The Experts below are selected from a list of 321 Experts worldwide ranked by ideXlab platform
Nori Satoh - One of the best experts on this subject based on the ideXlab platform.
-
Neuropeptides and their receptors of the protochordate,Ciona intestinalis:The evolutionary origin of vertebrate neuropeptides
Acta Biologica Hungarica, 2020Co-Authors: H. Satake, M. Aoyama, T. Kawada, T. Sekiguchi, T. Sakai, M. Fujie, Nori SatohAbstract:Ci-TK and Ci-TK-R are authentic tachykinin (TK) and TK receptor isolated from a protochordate, \ud Ciona intestinalis\ud . In this study, we investigated a novel function of TK as an enhancer of oocyte growth. Ci-TK-R is expressed specifically in the \ud Ciona\ud vitellogenic oocytes. Moreover, administration of Ci-TK to the \ud Ciona\ud ovary resulted in upregulation of gene expression and enzymatic activity of several proteases. Moreover, maturation of the \ud Ciona\ud oocytes from the vitellogenic stage to the post-vitellogenic stage was induced in the presence of Ci-TK, which was completely blocked by addition of protease inhibitors
-
SL RNA Genes of the Ascidian Tunicates Ciona intestinalis and Ciona savignyi
Zoological Science, 2010Co-Authors: Brendan Yeats, Eiichi Shoguchi, Nori Satoh, Jun Matsumoto, Sandra I. Mortimer, Kenneth E. M. HastingsAbstract:We characterized by bioinformatics the trans-spliced leader donor RNA (SL RNA) genes of two ascidians, Ciona intestinalis and Ciona savignyi. The Ciona intestinalis genome contains ∼670 copies of the SL RNA gene, principally on a 264-bp tandemly repeated element. Fluorescent in-situ hybridization mapped most of the repeats to a single site on the short arm of chromosome 8. The Ciona intestinalis genome also contains ∼100 copies of a >3.6-kb element that carries 1) an SL RNA-related sequence (possible a pseudogene) and 2) genes for the U6 snRNA and a histone-like protein. The Ciona savignyi genome contains two SL RNA gene classes having the same SL sequence as Ciona intestinalis but differing in the intron-like segments. These reside in similar but distinct repeat units of 575 bp (∼410 copies) and 552 bp (∼250 copies) that are arranged as separate tandem repeats. In neither Ciona species is the 5S RNA gene present within the SL RNA gene repeat unit. Although the number of SL RNA genes is similar, there is little sequence similarity between the intestinalis and savignyi repeat units, apart from the region encoding the SL RNA itself. This suggests that cis-regulatory elements involved in transcription and 3′-end processing are likely to be present within the transcribed region. The genomes of both Ciona species also include > 100 dispersed short elements containing the 16-nt SL sequence and up to 6 additional nucleotides of the SL RNA sequence.
-
Ciona intestinalis and Oxycomanthus japonicus, representatives of marine invertebrates.
Experimental Animals, 2009Co-Authors: Yasunori Sasakura, Nori Satoh, Kazuo Inaba, Mariko Kondo, Koji AkasakaAbstract:The study of marine invertebrates is useful in various biological research fields. However, genetic analyses of these animals are limited, mainly due to difficulties in culturing them, and the genetic resources of marine invertebrates have not been organized. Recently, advances have been made in the study of two deuterostomes, an ascidian Ciona intestinalis and a feather star Oxycomanthus japonicus. The draft genome sequence of Ciona intestinalis has been determined, and its compact genome, which has less redundancy of genes compared with vertebrates, provides us with a useful experimental system for analyzing the functions of genes during development. The life cycle of Ciona intestinalis is approximately 2-3 months, and the genetic techniques including a perfect inland culture system, germline transformation with a transposon Minos, enhancer detection and insertional mutagenesis, have been established. The feather star Oxycomanthus japonicus conserves the characteristics of the basic echinoderm body plan with a segmented mesoderm, which is a fascinating characteristic for understanding the evolution of echinoderms. Oxycomanthus japonicus shows strong regeneration ability and is a suitable subject for analysis of the mechanisms of regeneration. In consideration of these features, the National BioResource Project (NBRP) has started to support the supply of wild-types, transgenic lines and inbred lines of Ciona intestinalis and Oxycomanthus japonicus.
