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Han L, Quan Z, Wu Y, Hao P, Wang W, Li Y, Zhang X, Liu P, Gao C, Wang H, Wang L, Zhang W, Yin D, Chang Y, Ding J. Expression Regulation Mechanisms of Sea Urchin (Strongylocentrotus intermedius) Under the High Temperature: New Evidence for the miRNA-mRNA Interaction Involvement. Front Genet 2022; 13:876308. [PMID: 35846155 PMCID: PMC9277089 DOI: 10.3389/fgene.2022.876308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
In the context of global warming and continuous high temperatures in the northern part of China during summer, the mortality rate of our main breeding species, Strongylocentrotus intermedius, reached 80% in 2020. How sea urchins respond to high temperatures is of great concern to academia and industry. In this study, we examined the antioxidant enzyme activities of different color tube-footed sea urchins under heat stress and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. The results showed that the antioxidant enzyme activities of sea urchins were altered by thermal stress, and the changes in peroxidase activities of red tube-footed sea urchins were particularly significant. Investigations revealed that 1,079 differentially expressed genes (DEGs), 11 DE miRNAs, and 104 “DE miRNA-DEG” pairs in total were detected in sea urchins under high temperature stress. Several mRNA and miRNAs were significantly changed (e.g. HSP70, DnaJ11, HYAL, CALR, miR-184-p5, miR-92a, miR-92c, and miR-124-p5), suggesting these genes and miRNAs exerted important functions in response to high temperature. At the transcriptional level, red tube-footed sea urchins were found to be more sensitive to high temperature and could respond to high temperature rapidly. DE miRNA-mRNA network showed that miR-92b-3p and PC-5p-7420 were the most corresponding miRNAs. Five mRNAs (DnaJ11, SAR1B, CALR, HYOU1, TUBA) may be potential markers of sea urchin response to high temperature. Possible interaction between miRNA-mRNA could be linked to protein folding in the endoplasmic reticulum, Phagosomes, and calcium transport. This study provides a theoretical basis for the molecular mechanism of sea urchin heat tolerance and information that will aid in the selection and breeding of sea urchins with high temperature tolerance.
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Affiliation(s)
| | - Zijiao Quan
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Peng Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Heng Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
- *Correspondence: Jun Ding,
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Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA. The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev Biol 2019; 460:139-154. [PMID: 31816285 DOI: 10.1016/j.ydbio.2019.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 10/25/2022]
Abstract
Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.
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Affiliation(s)
- John D Hogan
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Lingqi Luo
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Jonas Ibn-Salem
- Evolution and Development Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany; Faculty of Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Arjun Lamba
- Biology Department, Boston University, Boston, MA, USA
| | | | - Michael L Piacentino
- Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA
| | - Daniel T Zuch
- Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA
| | - Amanda B Core
- Biology Department, Boston University, Boston, MA, USA
| | | | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - José Horacio Grau
- Dahlem Centre for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Berlin, Germany; Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Emily Speranza
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Naoki Irie
- Department of Biological Sciences, University of Tokyo, Tokyo, Japan
| | - Albert J Poustka
- Evolution and Development Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany; Dahlem Centre for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Berlin, Germany
| | - Cynthia A Bradham
- Program in Bioinformatics, Boston University, Boston, MA, USA; Biology Department, Boston University, Boston, MA, USA; Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA.
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Wang H, Ding J, Ding S, Chang Y. Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius. Genes Genomics 2019; 41:1397-1415. [PMID: 31485990 DOI: 10.1007/s13258-019-00864-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Sea urchin gonads of both sexes, commonly termed "roe", are highly valued seafood delicacies, and Strongylocentrotus intermedius is considered one of the tastiest sea urchins. In order to produce high-quality gonads for consumption and clarify the mechanism of gonad growth and development of the sea urchin, more genetic information, especially at the transcriptome level, is needed. OBJECTIVE A more thorough understanding of sea urchin gonad growth and development in both sexes could enable regulation of these processes at several stages with the aim of suppressing gametogenesis in order to produce high-quality gonads for consumption. METHODS The adult sea urchins S. intermedius were cultured for 3 months, and were sampled for the gonadal transcriptome analysis which has been performed on the RNAs of three male and female adults of S. intermedius in each gonad development stage. RESULTS Illumina sequencing raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) database (PRJNA532998). It generated 560,196,356 raw reads and 548,956,944 clean reads were acquired, which were assembled into 107,850 transcripts with 44,124 genes. Comparative analysis showed the differentially expressed genes (DEGs) from 114 to 2566. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to determine the functional significance of these DEGs. We have selected 9 genes related to growth and 12 genes related to fatty acid biosynthesis and metabolism in sea urchin gonads. CONCLUSION These data for sea urchins were intended to provide markers for gonad growth and development that can be accumulated for use in aquaculture applications.
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Affiliation(s)
- Heng Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Siyu Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
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Jain G, Pendola M, Koutsoumpeli E, Johnson S, Evans JS. Glycosylation Fosters Interactions between Model Sea Urchin Spicule Matrix Proteins. Implications for Embryonic Spiculogenesis and Biomineralization. Biochemistry 2018; 57:3032-3035. [PMID: 29757633 DOI: 10.1021/acs.biochem.8b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of embryonic mineralized skeletal elements (spicules) in the sea urchin requires the participation of proteins, many of which may interact with one another and assist in the creation of an extracellular matrix wherein mineral formation takes place. To probe this, we created a sea urchin spicule recombinant model protein pair system wherein we tested the interactions between two major spicule proteins, SpSM50 and the glycoprotein, SpSM30B/C. Both proteins are strong hydrogelators that manipulate early and later events in mineral formation. We discovered that the anionic glycan moieties of SpSM30B/C are required for interaction with the SpSM50 protein and that these interactions are Ca(II)-independent. In addition, when these proteins form a complex, they create hybrid hydrogel particles that are physically distinct from their individual counterparts. Thus, glycan-mediated interactions play an important role in in vitro spicule protein assembly and most likely within the spicule itself.
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Affiliation(s)
- Gaurav Jain
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Martin Pendola
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Eleni Koutsoumpeli
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - Steven Johnson
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - John Spencer Evans
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
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Armstrong AF, Grosberg RK. The developmental transcriptomes of two sea biscuit species with differing larval types. BMC Genomics 2018; 19:368. [PMID: 29776340 PMCID: PMC5960215 DOI: 10.1186/s12864-018-4768-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week. RESULTS Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression. CONCLUSION This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.
