Biomedical subjects

Eric H Davidson

Publications and source records attributed to Eric H Davidson.

At least 19 recordsLinked to original sources

PubMed2006

Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network.

The regulatory genome functions as a vast information processor through development. It processes the initial conditions that are set by asymmetric distributions of cellular components in the egg and translates them into the onset of spatially localized specification states. It regulates the timely differential activation of signaling molecules and transcription factors that divide the emerging domains into subdomains. It also governs the activation of groups of differentiation genes, the genes that encode, at the protein level, the functional and the structural properties of a cell type. The sea urchin endomesoderm gene regulatory network provides a window into the different levels of the regulatory apparatus. It demonstrates how the static physical genomic components define functional connections between the various regulatory genes that act together to conduct the dynamical developmental program.

Animals↗

PubMed2006

The transcriptome of the sea urchin embryo.

The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.

Animals↗

PubMed2006

Paleogenomics of echinoderms.

Paleogenomics propels the meaning of genomic studies back through hundreds of millions of years of deep time. Now that the genome of the echinoid Strongylocentrotus purpuratus is sequenced, the operation of its genes can be interpreted in light of the well-understood echinoderm fossil record. Characters that first appear in Early Cambrian forms are still characteristic of echinoderms today. Key genes for one of these characters, the biomineralized tissue stereom, can be identified in the S. purpuratus genome and are likely to be the same genes that were involved with stereom formation in the earliest echinoderms some 520 million years ago.

Animals↗

PubMed2006

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Animals↗

PubMed2006

The sea urchin genome: where will it lead us?

The sea urchin genome reveals large domains of biology heretofore unexplored at the genome level, as this is the first nonchordate deuterostome sequence. The sequence will accelerate progress toward complete understanding of the genomic regulatory system that controls developmental specification and morphogenetic function, thus illuminating basic developmental process in all animals.

Animals↗

PubMed2006

High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution.

A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total "regulome" of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity.

Animals↗

PubMed2006

Sea urchin Forkhead gene family: phylogeny and embryonic expression.

Transcription factors of the Forkhead (Fox) family have been identified in many metazoans, and play important roles in diverse biological processes. Here we define the set of fox genes present in the sea urchin genome, and survey their usage during development. This genome includes 22 fox genes, only three of which were previously known. Of the 23 fox gene subclasses identified in vertebrate genomes, the Strongylocentrotus purpuratus genome has orthologues of all but four (E, H, R and S). Phylogenetic analysis suggests that one S. purpuratus fox gene is equally related to foxA and foxB of vertebrates; this gene defines a new class. Two other genes appear to be specific to the sea urchin, with respect to the genomes so far sequenced. Fox genes orthologous with those of vertebrates but lacking in arthropod or nematode genomes may be deuterostome-specific (subclasses I, J1, J2, L1, M and Q1), while the majority are pan-bilaterian. All but one of the S. purpuratus fox genes (SpfoxQ1) are expressed during embryogenesis, most in a very specific temporal and spatial manner. The sea urchin fox genes clearly execute many different regulatory functions, and almost all of them participate in the process of embryonic development.

Animals↗

PubMed2006

The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development.

The C2H2 zinc finger is one of the most abundant protein domains and is thought to have been extensively replicated in diverse animal clades. Some well-studied proteins that contain this domain are transcriptional regulators. As part of an attempt to delineate all transcription factors encoded in the Strongylocentrotus purpuratus genome, we identified the C2H2 zinc finger genes indicated in the sequence, and examined their involvement in embryonic development. We found 377 zinc finger genes in the sea urchin genome, about half the number found in mice or humans. Their expression was measured by quantitative PCR. Up to the end of gastrulation less than a third of these genes is expressed, and about 75% of the expressed genes are maternal; both parameters distinguish these from all other classes of regulatory genes as measured in other studies. Spatial expression pattern was determined by whole mount in situ hybridization for 43 genes transcribed at a sufficient level, and localized expression was observed in diverse embryonic tissues. These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined.

Animals↗

PubMed2006

Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus.