-
Transposon mediated transgenesis in a marine invertebrate chordate: Ciona intestinalis
Genome Biology, 2007Co-Authors: Yasunori Sasakura, Nori Satoh, Terumi Matsuoka, Yuichi Oogai, Satoko AwazuAbstract:Achievement of transposon mediated germline transgenesis in a basal chordate, Ciona intestinalis , is discussed. A Tc1 / mariner superfamily transposon, Minos , has excision and transposition activities in Ciona . Minos enables the creation of stable transgenic lines, enhancer detection, and insertional mutagenesis.
-
culture of Ciona intestinalis in closed systems
Developmental Dynamics, 2007Co-Authors: Jeanstephane Joly, Nori Satoh, Terumi Matsuoka, Satoko Awazu, Shungo Kano, Helene Auger, Kazuko Hirayama, Laurent Legendre, Yasunori SasakuraAbstract:Improvements in closed-system culturing methods for marine invertebrates are important prerequisites for the generalized use of transgenic lines. We discuss here the effects of several closed-system conditions on the growth and survival of the solitary ascidian, Ciona intestinalis. In Shimoda, close to the sea, a small-tank system was used to ensure that tanks and systems were reasonably equipped, water exchange was rapid, and animals separated to minimize the risk of infection. In Gif-sur-Yvette, an inland site, we tried to determine the optimal conditions to limit handling operations, and to save artificial seawater by avoiding water pollution. A mixture of at least two types of live algae was better than any single-organism diet. With these maintenance protocols, we were able to obtain several generations of Ciona intestinalis, including several transgenic lines. Because these systems make it easier to rear Ciona intestinalis in laboratories, they increase the potentialities of this model organism for research. Developmental Dynamics 236:1832–1840, 2007. © 2007 Wiley-Liss, Inc.
Michael S Levine - One of the best experts on this subject based on the ideXlab platform.
-
diverse ets transcription factors mediate fgf signaling in the Ciona anterior neural plate
Developmental Biology, 2015Co-Authors: Blair T Gainous, Eileen Wagner, Michael S LevineAbstract:The ascidian Ciona intestinalis is a marine invertebrate belonging to the sister group of the vertebrates, the tunicates. Its compact genome and simple, experimentally tractable embryos make Ciona well-suited for the study of cell-fate specification in chordates. Tunicate larvae possess a characteristic chordate body plan, and many developmental pathways are conserved between tunicates and vertebrates. Previous studies have shown that FGF signals are essential for neural induction and patterning at sequential steps of Ciona embryogenesis. Here we show that two different ETS family transcription factors, Ets1/2 and Elk1/3/4, have partially redundant activities in the anterior neural plate of gastrulating embryos. Whereas Ets1/2 promotes pigment cell formation in lateral lineages, both Ets1/2 and Elk1/3/4 are involved in the activation of Myt1L in medial lineages and the restriction of Six3/6 expression to the anterior-most regions of the neural tube. We also provide evidence that photoreceptor cells arise from posterior regions of the presumptive sensory vesicle, and do not depend on FGF signaling. Cells previously identified as photoreceptor progenitors instead form ependymal cells and neurons of the larval brain. Our results extend recent findings on FGF-dependent patterning of anterior–posterior compartments in the Ciona central nervous system.
-
regulatory blueprint for a chordate embryo
Science, 2006Co-Authors: Kaoru S Imai, Michael S Levine, Nori Satoh, Yutaka SatouAbstract:Ciona is an emerging model system for elucidating gene networks in development. Comprehensive in situ hybridization assays have identified 76 regulatory genes with localized expression patterns in the early embryo, at the time when naive blastomeres are determined to follow specific cell fates. Systematic gene disruption assays provided more than 3000 combinations of gene expression profiles in mutant backgrounds. Deduced gene circuit diagrams describing the formation of larval tissues were computationally visualized. These diagrams constitute a blueprint for the Ciona embryo and provide a foundation for understanding the evolutionary origins of the chordate body plan.
-
uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis
Development, 2005Co-Authors: Brad Davidson, Michael S LevineAbstract:The bHLH transcription factor Mesp has an essential but ambiguous role in early chordate heart development. Here, we employ the genetic and morphological simplicity of the basal chordate Ciona intestinalis to elucidate Mesp regulation and function. Characterization of a minimal cardiac enhancer for the Ciona Mesp gene demonstrated direct activation by the T-box transcription factor Tbx6c . The Mesp enhancer was fused to GFP, permitting high-resolution visualization of heart cells as they migrate and divide. The enhancer was also used to drive targeted expression of an activator form of Mesp , which induces heart formation without migration. We discuss the implications of Tbx6- Mesp interactions for the evolution of cardiac mesoderm in invertebrates and vertebrates.