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Affiliation(s)
- Anne Frances Armstrong
- Center for Population Biology, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA. .,California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.
| | - Richard K Grosberg
- Coastal and Marine Sciences Institute, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA
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Abstract
The echinoderms are a phylum of invertebrate deuterostome animals that constitute important research models for a number of biological disciplines. EchinoBase ( www.echinobase.org ) is an echinoderm-specific genome database and web information system that provides a platform for the interrogation and exploration of echinoderm genomic data. This chapter outlines the datasets available on EchinoBase; from assembled genomes and genome annotations, to spatial and quantitative expression data, as well as functional genomics datasets. We also highlight the bioinformatic tools available on the website to facilitate rapid inquiries using these data (genome browsers, precompiled BLAST databases, etc.), and suggest optimized strategies for performing these inquiries. We conclude with a perspective on how one could integrate various genomic resources to predict putative noncoding regulatory regions. The available datasets and analyses they permit provide the basic components required for developing an understanding of how echinoderm genomes are regulated, especially during early development, and provides a platform for comparative genomic inquiries among species in this phylum.
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Semmens DC, Mirabeau O, Moghul I, Pancholi MR, Wurm Y, Elphick MR. Transcriptomic identification of starfish neuropeptide precursors yields new insights into neuropeptide evolution. Open Biol 2016; 6:150224. [PMID: 26865025 PMCID: PMC4772807 DOI: 10.1098/rsob.150224] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Neuropeptides are evolutionarily ancient mediators of neuronal signalling in nervous systems. With recent advances in genomics/transcriptomics, an increasingly wide range of species has become accessible for molecular analysis. The deuterostomian invertebrates are of particular interest in this regard because they occupy an ‘intermediate' position in animal phylogeny, bridging the gap between the well-studied model protostomian invertebrates (e.g. Drosophila melanogaster, Caenorhabditis elegans) and the vertebrates. Here we have identified 40 neuropeptide precursors in the starfish Asterias rubens, a deuterostomian invertebrate from the phylum Echinodermata. Importantly, these include kisspeptin-type and melanin-concentrating hormone-type precursors, which are the first to be discovered in a non-chordate species. Starfish tachykinin-type, somatostatin-type, pigment-dispersing factor-type and corticotropin-releasing hormone-type precursors are the first to be discovered in the echinoderm/ambulacrarian clade of the animal kingdom. Other precursors identified include vasopressin/oxytocin-type, gonadotropin-releasing hormone-type, thyrotropin-releasing hormone-type, calcitonin-type, cholecystokinin/gastrin-type, orexin-type, luqin-type, pedal peptide/orcokinin-type, glycoprotein hormone-type, bursicon-type, relaxin-type and insulin-like growth factor-type precursors. This is the most comprehensive identification of neuropeptide precursor proteins in an echinoderm to date, yielding new insights into the evolution of neuropeptide signalling systems. Furthermore, these data provide a basis for experimental analysis of neuropeptide function in the unique context of the decentralized, pentaradial echinoderm bauplan.
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Affiliation(s)
- Dean C Semmens
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Olivier Mirabeau
- Institut Curie, Genetics and Biology of Cancers Unit, INSERM U830, PSL Research University, Paris 75005, France
| | - Ismail Moghul
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mahesh R Pancholi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Chen Y, Chang Y, Wang X, Qiu X, Liu Y. De novo assembly and analysis of tissue-specific transcriptomes revealed the tissue-specific genes and profile of immunity from Strongylocentrotus intermedius. FISH & SHELLFISH IMMUNOLOGY 2015; 46:723-736. [PMID: 26253994 DOI: 10.1016/j.fsi.2015.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 07/02/2015] [Accepted: 07/19/2015] [Indexed: 06/04/2023]
Abstract
Strongylocentrotus intermedius is an important marine species in north China and Japan. Recent years, diseases are threating the sea urchin aquaculture industry seriously. To provide a genetic resource for S. intermedius as well as overview the immune-related genes of S. intermedius, we performed transcriptome sequencing of three cDNA libraries representing three tissues, coelomocytes, gut and peristomial membrane respectively. In total 138,421 contigs were assembled from all sequencing data. 96,764 contigs were annotated according to bioinformatics databases, including NT, nr, Swiss-Prot, KEGG, COG. 49,336 Contigs were annotated as CDS. In this study, we obtained 24,778 gene families from S. intermedius transcriptome. The gene expression analysis revealed that more genes were expressed in gut, more high expression level genes in coelomocytes when compared with other tissues. Specific expressed contigs in coelomocytes, gut, and peristomial membrane were 546, 1136, and 1012 respectively. Pathway analysis suggested 25, 17 and 36 potential specifically pathways may specific progressed in peristomial membrane, gut and coelomocytes respectively. Similarities and differences between S. intermedius and other echinoderms were analyzed. S. intermedius was more homology to Strongylocentrotus purpuratus than others sea urchin. Of 24,778 genes, 1074 genes are immune-related, immune genes were expressed with a higher level in coelomocytes than other tissues. Complement system may be the most important immune system in sea urchin. We also identified 2438 SSRs and 16,236 SNPs for S. intermedius. These results provide a transcriptome resource and foundation to study molecular mechanisms of sea urchin immune system.
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Affiliation(s)
- Yadong Chen
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, Liaoning, China; Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, Liaoning, China
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, Liaoning, China
| | - Xuemei Qiu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, Liaoning, China
| | - Yang Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, Liaoning, China.
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Abstract
In mature gametes and during the oocyte-to-embryo transition, transcription is generally silenced and gene expression is post-transcriptionally regulated. However, we recently discovered that major transcription can occur immediately after fertilization, prior to pronuclear fusion, and in the first cell division of the oocyte-to-embryo transition in the nematode Ascaris suum. We postulate that the balance between transcriptional and post-transcriptional regulation during the oocyte-to-embryo transition may largely be determined by cell cycle length and thus the time available for the genome to be transcribed.
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Affiliation(s)
- Jianbin Wang
- a Department of Biochemistry and Molecular Genetics ; University of Colorado School of Medicine ; Aurora , CO USA
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de Araujo Leite JC, de Castro TMX, Barbosa-Filho JM, de Siqueira-Junior JP, Marques-Santos LF. Photoprotective effect of coumarin and 3-hydroxycoumarin in sea urchin gametes and embryonic cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 146:44-51. [DOI: 10.1016/j.jphotobiol.2015.02.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/02/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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Stepicheva N, Nigam PA, Siddam AD, Peng CF, Song JL. microRNAs regulate β-catenin of the Wnt signaling pathway in early sea urchin development. Dev Biol 2015; 402:127-41. [PMID: 25614238 DOI: 10.1016/j.ydbio.2015.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 12/18/2014] [Accepted: 01/09/2015] [Indexed: 12/19/2022]
Abstract
Development of complex multicellular organisms requires careful regulation at both transcriptional and post-transcriptional levels. Post-transcriptional gene regulation is in part mediated by a class of non-coding RNAs of 21-25 nucleotides in length known as microRNAs (miRNAs). β-catenin, regulated by the canonical Wnt signaling pathway, has a highly evolutionarily conserved function in patterning early metazoan embryos, in forming the Anterior-Posterior axis, and in establishing the endomesoderm. Using reporter constructs and site-directed mutagenesis, we identified at least three miRNA binding sites within the 3' untranslated region (3'UTR) of the sea urchin β-catenin. Further, blocking these three miRNA binding sites within the β-catenin 3'UTR to prevent regulation of endogenous β-catenin by miRNAs resulted in a minor increase in β-catenin protein accumulation that is sufficient to induce aberrant gut morphology and circumesophageal musculature. These phenotypes are likely the result of increased transcript levels of Wnt responsive endomesodermal regulatory genes. This study demonstrates the importance of miRNA regulation of β-catenin in early development.