All genes encoding transcription factors of the bHLH, Nuclear Receptor, Basic Leucine Zipper, T-box, Smad, Sox, and other smaller families were identified in the Strongylocentrotus purpuratus genome by means of a permissive blast search of the genome using a database of known transcription factors. Phylogenetic trees were constructed for the major families, permitting a comparison of the regulatory protein repertoire of the sea urchin and other species. QPCR and whole mount in situ hybridization experiments revealed the temporal and spatial expression patterns of these genes during early development. These regulatory genes are initially expressed at a broad range of time points, and the large majority of genes of all families are expressed within the first 48 h of development. The observations suggest assignment of many regulatory genes to specific developmental sub-networks, including endomesodermal, oral, aboral, and apical.

Animals↗

PubMed2006

Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development.

A set of 96 homeobox transcription factors was identified in the Strongylocentrotus purpuratus genome using permissive blast searches with a large collection of authentic homeodomain sequences from mouse, human and fly. A phylogenetic tree was constructed to compare the sea urchin homeobox gene family to those of vertebrates, with the result that with the only a few exceptions, orthologs of all vertebrate homeodomain genes were uncovered by our search. QPCR time course measurements revealed that 65% of these genes are expressed within the first 48 h of development (late gastrula). For genes displaying sufficiently high levels of transcript during the first 24 h of development (late blastula), whole mount in situ hybridization was carried out up to 48 h to determine spatial patterns of expression. The results demonstrate that homeodomain transcription factors participate in multiple and diverse developmental functions, in that they are used at a range of time points and in every territory of the developing embryo.

Animals↗

PubMed2006

Phosphatized polar lobe-forming embryos from the Precambrian of southwest China.

In developing embryos of some extant spiralian animals, polar lobe formation is one of the symmetry-breaking mechanisms for segregation of maternal cytoplasmic substances to certain blastomeres and not others. Polar lobe formation leads to unique early cleavage morphologies that include trilobed, J-shaped, and five-lobed structures. Fossil embryos similar to modern lobeforming embryos are recognized from the Precambrian Doushantuo Formation phosphates, Weng'an, Guizhou Province, China. These embryos are abundant and form a developmental sequence comparable to different developing stages observed in lobe-forming embryos of extant spiralians. These data imply that lobe formation is an evolutionarily ancient process of embryonic specification.

Animals↗

PubMed2006

Confocal quantification of cis-regulatory reporter gene expression in living sea urchin.

Quantification of GFP reporter gene expression at single cell level in living sea urchin embryos can now be accomplished by a new method of confocal laser scanning microscopy (CLSM). Eggs injected with a tissue-specific GFP reporter DNA construct were grown to gastrula stage and their fluorescence recorded as a series of contiguous Z-section slices that spanned the entire embryo. To measure the depth-dependent signal decay seen in the successive slices of an image stack, the eggs were coinjected with a freely diffusible internal fluorescent standard, rhodamine dextran. The measured rhodamine fluorescence was used to generate a computational correction for the depth-dependent loss of GFP fluorescence per slice. The intensity of GFP fluorescence was converted to the number of GFP molecules using a conversion constant derived from CLSM imaging of eggs injected with a measured quantity of GFP protein. The outcome is a validated method for accurately counting GFP molecules in given cells in reporter gene transfer experiments, as we demonstrate by use of an expression construct expressed exclusively in skeletogenic cells.

Animals↗

PubMed2006

cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification.

The glial cells missing regulatory gene of Strongylocentrotus purpuratus (spgcm) was proposed earlier to be the genomic target of Delta/Notch (D/N) signaling required for specification of the mesodermal precursors of pigment cells. Here, we show that microinjection of a spgcm antisense morpholino oligonucleotide results in larvae without pigment cells. Microinjection of an mRNA encoding a dominant negative form of Suppressor of Hairless (dn-Su(H)) results in reduced levels of spgcm mRNA, disruption of mesodermal founder cell specification and failure to produce pigment cells. These results confirm that this gene is required for pigment cell specification. Three cis-regulatory modules of the spgcm gene were identified, which when incorporated in a GFP expression construct recapitulate the early expression pattern of this gene. Spatial expression of this GFP expression construct is severely disrupted by co-expression of dn-Su(H) mRNA, confirming that spgcm is a direct target of canonical N signaling mediated through Su(H) inputs. cis-perturbation analysis by mutation of consensus Su(H) sites identified a conserved motif paired-site and a lone site in the middle module that function both to drive expression in SMC precursors which receive the Delta signal and to repress expression in ectopic locations which lack this signal. While these Su(H) target sites provide the cis-regulatory architecture with the core of an N signaling transcriptional response switch, both the on and off outputs from this module require additional inputs.