-
evolutionary origins of the vertebrate heart specification of the cardiac lineage in Ciona intestinalis
Proceedings of the National Academy of Sciences of the United States of America, 2003Co-Authors: Brad Davidson, Michael S LevineAbstract:Here we exploit the extensive cell lineage information and streamlined genome of the ascidian, Ciona intestinalis, to investigate heart development in a basal chordate. Several cardiac genes were analyzed, including the sole Ciona ortholog of the Drosophila tinman gene, and tissue-specific enhancers were isolated for some of the genes. Conserved sequence motifs within these enhancers facilitated the isolation of a heart enhancer for the Ciona Hand-like gene. Altogether, these studies provide a regulatory framework for the differentiation of the cardiac mesoderm, beginning at the 110-cell stage, and extending through the fusion of cardiac progenitors during tail elongation. The cardiac lineage shares a common origin with the germ line, and zygotic transcription is first detected in the heart progenitors only after its separation from the germ line at the 64-cell stage. We propose that germ-line determinants influence the specification of the cardiac mesoderm, both by inhibiting inductive signals required for the development of noncardiac mesoderm lineages, and by providing a localized source of Wnt-5 and other signals required for heart development. We discuss the possibility that the germ line also influences the specification of the vertebrate heart.
-
Ciona intestinalis an emerging model for whole genome analyses
Trends in Genetics, 2003Co-Authors: Nori Satoh, Yutaka Satou, Brad Davidson, Michael S LevineAbstract:Abstract The tadpole larvae of the ascidian Ciona intestinalis possess the most simplified chordate body plan. Analysis of the Ciona draft genome indicates that the ∼153–159Mb genome contains ∼16 000 protein-coding genes. Among these is a fundamental set of conserved chordate proteins involved in cell signaling and development. A thorough examination of Ciona gene expression (the transcriptome) is ongoing, including large-scale expressed sequence tag analyses, cDNA sequencing and in situ hybridization screens. Together with recent advances in the methodology used to investigate gene regulation and function, these make Ciona an attractive experimental system for genome level analysis of chordate developmental genetics.
Yasunori Sasakura - One of the best experts on this subject based on the ideXlab platform.
-
The ventral peptidergic system of the adult ascidian Ciona robusta ( Ciona intestinalis Type A) insights from a transgenic animal model
Scientific Reports, 2020Co-Authors: Tomohiro Osugi, Yasunori Sasakura, Honoo SatakeAbstract:Ascidians are the sister group of vertebrates and occupy a critical position in explorations of the evolution of the endocrine and nervous systems of chordates. Here, we describe the complete ventral peptidergic system in adult transgenic Ciona robusta (Ciona intestinalis Type A) which expresses the Kaede reporter gene driven by the prohormone convertase 2 (PC2) gene promoter. Numerous PC2 promoter-driven fluorescent (Kaede-positive) non-neural cells were distributed in the blood sinus located at the anterior end of the pharynx, suggesting the acquisition of a peptidergic circulatory system in Ciona. Kaede-positive ciliated columnar cells, rounded cells, and tall ciliated cells were observed in the alimentary organs, including the endostyle, pharynx, esophagus, stomach, and intestine, suggesting that digestive functions are regulated by multiple peptidergic systems. In the heart, Kaede-positive neurons were located in the ring-shaped plexus at both ends of the myocardium. Nerve fiber–like tracts ran along the raphe and appeared to be connected with the plexuses. Such unique structures suggest a role for the peptidergic system in cardiac function. Collectively, the present anatomic analysis revealed the major framework of the ventral peptidergic system of adult Ciona, which could facilitate investigations of peptidergic regulation of the pharynx, endostyle, alimentary tissues, and heart.
-
Germline Transgenesis in Ciona.