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Affiliation(s)
- Nadezda Stepicheva
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Priya A Nigam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Chieh Fu Peng
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA.
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Isolation and assessment of signaling proteins from synchronized cultures during egg activation and through the egg-to-embryo transition in sea urchins. Methods Mol Biol 2014; 1128:277-94. [PMID: 24567222 DOI: 10.1007/978-1-62703-974-1_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sea urchins are an excellent model system for investigating fertilization mechanisms and fundamental cell biological phenomenon such as release from quiescence, cell division, secretion, and basic signal transduction. The ease of gamete collection, fertilization, and culture is complemented by exquisite developmental synchronicity and the ability to carry out both large-scale biochemical studies and single-cell experiments. In particular, fertilization in echinoderms serves as a paradigm for a digital signaling event-a one-time only switch that launches the egg into the developmental pathway. Sperm-induced egg activation is dependent on the release of calcium from internal stores and subsequent effects on a myriad of cellular events such as exocytosis, cytoskeletal remodeling, and cell cycle reentry. Here we describe methods to investigate individual signaling proteins as well as global proteomic and phosphoproteomic changes involved in the initial steps of egg activation through the egg-to-embryo transition.
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Holland A, Ohlendieck K. Comparative profiling of the sperm proteome. Proteomics 2014; 15:632-48. [DOI: 10.1002/pmic.201400032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/27/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Ashling Holland
- Department of Biology; National University of Ireland; Maynooth County Kildare Ireland
| | - Kay Ohlendieck
- Department of Biology; National University of Ireland; Maynooth County Kildare Ireland
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15
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Transcriptome information of the Arctic green sea urchin and its use in environmental monitoring. Polar Biol 2014. [DOI: 10.1007/s00300-014-1507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wang C, Wachholtz M, Wang J, Liao X, Lu G. Analysis of the skin transcriptome in two oujiang color varieties of common carp. PLoS One 2014; 9:e90074. [PMID: 24603653 PMCID: PMC3946065 DOI: 10.1371/journal.pone.0090074] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 01/29/2014] [Indexed: 11/18/2022] Open
Abstract
Background Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding. Methodology/Principal Findings In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW. Conclusions The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.
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Affiliation(s)
- Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
- * E-mail: (CW); (GL)
| | - Michael Wachholtz
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Jun Wang
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Xiaolin Liao
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem, Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
- * E-mail: (CW); (GL)
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17
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Abstract
The Sea Urchin Genome Project Web site, SpBase ( http://SpBase.org ), in association with a suite of publicly available sequence comparison tools provides a platform from which to analyze genes and genomic sequences of sea urchin. This information system is specifically designed to support laboratory bench studies in cell and molecular biology. In particular these tools and datasets have supported the description of the gene regulatory networks of the purple sea urchin S. purpuratus. This chapter details methods to undertake in the first steps to find genes and noncoding regulatory sequences for further analysis.
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Affiliation(s)
- R Andrew Cameron
- Center for Computational Regulatory Genomics, Beckman Institute, Caltech, Pasadena, CA, USA
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18
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Leite JCDA, de Vasconcelos RB, da Silva SG, de Siqueira-Junior JP, Marques-Santos LF. ATP-binding cassette transporters protect sea urchin gametes and embryonic cells against the harmful effects of ultraviolet light. Mol Reprod Dev 2013; 81:66-83. [PMID: 24254332 DOI: 10.1002/mrd.22283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/14/2013] [Indexed: 12/22/2022]
Abstract
Embryos of marine organisms whose development occurs externally are particularly sensitive to ultraviolet (UV) light (bands A and B, respectively, UVA and UVB). ATP-binding cassette (ABC) transporters are the first line of cellular defense against chemical or physical stress. The present work investigated the involvement of ABC transporters on UVA or UVB effects on eggs, spermatozoa, and embryonic cells of the sea urchin Echinometra lucunter. Gametes or embryos were exposed to UVA (3.6-14.4 kJ m(-2)) or UVB (0.112-14.4 kJ m(-2)), and embryonic development was monitored by optical microscopy at different developmental stages in the presence or absence of the ABC-transporter blockers reversin205 (ABCB1 blocker) or MK571 (ABCC1 blocker). E. lucunter eggs, spermatozoa and embryos were resistant to UVA exposure. Resistance to the harmful effects of UVB was strongly associated to ABC transporter activity (embryos > eggs > spermatozoa). ABCB1 or ABCC1 blockage promoted the injurious effects of UVA on spermatozoa. ABCC1 transporter blockage increased UVB-dependent damage in eggs while ABCB1 transporter inhibition increased harmful effects of UVB in embryonic cells. ABC-transporter activity was not, however, affected by UVB exposure. In conclusion, the present study is the first report on the protective role of ABC transporters against harmful effects of UVA and UVB on sea urchin eggs and embryonic cells.
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Affiliation(s)
- Jocelmo Cássio de Araujo Leite
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
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19
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Adams NL, Campanale JP, Foltz KR. Proteomic responses of sea urchin embryos to stressful ultraviolet radiation. Integr Comp Biol 2012; 52:665-80. [PMID: 22576820 DOI: 10.1093/icb/ics058] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Solar ultraviolet radiation (UVR, 290-400 nm) penetrates into seawater and can harm shallow-dwelling and planktonic marine organisms. Studies dating back to the 1930s revealed that echinoids, especially sea urchin embryos, are powerful models for deciphering the effects of UVR on embryonic development and how embryos defend themselves against UV-induced damage. In addition to providing a large number of synchronously developing embryos amenable to cellular, biochemical, molecular, and single-cell analyses, the purple sea urchin, Strongylocentrotus purpuratus, also offers an annotated genome. Together, these aspects allow for the in-depth study of molecular and biochemical signatures of UVR stress. Here, we review the effects of UVR on embryonic development, focusing on the early-cleavage stages, and begin to integrate data regarding single-protein responses with comprehensive proteomic assessments. Proteomic studies reveal changes in levels of post-translational modifications to proteins that respond to UVR, and identify proteins that can then be interrogated as putative targets or components of stress-response pathways. These responsive proteins are distributed among systems upon which targeted studies can now begin to be mapped. Post-transcriptional and translational controls may provide early embryos with a rapid, fine-tuned response to stress during early stages, especially during pre-blastula stages that rely primarily on maternally derived defenses rather than on responses through zygotic gene transcription.
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Affiliation(s)
- N L Adams
- California Polytechnic State University, San Luis Obispo, CA, USA.