Animals↗

PubMed2006

Expression and function of blimp1/krox, an alternatively transcribed regulatory gene of the sea urchin endomesoderm network.

The blimp1/krox gene of Strongylocentrotus purpuratus, formerly krox1, encodes zinc finger transcription factors which play a central role in both early and late endomesoderm specification. Here we show that there are two alternative splice forms transcribed under the control of different regulatory regions. The blimp/krox1b form was previously unknown, and is the form expressed during cleavage, beginning 6-9 h postfertilization. This form is required for the early events of endomesoderm specification. A different splice variant, blimp1/krox1a, is expressed only from gastrula stage onward. During cleavage stages the blimp1/krox gene is expressed in the large micromeres and veg2 descendents. Soon after, it is expressed in the ring of specified mesoderm cells at the vegetal pole of the blastula. Its expression is later restricted to the blastopore region and the posterior of the invaginating archenteron, and finally to the midgut and hindgut of the pluteus larva. The expression of blimp1/krox is dynamic, and involves several distinct spatial territories. A GFP recombinant BAC was created by substituting the GFP coding sequence for that of the second exon (1b), in order to distinguish the expression pattern of the early form from that of the late form. This construct closely mimics blimp1/krox1b expression during early stages of sea urchin development. To expand our knowledge of the downstream linkages of this gene, additional experiments were carried out using antisense morpholino oligos (MASO). We confirmed previously published data that blimp1/krox autoregulates its own expression, but discovered, surprisingly, that this gene represses rather than activates itself. This negative autoregulation is restricted to the mesodermal and probably skeletogenic territories during the blastula stage, as shown by in situ hybridization analysis of MASO injected embryos. The MASO perturbation analysis also revealed blimp1/krox inputs into other genes of the endomesoderm regulatory network.

Alternative Splicing↗

PubMed2006

Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula.

The sea urchin regulatory gene Spblimp1/krox produces alternatively transcribed and spliced isoforms, 1a and 1b, which have different temporal and spatial patterns of expression. Here we describe a cis-regulatory module that controls the expression of the 1a splice form in the midgut and hindgut at the beginning of gastrulation. Conserved sequence patches revealed by a comparison of the blimp1/krox locus in Strongylocentrotus purpuratus and Lytechinus variegatus genomes were tested by gene transfer, in association with GFP or CAT reporter genes. An expression construct containing a conserved sequence patch immediately 5' of exon 1a included the transcription initiation site for blimp1/krox1a. This construct displays specific mid and hindgut expression, indicating that these are the locations of endogenous blimp1/krox1a transcription during the gastrula stage. Its sequence contains binding sites for Brn1/2/4, Otx, and Blimp1/Krox itself, as predicted in a prior regulatory network analysis.

Alternative Splicing↗

PubMed2006

cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo.

The Strongylocentrotus purpuratus cyclophilin1 gene (Sp-cyp1) is expressed exclusively in skeletogenic mesenchyme cells of the embryo, beginning in the micromere lineage of the early blastula stage and continuing after gastrulation during the syncytial deposition of the skeleton. This gene encodes a protein which is a member of the peptidyl-prolyl cis-trans isomerase (PPIase) family. Sp-cyp1 is among the differentiation genes activated in the skeletogenic territory as a terminal function of the endomesodermal gene regulatory network. Network perturbation analysis had predicted the skeletogenic regulators Ets1 and Deadringer (Dri) to be its driver inputs. Here, we show that a 218-bp cis-regulatory DNA fragment recapitulates skeletogenic Sp-cyp1 expression; that elimination of either Ets1 or Dri inputs severely depresses the activity of expression constructs containing this DNA fragment; and that Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. Other studies indicate that the same inputs are evidently necessary for expression of several other skeletogenic differentiation genes, and these genes probably constitute a skeletogenic gene battery, defined by its Ets plus Dri regulatory inputs.

Amino Acid Sequence↗

PubMed2006

Gene regulatory networks and the evolution of animal body plans.

Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early "Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the kernels" of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.

Adaptation, Biological↗

PubMed2006

Unusual gene order and organization of the sea urchin hox cluster.

While the highly consistent gene order and axial colinear patterns of expression seem to be a feature of vertebrate hox gene clusters, this pattern may be less well conserved across the rest of the bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3' gene is Hox5. (The gene order is 5'-Hox1, 2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5-3'.) The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.

Animals↗