Advances in Experimental Medicine and Biology, 2018Co-Authors: Yasunori SasakuraAbstract:Transgenesis is an indispensable method for elucidating the cellular and molecular mechanisms underlying biological phenomena. In Ciona, transgenic lines that have a transgene insertion in their genomes have been created. The transgenic lines are valuable because they express reporter genes in a nonmosaic manner. This nonmosaic manner allows us to accurately observe tissues and organs. The insertions of transgenes can destroy genes to create mutants. The insertional mutagenesis is a splendid method for investigating functions of genes. In Ciona intestinalis, expression of the gfp reporter gene is subjected to epigenetic silencing in the female germline. This epigenetic silencing has been used to establish a novel method for knocking down maternal expression of genes. The genetic procedures based on germline transgenesis facilitate studies for addressing gene functions in Ciona.
-
The nervous system of the adult ascidian Ciona intestinalis Type A (Ciona robusta): Insights from transgenic animal models
PLOS ONE, 2017Co-Authors: Tomohiro Osugi, Yasunori Sasakura, Honoo SatakeAbstract:The nervous system of ascidians is an excellent model system to provide insights into the evolutionary process of the chordate nervous system due to their phylogenetic positions as the sister group of vertebrates. However, the entire nervous system of adult ascidians has yet to be functionally and anatomically investigated. In this study, we have revealed the whole dorsal and siphon nervous system of the transgenic adult ascidian of Ciona intestinalis Type A (Ciona robusta) in which a Kaede reporter gene is expressed in a pan-neuronal fashion. The fluorescent signal of Kaede revealed the innervation patterns and distribution of neurons in the nervous system of Ciona. Precise microscopic observation demonstrated the clear innervation of the anterior and posterior main nerves to eight and six lobes of the oral and atrial siphons, respectively. Moreover, visceral nerves, previously identified as unpaired nerves, were found to be paired; one nerve was derived from the posterior end of the cerebral ganglion and the other from the right posterior nerve. This study further revealed the full trajectory of the dorsal strand plexus and paired visceral nerves on either side from the cerebral ganglion to the ovary, and precise innervation between the cerebral ganglion and the peripheral organs including the gonoduct, cupular organ, rectum and ovary. The differential innervation patterns of visceral nerves and the dorsal strand plexus indicate that the peripheral organs including the ovary undergo various neural regulations. Collectively, the present anatomical analysis revealed the major innervation of the dorsal and siphon nervous systems of adult Ciona.
-
Genome Editing of the Ascidian Ciona intestinalis with TALE Nuclease
Methods of Molecular Biology, 2017Co-Authors: Yasunori Sasakura, Keita Yoshida, Nicholas TreenAbstract:: The ascidian Ciona intestinalis is an important model animal for studying developmental mechanisms for constructing the chordate body. Although molecular and embryological techniques for manipulating Ciona genes were developed a long time ago, recent achievements of genome editing in this animal have innovated functional analyses of genes in Ciona. Particularly, knockout of genes in the G0 generation coupled with tissue-specific expression of TALENs enables us to rapidly address gene functions that were difficult using previous methods.
-
CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis.
Development Growth & Differentiation, 2014Co-Authors: Haruka Sasaki, Akiko Hozumi, Keita Yoshida, Yasunori SasakuraAbstract:Knockout of genes with CRISPR/Cas9 is a newly emerged approach to investigate functions of genes in various organisms. We demonstrate that CRISPR/Cas9 can mutate endogenous genes of the ascidian Ciona intestinalis, a splendid model for elucidating molecular mechanisms for constructing the chordate body plan. Short guide RNA (sgRNA) and Cas9 mRNA, when they are expressed in Ciona embryos by means of microinjection or electroporation of their expression vectors, introduced mutations in the target genes. The specificity of target choice by sgRNA is relatively high compared to the reports from some other organisms, and a single nucleotide mutation at the sgRNA dramatically reduced mutation efficiency at the on-target site. CRISPR/Cas9-mediated mutagenesis will be a powerful method to study gene functions in Ciona along with another genome editing approach using TALE nucleases.
Yutaka Satou - One of the best experts on this subject based on the ideXlab platform.
-
a nearly complete genome of Ciona intestinalis type a c robusta reveals the contribution of inversion to chromosomal evolution in the genus Ciona
Genome Biology and Evolution, 2019Co-Authors: Yutaka Satou, Reiko Yoshida, Manabu Fujie, Ryohei Nakamura, Deli Yu, Mayuko Hamada, Kanako Hisata, Hiroyuki Takeda, Noriyuki SatohAbstract:: Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.