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20
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Shipp LE, Hamdoun A. ATP-binding cassette (ABC) transporter expression and localization in sea urchin development. Dev Dyn 2012; 241:1111-24. [PMID: 22473856 DOI: 10.1002/dvdy.23786] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND ATP-binding cassette (ABC) transporters are membrane proteins that regulate intracellular concentrations of myriad compounds and ions. There are >100 ABC transporter predictions in the Strongylocentrotus purpuratus genome, including 40 annotated ABCB, ABCC, and ABCG "multidrug efflux" transporters. Despite the importance of multidrug transporters for protection and signaling, their expression patterns have not been characterized in deuterostome embryos. RESULTS Sea urchin embryos expressed 20 ABCB, ABCC, and ABCG transporter genes in the first 58 hr of development, from unfertilized egg to early prism. We quantified transcripts of ABCB1a, ABCB4a, ABCC1, ABCC5a, ABCC9a, and ABCG2b, and found that ABCB1a mRNA was 10-100 times more abundant than other transporter mRNAs. In situ hybridization showed ABCB1a was expressed ubiquitously in embryos, while ABCC5a was restricted to secondary mesenchyme cells and their precursors. Fluorescent protein fusions showed localization of ABCB1a on apical cell surfaces, and ABCC5a on basolateral surfaces. CONCLUSIONS Embryos use many ABC transporters with predicted functions in cell signaling, lysosomal and mitochondrial homeostasis, potassium channel regulation, pigmentation, and xenobiotic efflux. Detailed characterization of ABCB1a and ABCC5a revealed that they have different temporal and spatial gene expression profiles and protein localization patterns that correlate to their predicted functions in protection and development, respectively.
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Affiliation(s)
- Lauren E Shipp
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, California 92093-0202, USA
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21
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Pantropic retroviruses as a transduction tool for sea urchin embryos. Proc Natl Acad Sci U S A 2012; 109:5334-9. [PMID: 22431628 DOI: 10.1073/pnas.1117846109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sea urchins are an important model for experiments at the intersection of development and systems biology, and technical innovations that enhance the utility of this model are of great value. This study explores pantropic retroviruses as a transduction tool for sea urchin embryos, and demonstrates that pantropic retroviruses infect sea urchin embryos with high efficiency and genomically integrate at a copy number of one per cell. We successfully used a self-inactivation strategy to both insert a sea urchin-specific enhancer and disrupt the endogenous viral enhancer. The resulting self-inactivating viruses drive global and persistent gene expression, consistent with genomic integration during the first cell cycle. Together, these data provide substantial proof of principle for transduction technology in sea urchin embryos.
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22
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Veldhoen N, Ikonomou MG, Helbing CC. Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 76:23-38. [PMID: 22036265 DOI: 10.1016/j.ecoenv.2011.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 09/16/2011] [Accepted: 10/06/2011] [Indexed: 05/31/2023]
Abstract
Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems.
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Affiliation(s)
- Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 Stn CSC, Victoria, B.C., Canada
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23
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Rafiq K, Cheers MS, Ettensohn CA. The genomic regulatory control of skeletal morphogenesis in the sea urchin. Development 2011; 139:579-90. [PMID: 22190640 DOI: 10.1242/dev.073049] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A central challenge of developmental and evolutionary biology is to understand how anatomy is encoded in the genome. Elucidating the genetic mechanisms that control the development of specific anatomical features will require the analysis of model morphogenetic processes and an integration of biological information at genomic, cellular and tissue levels. The formation of the endoskeleton of the sea urchin embryo is a powerful experimental system for developing such an integrated view of the genomic regulatory control of morphogenesis. The dynamic cellular behaviors that underlie skeletogenesis are well understood and a complex transcriptional gene regulatory network (GRN) that underlies the specification of embryonic skeletogenic cells (primary mesenchyme cells, PMCs) has recently been elucidated. Here, we link the PMC specification GRN to genes that directly control skeletal morphogenesis. We identify new gene products that play a proximate role in skeletal morphogenesis and uncover transcriptional regulatory inputs into many of these genes. Our work extends the importance of the PMC GRN as a model developmental GRN and establishes a unique picture of the genomic regulatory control of a major morphogenetic process. Furthermore, because echinoderms exhibit diverse programs of skeletal development, the newly expanded sea urchin skeletogenic GRN will provide a foundation for comparative studies that explore the relationship between GRN evolution and morphological evolution.
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Affiliation(s)
- Kiran Rafiq
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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24
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Select microRNAs are essential for early development in the sea urchin. Dev Biol 2011; 362:104-13. [PMID: 22155525 DOI: 10.1016/j.ydbio.2011.11.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 10/22/2011] [Accepted: 11/22/2011] [Indexed: 11/22/2022]
Abstract
microRNAs (miRNAs) are small noncoding RNAs that mediate post-transcriptional gene regulation and have emerged as essential regulators of many developmental events. The transcriptional network during early embryogenesis of the purple sea urchin, Strongylocentrotus purpuratus, is well described and can serve as an excellent model to test functional contributions of miRNAs in embryogenesis. We examined the loss of function phenotypes of major components of the miRNA biogenesis pathway. Inhibition of de novo synthesis of Drosha and Dicer in the embryo led to consistent developmental defects, a failure to gastrulate, and embryonic lethality, including changes in the steady state levels of transcription factors and signaling molecules involved in germ layer specification. We annotated and profiled small RNA expression from the ovary and several early embryonic stages by deep sequencing followed by computational analysis. miRNAs as well as a large population of putative piRNAs (piwi-interacting RNAs) had dynamic accumulation profiles through early development. Defects in morphogenesis caused by loss of Drosha could be rescued with four miRNAs. Taken together our results indicate that post-transcriptional gene regulation directed by miRNAs is functionally important for early embryogenesis and is an integral part of the early embryonic gene regulatory network in S. purpuratus.
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25
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Beeble A, Calestani C. Expression pattern of polyketide synthase-2 during sea urchin development. Gene Expr Patterns 2011; 12:7-10. [PMID: 22001775 DOI: 10.1016/j.gep.2011.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 10/17/2022]
Abstract
Polyketide synthases (PKSs) are a large group of proteins responsible for the biosynthesis of polyketide compounds, which are mainly found in bacteria, fungi, and plants. Polyketides have a wide array of biological functions, including antibiotic, antifungal, predator defense, and light responses. In this study, we describe the developmental expression pattern of pks2, one of two pks found in the sea urchin genome. Throughout development, pks2 expression was restricted to skeletogenic cells and their precursors. Pks2 was first detected during the blastula stage. The transcript level peaked at hatched blastula, when all skeletogenic cell precursors expressed pks2. This was followed by a steady decline in expression in the skeletogenic cells on the aboral side of the embryo. By the prism stage, pks2 expression was limited to only 3-4 skeletogenic cells localized on the oral side.
