ciona intestinalis, and the pelagic appendicularians, in particular Oikopleura dioica. However, there exists a third group of tunicates with a pelagic lifestyle, the thaliaceans, which include salps, pyrosomes, and doliolids. Although thaliaceans have raised the curi...

This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult ana...

Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highl...

Recent microscopy techniques allow imaging temporal 3D stacks of developing organs or embryos with a cellular level of resolution and with a sufficient acquisition frequency to accurately track cell lineages. Imaging multiple organs or embryos in different experimental conditions may help decipher the impact of genetic backgrounds and environmental...

Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans and appendicularians. With the advent of inexpensive high throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facili...

In chordates, neural induction is the first step of a complex developmental process through which ectodermal cells acquire a neural identity. In ascidians, FGF-mediated neural induction occurs at the 32-cell stage in two blastomere pairs, precursors respectively of anterior and posterior neural tissue. We combined molecular embryology and cis-regul...

Current imaging techniques can capture temporal sequences of 3D images with very high time resolution over several hours. Comparing sequences covering the same time period opens the way to the study of developmental variability. Stitching together sequences captured from different embryos may help producing a sequence covering the whole development...

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed du...

Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distin...

Vertebrate embryos exploit the mutual inhibition between the RA and FGF signalling pathways to coordinate the proliferative elongation of the main body axis with the progressive patterning and differentiation of its neuroectodermal and paraxial mesodermal structures. The evolutionary history of this patterning system is still poorly understood. Her...

(A): Ci-LRP5/6, the Ciona homologue of LRP5/6, the WNT co-receptor required for canonical pathway activation, is expressed in the ventral midline epidermis. Left panel, side view of an early tailbud stage embryo, anterior is to the left. Right panel, ventral view of the same embryo, anterior is to the top. (B): X-Gal staining of embryos electropora...

(A): treatment with DEAB blocks the activity of the pCi-Hox1(intron2)::lacZ reporter construct, while treatment with RA leads to its ectopic activation throughout the embryo. (B): treatment with RA at late gastrula stage rescues the U0126-induced loss of Ci-cyp26 expression in the anterior tail epidermis. (C): bFGF treatment of pCi-Hox1(intron2)::l...

(A): treatment with recombinant bFGF leads to the ectopic diphosphorylation of Erk, while treatment with U0126 results in a loss of the dpErk signal throughout the embryo, distinct from the tailtip specific loss due to RA treatment shown in Fig. 2L–O. (B): Ci-fgf9/16/20 is expressed by a few muscle posterior muscle cells close to the tail tip (imag...

During embryonic development, cell behaviors that are tightly coordinated both spatially and temporally integrate at the tissue level and drive embryonic morphogenesis. Over the past 20 years, advances in imaging techniques, in particular, the development of confocal imaging, have opened a new world in biology, not only giving us access to a wealth...

During embryonic development, cell behaviors that are tightly coordinated both spatially and temporally integrate at the tissue level and drive embryonic morphogenesis. Over the past 20 years, advances in imaging techniques, in particular, the development of confocal imaging, have opened a new world in biology, not only giving us access to a wealth...

During embryonic development, cell behaviors that are tightly coordinated both spatially and temporally integrate at the tissue level and drive embryonic morphogenesis. Over the past 20 years, advances in imaging techniques, in particular, the development of confocal imaging, have opened a new world in biology, not only giving us access to a wealth...

The tunicates, or urochordates, constitute a large group of marine animals whose recent common ancestry with vertebrates is reflected in the tadpole-like larvae of most tunicates. Their diversity and key phylogenetic position are enhanced, from a research viewpoint, by anatomically simple and transparent embryos, compact rapidly evolving genomes, a...

Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at...

Epithelial invagination is a fundamental morphogenetic behavior that transforms a flat cell sheet into a pit or groove. Previous studies of invagination have focused on the role of actomyosin-dependent apical contraction; other mechanisms remain largely unexplored. We combined experimental and computational approaches to identify a two-step mechani...

Transcription initiation is controlled by cis-regulatory modules. Although these modules are usually made of clusters of short transcription factor binding sites, a small minority of such clusters in the genome have cis-regulatory activity. This paradox is currently unsolved. To identify what discriminates active from inactive clusters, we focused...

The diversity of animal morphologies is thought to result largely from spatial or temporal variations in gene expression. Conversely, we explored here the extent of divergence in transcriptional expression patterns compatible with a common morphological output, the chordate larva. We compared two organisms that share a prototypical tadpole larval b...

16th Annual Conference of the International-Society-of-Development-Biologists, Edinburgh, SCOTLAND, SEP 06-10, 2009

Ascidians were historically the first metazoans in which experimental embryology was carried out. These early works by Chabry and Conklin [Chabry, L., 1887. Embryologie normale et tératologique des Ascidie. Felix Alcan Editeur, Paris; Conklin, E., 1905. The organization and cell lineage of the ascidian egg. J. Acad., Nat. Sci. Phila. 13, 1], in par...

NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because...