-
high throughput protein production combined with high throughput selex identifies an extensive atlas of Ciona robusta transcription factor dna binding specificities
Methods of Molecular Biology, 2019Co-Authors: Kazuhiro R Nitta, Yutaka Satou, Renaud Vincentelli, Edwin Jacox, Agnes Cimino, Yukio Ohtsuka, Daniel Sobral, Christian Cambillau, Patrick LemaireAbstract:: 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 method, which can be used to determine the DNA-binding specificity of TFs. Thanks to the development of high-throughput (HT) DNA cloning system and protein production technology, the classical SELEX assay has be extended to high-throughput scale (HT-SELEX).We report here the detailed protocol for the cloning, production, and purification of 420 Ciona robusta DNA BD. 263 Ciona robusta TF DNA-binding domain proteins were purified in milligram quantities and analyzed by HT-SELEX. The identification of 139 recognition sequences generates an atlas of protein-DNA-binding specificities that is crucial for the understanding of the gene regulatory network (GRN) of Ciona robusta. Overall, our analysis suggests that the Ciona robusta repertoire of sequence-specific transcription factors comprises less than 500 genes. The protocols for high-throughput protein production and HT-SELEX described in this article for the study of Ciona robusta TF DNA-binding specificity are generic and have been successfully applied to a wide range of TFs from other species, including human, mouse, and Drosophila.
-
Microinjection of Exogenous Nucleic Acids into Eggs: Ciona Species.
Advances in Experimental Medicine and Biology, 2018Co-Authors: Kenji Kobayashi, Yutaka SatouAbstract:Microinjection is a common technique used to deliver nucleic acids into eggs and embryos in Ciona species. There are three Ciona species that are commonly used for research—Ciona intestinalis type A (C. robusta), C. intestinalis type B (C. intestinalis), and C. savignyi. Here, we present the microinjection methods using eggs and embryos of C. intestinalis type A and C. savignyi; however, our methods would also be applicable to eggs and embryos of C. intestinalis type B. Microinjection is a classical and widely used delivery method, which involves the use of a glass micropipette, a hollow glass needle with a microscopic tip, to inject nucleic acids into eggs and embryos under a stereo microscope. The required amount of nucleic acids is much smaller for microinjection than for electroporation, another delivery method. Proteins, and other chemicals, such as fluorescent dye, can be introduced with nucleic acids using a microinjection.
-
regulatory blueprint for a chordate embryo
Science, 2006Co-Authors: Kaoru S Imai, Michael S Levine, Nori Satoh, Yutaka SatouAbstract:Ciona is an emerging model system for elucidating gene networks in development. Comprehensive in situ hybridization assays have identified 76 regulatory genes with localized expression patterns in the early embryo, at the time when naive blastomeres are determined to follow specific cell fates. Systematic gene disruption assays provided more than 3000 combinations of gene expression profiles in mutant backgrounds. Deduced gene circuit diagrams describing the formation of larval tissues were computationally visualized. These diagrams constitute a blueprint for the Ciona embryo and provide a foundation for understanding the evolutionary origins of the chordate body plan.
-
genomic overview of mrna 5 leader trans splicing in the ascidian Ciona intestinalis
Nucleic Acids Research, 2006Co-Authors: Yutaka Satou, Makoto Hamaguchi, Kenneth E. M. Hastings, Keisuke Takeuchi, Nori SatohAbstract:: Although spliced leader (SL) trans-splicing in the chordates was discovered in the tunicate Ciona intestinalis there has been no genomic overview analysis of the extent of trans-splicing or the make-up of the trans-spliced and non-trans-spliced gene populations of this model organism. Here we report such an analysis for Ciona based on the oligo-capping full-length cDNA approach. We randomly sampled 2078 5'-full-length ESTs representing 668 genes, or 4.2% of the entire genome. Our results indicate that Ciona contains a single major SL, which is efficiently trans-spliced to mRNAs transcribed from a specific set of genes representing approximately 50% of the total number of expressed genes, and that individual trans-spliced mRNA species are, on average, 2-3-fold less abundant than non-trans-spliced mRNA species. Our results also identify a relationship between trans-splicing status and gene functional classification; ribosomal protein genes fall predominantly into the non-trans-spliced category. In addition, our data provide the first evidence for the occurrence of polycistronic transcription in Ciona. An interesting feature of the Ciona polycistronic transcription units is that the great majority entirely lack intercistronic sequences.