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Affiliation(s)
- Adam Beeble
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
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26
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Russo R, Zito F, Costa C, Bonaventura R, Matranga V. Transcriptional increase and misexpression of 14-3-3 epsilon in sea urchin embryos exposed to UV-B. Cell Stress Chaperones 2010; 15:993-1001. [PMID: 20607471 PMCID: PMC3024062 DOI: 10.1007/s12192-010-0210-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/15/2010] [Accepted: 06/17/2010] [Indexed: 12/19/2022] Open
Abstract
Members of the 14-3-3 protein family are involved in many important cellular events, including stress response, survival and apoptosis. Genes of the 14-3-3 family are conserved from plants to humans, and some members are responsive to UV radiation. Here, we report the isolation of the complete cDNA encoding the 14-3-3 epsilon isoform from Paracentrotus lividus sea urchin embryos, referred to as Pl14-3-3ε, and the phylogenetic relationship with other homologues described in different phyla. Pl14-3-3ε mRNA levels were measured by QPCR during development and found to increase from the mesenchyme blastula to the prism stage. In response to UV-B (312 nm) exposure, early stage embryos collected 2 h later showed a 2.3-fold (at 400 J/m(2)) and a 2.7-fold (at 800 J/m(2)) increase in Pl14-3-3ε transcript levels compared with controls. The spatial expression of Pl14-3-3ε mRNA, detected by whole mount in situ hybridization in both control and UV-B exposed embryos, harvested at late developmental stages, showed transcripts to be located in the archenteron of gastrula stage and widely distributed in all germ layers, respectively. The Pl14-3-3ε mRNA delocalization parallels the failure in archenteron elongation observed morphologically, as well as the lack of specific endoderm markers, investigated by indirect immuno-fluorescence on whole mount embryos. Results confirm the involvement of 14-3-3ε in the stress response elicited by UV-B and demonstrate, for the first time, its contribution at the transcriptional level in the sea urchin embryo.
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Affiliation(s)
- Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, “Alberto Monroy”, Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, “Alberto Monroy”, Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, “Alberto Monroy”, Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Rosa Bonaventura
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, “Alberto Monroy”, Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare, “Alberto Monroy”, Via Ugo La Malfa 153, 90146 Palermo, Italy
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27
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Oliver TA, Garfield DA, Manier MK, Haygood R, Wray GA, Palumbi SR. Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin. Genome Biol Evol 2010; 2:800-14. [PMID: 20935062 PMCID: PMC2975446 DOI: 10.1093/gbe/evq063] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Comparisons of genomic sequence between divergent species can provide insight into the action of natural selection across many distinct classes of proteins. Here, we examine the extent of positive selection as a function of tissue-specific and stage-specific gene expression in two closely-related sea urchins, the shallow-water Strongylocentrotus purpuratus and the deep-sea Allocentrotus fragilis, which have diverged greatly in their adult but not larval habitats. Genes that are expressed specifically in adult somatic tissue have significantly higher dN/dS ratios than the genome-wide average, whereas those in larvae are indistinguishable from the genome-wide average. Testis-specific genes have the highest dN/dS values, whereas ovary-specific have the lowest. Branch-site models involving the outgroup S. franciscanus indicate greater selection (ωFG) along the A. fragilis branch than along the S. purpuratus branch. The A. fragilis branch also shows a higher proportion of genes under positive selection, including those involved in skeletal development, endocytosis, and sulfur metabolism. Both lineages are approximately equal in enrichment for positive selection of genes involved in immunity, development, and cell–cell communication. The branch-site models further suggest that adult-specific genes have experienced greater positive selection than those expressed in larvae and that ovary-specific genes are more conserved (i.e., experienced greater negative selection) than those expressed specifically in adult somatic tissues and testis. Our results chart the patterns of protein change that have occurred after habitat divergence in these two species and show that the developmental or functional context in which a gene acts can play an important role in how divergent species adapt to new environments.
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Affiliation(s)
- Thomas A Oliver
- Department of Biology, Hopkins Marine Station, Stanford University, USA
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28
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Aze A, Fayet C, Lapasset L, Genevière A. Replication origins are already licensed in G1 arrested unfertilized sea urchin eggs. Dev Biol 2010; 340:557-70. [DOI: 10.1016/j.ydbio.2010.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2009] [Revised: 02/02/2010] [Accepted: 02/04/2010] [Indexed: 11/24/2022]
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29
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Istrail S, Tarpine R, Schutter K, Aguiar D. Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks. Methods Mol Biol 2010; 674:369-99. [PMID: 20827603 DOI: 10.1007/978-1-60761-854-6_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The CYRENE Project focuses on the study of cis-regulatory genomics and gene regulatory networks (GRN) and has three components: a cisGRN-Lexicon, a cisGRN-Browser, and the Virtual Sea Urchin software system. The project has been done in collaboration with Eric Davidson and is deeply inspired by his experimental work in genomic regulatory systems and gene regulatory networks. The current CYRENE cisGRN-Lexicon contains the regulatory architecture of 200 transcription factors encoding genes and 100 other regulatory genes in eight species: human, mouse, fruit fly, sea urchin, nematode, rat, chicken, and zebrafish, with higher priority on the first five species. The only regulatory genes included in the cisGRN-Lexicon (CYRENE genes) are those whose regulatory architecture is validated by what we call the Davidson Criterion: they contain functionally authenticated sites by site-specific mutagenesis, conducted in vivo, and followed by gene transfer and functional test. This is recognized as the most stringent experimental validation criterion to date for such a genomic regulatory architecture. The CYRENE cisGRN-Browser is a full genome browser tailored for cis-regulatory annotation and investigation. It began as a branch of the Celera Genome Browser (available as open source at http://sourceforge.net/projects/celeragb /) and has been transformed to a genome browser fully devoted to regulatory genomics. Its access paradigm for genomic data is zoom-to-the-DNA-base in real time. A more recent component of the CYRENE project is the Virtual Sea Urchin system (VSU), an interactive visualization tool that provides a four-dimensional (spatial and temporal) map of the gene regulatory networks of the sea urchin embryo.
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Affiliation(s)
- Sorin Istrail
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI, USA.
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30
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Abstract
All animal embryos pass through a stage during which developmental control is handed from maternally provided gene products to those synthesized from the zygotic genome. This maternal-to-zygotic transition (MZT) has been extensively studied in model organisms, including echinoderms, nematodes, insects, fish,amphibians and mammals. In all cases, the MZT can be subdivided into two interrelated processes: first, a subset of maternal mRNAs and proteins is eliminated; second, zygotic transcription is initiated. The timing and scale of these two events differ across species, as do the cellular and morphogenetic processes that sculpt their embryos. In this article, we discuss conserved and distinct features within the two component processes of the MZT.
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Affiliation(s)
- Wael Tadros
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, TMDT Building, 101 College Street, Toronto,Ontario, Canada M5G 1L7
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, TMDT Building, 101 College Street, Toronto,Ontario, Canada M5G 1L7
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31
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Abstract
Animal development is an elaborate process programmed by genomic regulatory instructions. Regulatory genes encode transcription factors and signal molecules, and their expression is under the control of cis-regulatory modules that define the logic of transcriptional responses to the inputs of other regulatory genes. The functional linkages among regulatory genes constitute the gene regulatory networks (GRNs) that govern cell specification and patterning in development. Constructing such networks requires identification of the regulatory genes involved and characterization of their temporal and spatial expression patterns. Interactions (activation/repression) among transcription factors or signals can be investigated by large-scale perturbation analysis, in which the function of each gene is specifically blocked. Resultant expression changes are then integrated to identify direct linkages, and to reveal the structure of the GRN. Predicted GRN linkages can be tested and verified by cis-regulatory analysis. The explanatory power of the GRN was shown in the lineage specification of sea urchin endomesoderm. Acquiring such networks is essential for a systematic and mechanistic understanding of the developmental process.
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Affiliation(s)
- Enhu Li
- Division of Biology, California Institute of Technology, Pasadena, California 911025, USA
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32
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Abstract
Organisms must continually adapt to changing cellular and environmental factors (e.g., oxygen levels) by altering their gene expression patterns. At the same time, all organisms must have stable gene expression patterns that are robust to small fluctuations in environmental factors and genetic variation. Learning and characterizing the structure and dynamics of Regulatory Networks (RNs), on a whole-genome scale, is a key problem in systems biology. Here, we review the challenges associated with inferring RNs in a solely data-driven manner, concisely discuss the implications and contingencies of possible procedures that can be used, specifically focusing on one such procedure, the Inferelator. Importantly, the Inferelator explicitly models the temporal component of regulation, can learn the interactions between transcription factors and environmental factors, and attaches a statistically meaningful weight to every edge. The result of the Inferelator is a dynamical model of the RN that can be used to model the time-evolution of cell state.
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33
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Shen X, Tian M, Liu Z, Cheng H, Tan J, Meng X, Ren J. Complete mitochondrial genome of the sea cucumber Apostichopus japonicus (Echinodermata: Holothuroidea): The first representative from the subclass Aspidochirotacea with the echinoderm ground pattern. Gene 2009; 439:79-86. [DOI: 10.1016/j.gene.2009.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 03/07/2009] [Accepted: 03/13/2009] [Indexed: 11/30/2022]
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34
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Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009; 10:219. [PMID: 19435504 PMCID: PMC2689275 DOI: 10.1186/1471-2164-10-219] [Citation(s) in RCA: 383] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 05/12/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. RESULTS More than 600,000 reads produced in a single 454 sequencing run were assembled into approximately 40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified approximately 11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed approximately 8,500 pairs of orthologs and approximately 100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. CONCLUSION The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.
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Affiliation(s)
- Eli Meyer
- University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA
| | - Galina V Aglyamova
- University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA
| | - Shi Wang
- University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA
| | - Jade Buchanan-Carter
- The Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA
| | - David Abrego
- ARC Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - John K Colbourne
- The Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN, 47405, USA
| | - Bette L Willis
- ARC Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Mikhail V Matz
- University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA
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Wang X, Yu Z, Yang X, Deng XW, Li L. Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. ACTA ACUST UNITED AC 2009; 25:1215-8. [PMID: 19289447 DOI: 10.1093/bioinformatics/btp147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The unprecedented complexity of the transcriptomic data obtained in recent years creates opportunities for new genomic studies aimed at interpolating regulatory code of gene expression and tracing genome evolution. We report here the identification and characterization of a set of 851 intergenic loci that represent transcribed gene fragments (TGFs) ectopically duplicated from 1030 non-transposable element (non-TE) donor genes in the rice genome. We analyzed the genomic context of the TGFs and donor genes. We show that the TGFs have adopted transcriptional orientation and pattern independent of the donor genes. We further show that TGFs have undergone relaxed purifying selection, consistent with their being pseudogenized. We found that the donor genes, which are biased toward certain molecular functions, exhibit an accelerated evolution rate comparing to the genome average. Our results demonstrated a large number of actively TGFs in the rice genome and shed light on the origin, mode of action and function of the TGFs.
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Affiliation(s)
- Xiangfeng Wang
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT 06520, USA
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Bradham CA, Oikonomou C, Kühn A, Core AB, Modell JW, McClay DR, Poustka AJ. Chordin is required for neural but not axial development in sea urchin embryos. Dev Biol 2009; 328:221-33. [PMID: 19389361 DOI: 10.1016/j.ydbio.2009.01.027] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 01/12/2009] [Indexed: 11/27/2022]
Abstract
The oral-aboral (OA) axis in the sea urchin is specified by the TGFbeta family members Nodal and BMP2/4. Nodal promotes oral specification, whereas BMP2/4, despite being expressed in the oral territory, is required for aboral specification. This study explores the role of Chordin (Chd) during sea urchin embryogenesis. Chd is a secreted BMP inhibitor that plays an important role in axial and neural specification and patterning in Drosophila and vertebrate embryos. In Lytechinus variegatus embryos, Chd and BMP2/4 are functionally antagonistic. Both are expressed in overlapping domains in the oral territory prior to and during gastrulation. Perturbation shows that, surprisingly, Chd is not involved in OA axis specification. Instead, Chd is required both for normal patterning of the ciliary band at the OA boundary and for development of synaptotagmin B-positive (synB) neurons in a manner that is reciprocal with BMP2/4. Chd expression and synB-positive neural development are both downstream from p38 MAPK and Nodal, but not Goosecoid. These data are summarized in a model for synB neural development.
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Affiliation(s)
- Cynthia A Bradham
- Biology Department, Boston University, 24 Cummington, Boston, MA, USA.
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Townley IK, Schuyler E, Parker-Gür M, Foltz KR. Expression of multiple Src family kinases in sea urchin eggs and their function in Ca2+ release at fertilization. Dev Biol 2009; 327:465-77. [PMID: 19150445 DOI: 10.1016/j.ydbio.2008.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 12/19/2008] [Accepted: 12/22/2008] [Indexed: 01/22/2023]
Abstract
Egg activation at fertilization in deuterostomes requires a rise in intracellular Ca(2+), which is released from the egg's endoplasmic reticulum. In sea urchins, a Src Family Kinase (SpSFK1) is necessary for the PLCgamma-mediated signaling event that initiates this Ca(2+) release (Giusti, A.F., O'Neill, F.J., Yamasu, K., Foltz, K.R. and Jaffe, L.A., 2003. Function of a sea urchin egg Src family kinase in initiating Ca2+ release at fertilization. Dev. Biol. 256, 367-378.). Annotation of the Strongylocentrotus purpuratus genome sequence led to the identification of additional, predicted SFKs (Bradham, C.A., Foltz, D.R., Beane, W.S., Amone, M.I., Rizzo, F., Coffman, J.A., Mushegian, A., Goel, M., Morales, J., Geneviere, A.M., Lapraz, F., Robertson, A.J., Kelkar, H., Loza-Coll, M., Townley, I.K., Raisch, M., Roux, M.M., Lepage, T., Gache, C., McClay, D.R., Manning, G., 2006. The sea urchin kinome: a first look. Dev. Biol. 300, 180-193.; Roux, M.M., Townley, I.K., Raisch, M., Reade, A., Bradham, C., Humphreys, G., Gunaratne, H.J., Killian, C.E., Moy, G., Su, Y.H., Ettensohn, C.A., Wilt, F., Vacquier, V.D., Burke, R.D., Wessel, G. and Foltz, K.R., 2006. A functional genomic and proteomic perspective of sea urchin calcium signaling and egg activation. Dev. Biol. 300, 416-433.). Here, we describe the cloning and characterization of these 4 additional SFKs and test their function during the initial Ca(2+) release at fertilization using the dominant-interfering microinjection method coupled with Ca(2+) recording. While two of the new SFKs (SpFrk and SpSFK3) are necessary for Ca(2+) release, SpSFK5 appears dispensable for early egg to embryo transition events. Interestingly, SpSFK7 may be involved in preventing precocious release of Ca(2+). Binding studies indicate that only SpSFK1 is capable of direct interaction with PLCgamma. Immunolocalization studies suggest that one or more SpSFK and PLCgamma are localized to the egg cortex and at the site of sperm-egg interaction. Collectively, these data indicate that more than one SFK is involved in the Ca(2+) release pathway at fertilization.