Brad Davidson - One of the best experts on this subject based on the ideXlab platform.
-
Heart Development in Ciona
Reference Module in Life Sciences, 2017Co-Authors: Christina D. Cota, Karl Palmquist, Brad DavidsonAbstract:Abstract Ciona intestinalis is an important model for studying the genetic and cellular basis of heart development. In this article we summarize the anatomy, physiology, and formation of the heart in developing Ciona embryos. We also review recent studies characterizing the gene network encoding Ciona cardiogenesis and how cellular processes interface with this network. Additionally, we discuss how insights into Ciona heart development inform vertebrate cardiogenesis. More broadly, we consider the potential for Ciona heart research to shed light on the morphogenetic circuitry regulating cell identity and behavior in developing embryos, stem cells, and tumors.
-
Ciona intestinalis as a model for cardiac development
Seminars in Cell & Developmental Biology, 2007Co-Authors: Brad DavidsonAbstract:The primitive chordate Ciona intestinalis has emerged as a significant model system for the study of heart development. The Ciona embryo employs a conserved heart gene network in the context of extremely low cell numbers and reduced genetic redundancy. Here, I review recent studies on the molecular genetics of Ciona cardiogenesis as well as classic work on heart anatomy and physiology. I also discuss the potential of employing Ciona to decipher a comprehensive chordate gene network and to determine how this network controls heart morphogenesis.
-
Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
Genome Research, 2005Co-Authors: Michael Levine, Brad DavidsonAbstract:The draft genome of the primitive chordate, Ciona intestinalis, was published three years ago. Since then, significant progress has been made in utilizing Ciona's genomic and morphological simplicity to better understand conserved chordate developmental processes. Extensive annotation and sequencing of staged EST libraries make the Ciona genome one of the best annotated among those that are publicly available. The formation of the Ciona tadpole depends on simple, well-defined cellular lineages, and it is possible to trace the lineages of key chordate tissues such as the notochord and neural tube to the fertilized egg. Electroporation methods permit the targeted expression of regulatory genes and signaling molecules in defined cell lineages, as well as the rapid identification of regulatory DNAs underlying cell-specific gene expression. The recent sequencing of a second Ciona genome (C savignyi) permits the use of simple alignment algorithms for the identification of conserved noncoding sequences, including microRNA genes and enhancers. Detailed expression profiles are now available for almost every gene that encodes a regulatory protein or cell-signaling molecule. The combination of gene-expression profiles, comparative genome analysis, and gene-disruption assays should permit the determination of high-resolution genomic regulatory networks underlying the specification of basic chordate tissues such as the heart, blood, notochord, and neural tube.
-
uncoupling heart cell specification and migration in the simple chordate Ciona intestinalis
Development, 2005Co-Authors: Brad Davidson, Michael S LevineAbstract:The bHLH transcription factor Mesp has an essential but ambiguous role in early chordate heart development. Here, we employ the genetic and morphological simplicity of the basal chordate Ciona intestinalis to elucidate Mesp regulation and function. Characterization of a minimal cardiac enhancer for the Ciona Mesp gene demonstrated direct activation by the T-box transcription factor Tbx6c . The Mesp enhancer was fused to GFP, permitting high-resolution visualization of heart cells as they migrate and divide. The enhancer was also used to drive targeted expression of an activator form of Mesp , which induces heart formation without migration. We discuss the implications of Tbx6- Mesp interactions for the evolution of cardiac mesoderm in invertebrates and vertebrates.
-
noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance
Genome Research, 2004Co-Authors: David S Johnson, Brad Davidson, William C Smith, Christopher D Brown, Arend SidowAbstract:We show that sequence comparisons at different levels of resolution can efficiently guide functional analyses of regulatory regions in the ascidians Ciona savignyi and Ciona intestinalis. Sequence alignments of several tissue-specific genes guided discovery of minimal regulatory regions that are active in whole-embryo reporter assays. Using the Troponin I (TnI) locus as a case study, we show that more refined local sequence analyses can then be used to reveal functional substructure within a regulatory region. A high-resolution saturation mutagenesis in conjunction with comparative sequence analyses defined essential sequence elements within the TnI regulatory region. Finally, we found a significant, quantitative relationship between function and sequence divergence of noncoding functional elements. This work demonstrates the power of comparative sequence analysis between the two Ciona species for guiding gene regulatory experiments.