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Affiliation(s)
- Ian K Townley
- Department of Molecular, Cellular and Developmental Biology and the Marine Science Institute, UC Santa Barbara Santa Barbara, CA 93106-9610, USA.
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Cameron RA, Samanta M, Yuan A, He D, Davidson E. SpBase: the sea urchin genome database and web site. Nucleic Acids Res 2009; 37:D750-4. [PMID: 19010966 PMCID: PMC2686435 DOI: 10.1093/nar/gkn887] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Accepted: 10/20/2008] [Indexed: 11/29/2022] Open
Abstract
SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided.
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Affiliation(s)
- R Andrew Cameron
- Center for Computational Regulatory Genomics, Beckman Institute 139-74, California Institute of Technology, Pasadena, CA 91104, USA.
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Freeman RM, Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ, Gerhart J, Kirschner M. cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism. THE BIOLOGICAL BULLETIN 2008; 214:284-302. [PMID: 18574105 DOI: 10.2307/25470670] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a direct-developing hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (< or = 10(-10)), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGFbeta, Wnt, Hh, Delta/Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3' untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism.
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Affiliation(s)
- R M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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41
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Page-McCaw A. Remodeling the model organism: matrix metalloproteinase functions in invertebrates. Semin Cell Dev Biol 2008; 19:14-23. [PMID: 17702617 PMCID: PMC2248213 DOI: 10.1016/j.semcdb.2007.06.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 06/23/2007] [Indexed: 11/17/2022]
Abstract
The matrix metalloproteinase (MMP) family of extracellular proteases is conserved throughout the animal kingdom. Studies of invertebrate MMPs have demonstrated they are involved in tissue remodeling. In Drosophila, MMPs are required for histolysis, tracheal growth, tissue invasion, axon guidance, and dendritic remodeling. Recent work demonstrates that MMPs also participate in Drosophila tumor invasion. In Caenorhabditis elegans an MMP is involved in anchor cell invasion; a Hydra MMP is important for regeneration and maintaining cell identity; and a sea urchin MMP degrades matrix to allow hatching. In worms and in flies, MMPs are regulated by the JNK pathway.
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Affiliation(s)
- Andrea Page-McCaw
- Center for Biotechnology and Interdisciplinary Studies and Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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42
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Yazgan O, Krebs JE. Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem Cell Biol 2008; 85:484-96. [PMID: 17713583 DOI: 10.1139/o07-061] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome sequencing and annotation has advanced our understanding of genome organization and gene structure but initially only allowed predictions of how many genes might be present. Mechanisms such as alternative splicing reveal that these predictions only scratch the surface of the true nature of the transcriptome. Several thousand expressed partial gene fragments have been cloned but were considered transcriptional noise or cloning artifacts. We now know that genomes are indeed expressed at much higher levels than was previously predicted, and much of the additional transcription maps to intergenic regions, intron sequences, and untranslated regions of mRNAs. These transcripts are expressed from either the sense or the antisense strand and can be confirmed by conventional techniques. In addition to the already established roles for small RNAs in gene regulation, large noncoding RNAs (ncRNAs) are also emerging as potent regulators of gene expression. In this review, we summarize several illustrative examples of gene regulatory mechanisms that involve large ncRNAs. We describe several distinct regulatory mechanisms that involve large ncRNAs, such as transcriptional interference and promoter inactivation, as well as indirect effects on transcription regulatory proteins and in genomic imprinting. These diverse functions for large ncRNAs are likely to be only the first of many novel regulatory mechanisms emerging from this growing field.
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Affiliation(s)
- Oya Yazgan
- Department of Biological Sciences, University of AK Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
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Lotze MT, Zeh HJ, Rubartelli A, Sparvero LJ, Amoscato AA, Washburn NR, Devera ME, Liang X, Tör M, Billiar T. The grateful dead: damage-associated molecular pattern molecules and reduction/oxidation regulate immunity. Immunol Rev 2008; 220:60-81. [PMID: 17979840 DOI: 10.1111/j.1600-065x.2007.00579.x] [Citation(s) in RCA: 435] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The response to pathogens and damage in plants and animals involves a series of carefully orchestrated, highly evolved, molecular mechanisms resulting in pathogen resistance and wound healing. In metazoans, damage- or pathogen-associated molecular pattern molecules (DAMPs, PAMPs) execute precise intracellular tasks and are also able to exert disparate functions when released into the extracellular space. The emergent consequence for both inflammation and wound healing of the abnormal extracellular persistence of these factors may underlie many clinical disorders. DAMPs/PAMPs are recognized by hereditable receptors including the Toll-like receptors, the NOD1-like receptors and retinoic-acid-inducible gene I-like receptors, as well as the receptor for advanced glycation end products. These host molecules 'sense' not only pathogens but also misfolded/glycated proteins or exposed hydrophobic portions of molecules, activating intracellular cascades that lead to an inflammatory response. Equally important are means to not only respond to these molecules but also to eradicate them. We have speculated that their destruction through oxidative mechanisms normally exerted by myeloid cells, such as neutrophils and eosinophils, or their persistence in the setting of pathologic extracellular reducing environments, maintained by exuberant necrotic cell death and/or oxidoreductases, represent important molecular means enabling chronic inflammatory states.
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Affiliation(s)
- Michael T Lotze
- Department of Surgery, G.27A Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
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Roux MM, Radeke MJ, Goel M, Mushegian A, Foltz KR. 2DE identification of proteins exhibiting turnover and phosphorylation dynamics during sea urchin egg activation. Dev Biol 2008; 313:630-47. [DOI: 10.1016/j.ydbio.2007.10.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 10/29/2007] [Accepted: 10/31/2007] [Indexed: 10/22/2022]
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Abstract
The application of genomic technologies to the study of mRNA processing is increasingly conducted in metazoan organisms in order to understand the complex events that occur during and after transcription. Large-scale systems analyses of mRNA-protein interactions and mRNA dynamics have revealed specificity in mRNA transcription, splicing, transport, translation, and turnover, and have begun to make connections between the different layers of mRNA processing. Here, we review global studies of post-transcriptional processes and discuss the challenges facing our understanding of mRNA regulation in metazoan organisms. In parallel, we examine genome-scale investigations that have expanded our knowledge of RNA-binding proteins and the networks of mRNAs that they regulate.
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Affiliation(s)
- Adrienne E McKee
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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46
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Poustka AJ, Kühn A, Groth D, Weise V, Yaguchi S, Burke RD, Herwig R, Lehrach H, Panopoulou G. A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks. Genome Biol 2007; 8:R85. [PMID: 17506889 PMCID: PMC1929154 DOI: 10.1186/gb-2007-8-5-r85] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 04/12/2007] [Accepted: 05/16/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genome of the sea urchin Strongylocentrotus purpuratus has recently been sequenced because it is a major model system for the study of gene regulatory networks. Embryonic expression patterns for most genes are unknown, however. RESULTS Using large-scale screens on arrays carrying 50% to 70% of all genes, we identified novel territory-specific markers. Our strategy was based on computational selection of genes that are differentially expressed in lithium-treated embryos, which form excess endomesoderm, and in zinc-treated embryos, in which endomesoderm specification is blocked. Whole-mount in situ hybridization (WISH) analysis of 700 genes indicates that the apical organ region is eliminated in lithium-treated embryos. Conversely, apical and specifically neural markers are expressed more broadly in zinc-treated embryos, whereas endomesoderm signaling is severely reduced. Strikingly, the number of serotonergic neurons is amplified by at least tenfold in zinc-treated embryos. WISH analysis further indicates that there is crosstalk between the Wnt (wingless int), Notch, and fibroblast growth factor signaling pathways in secondary mesoderm cell specification and differentiation, similar to signaling cascades that function during development of presomitic mesoderm in mouse embryogenesis. We provide differential expression data for more than 4,000 genes and WISH patterns of more than 250 genes, and more than 2,400 annotated WISH images. CONCLUSION Our work provides tissue-specific expression patterns for a large fraction of the sea urchin genes that have not yet been included in existing regulatory networks and await functional integration. Furthermore, we noted neuron-inducing activity of zinc on embryonic development; this is the first observation of such activity in any organism.
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Affiliation(s)
- Albert J Poustka
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Alexander Kühn
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Detlef Groth
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Vesna Weise
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Shunsuke Yaguchi
- University of Victoria, Departments of Biology and Biochemistry/Microbiology, 3800 Finnerty Road, Victoria, British Columbia, Canada V8P 5C5
- US National Institutes of Health, National Institute of Dental and Craniofacial Research, 30 Convent Drive, MSC 4326, Bethesda. Maryland 20815, USA
| | - Robert D Burke
- University of Victoria, Departments of Biology and Biochemistry/Microbiology, 3800 Finnerty Road, Victoria, British Columbia, Canada V8P 5C5
| | - Ralf Herwig
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Hans Lehrach
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
| | - Georgia Panopoulou
- Max-Planck Institut für Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195 Berlin, Germany
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Hauser F, Pessi G, Friberg M, Weber C, Rusca N, Lindemann A, Fischer HM, Hennecke H. Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation. Mol Genet Genomics 2007; 278:255-71. [PMID: 17569992 DOI: 10.1007/s00438-007-0246-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
Hierarchically organized regulatory proteins form a complex network for expression control of symbiotic and accessory genes in the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum. A genome-wide survey of regulatory interactions was made possible with the design of a custom-made gene chip. Here, we report the first use of the microarray in a comprehensive and complete characterization of the B. japonicum NifA+sigma(54) regulon which forms an important node in the entire network. Comparative transcript profiles of anaerobically grown wild-type, nifA, and rpoN (1/2) mutant cells were complemented with a position-specific frequency matrix-based search for NifA- and sigma(54)-binding sites plus a simple operon definition. One of the newly identified NifA+sigma(54)-dependent genes, fdxN, encodes a ferredoxin required for efficient symbiotic nitrogen fixation, which makes it a candidate for being a direct electron donor to nitrogenase. The fdxN gene has an unconventional, albeit functional sigma(54 )promoter with the dinucleotide GA instead of the consensus GC motif at position -12. A GC-containing mutant promoter and the atypical GA-containing promoter of the wild type were disparately activated. Expression analyses were also carried out with two other NifA+sigma(54) targets (ectC; ahpC). Incidentally, the tiling-like design of the microarray has helped to arrive at completely revised annotations of the ectC- and ahpC-upstream DNA regions, which are now compatible with promoter locations. Taken together, the approaches used here led to a substantial expansion of the NifA+sigma(54 )regulon size, culminating in a total of 65 genes for nitrogen fixation and diverse other processes.
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Affiliation(s)
- Felix Hauser
- Institute of Microbiology, Eidgenössische Technische Hochschule, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007; 8:413-23. [PMID: 17486121 DOI: 10.1038/nrg2083] [Citation(s) in RCA: 529] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations suggest that genomic architecture is not colinear, but is instead interleaved and modular, and that the same genomic sequences are multifunctional: that is, used for multiple independently regulated transcripts and as regulatory regions. What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?
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Affiliation(s)
- Philipp Kapranov
- Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA
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Andrew Cameron R, Davidson EH. A basal deuterostome genome viewed as a natural experiment. Gene 2007; 406:1-7. [PMID: 17550788 PMCID: PMC2200295 DOI: 10.1016/j.gene.2007.04.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 04/26/2007] [Accepted: 04/26/2007] [Indexed: 11/26/2022]
Abstract
With the determination of its genome sequence the utility of the sea urchin model system increases. The phylogenetic position of the sea urchin among the deuterostomes allows for informative comparisons to vertebrate research models. A combined whole genome shotgun and bacterial artificial chromosome based strategy yielded a high quality draft genome sequence of 814 Mb. The predicted gene set estimated to include 23,300 genes was annotated and compared to those of other metazoan animals. Gene family expansions in the innate immune system are large and offer a first glimpse of how the long-lived sea urchin defends itself. The gene sets of the sea urchin place it firmly among the deuterostomes and indicate that various gene family-specific expansions and contractions characterize the evolution of animal genomes rather than the invention of new genes.
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Affiliation(s)
- R Andrew Cameron
- Beckman Institute 139-74, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, United States.
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50
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Lapraz F, Duboc V, Lepage T. A genomic view of TGF-β signal transduction in an invertebrate deuterostome organism and lessons from the functional analyses of Nodal and BMP2/4 during sea urchin development. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/sita.200600125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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