Stage- and tissue-specific expression of two homeo box genes in sea urchin embryos and adults

Homeobox protein A1-like and DNA methylation regulate embryo-specific Zinc finger protein 615 gene expression and embryonic development in the silkworm Bombyx mori

DNA methylation and transcription factors play roles in gene expression and animal development. In insects, DNA methylation modifies gene bodies, but how DNA methylation and transcription factors regulate gene expression is unclear. In this study, we investigated the mechanism that regulates the expression of Bombyx mori Zinc finger protein 615 (ZnF 615), which is a downstream gene of DNA methyltransferase 1 (Dnmt1), and its effects on the regulation of embryonic development. By progressively truncating the ZnF 615 promoter, it was found that the -223 and -190 nt region, which contains homeobox (Hox) protein cis-regulatory elements (CREs), had the greatest impact on the transcription of ZnF 615. RNA interference (RNAi)-mediated knockdown and overexpression of Hox family genes showed that Hox A1-like can enhance the messenger RNA level of ZnF 615. Further studies showed that Hox A1-like regulates ZnF 615 expression by directly binding to the -223 and -190 nt region of its promoter. Simultaneous RNAi-mediated knockdown or overexpression of Hox A1-like and Dnmt1 significantly inhibited or enhanced the regulatory effect of either gene alone on ZnF 615 expression, suggesting that both DNA methylation of gene bodies and binding of transcription factors to promoters are essential for gene expression. RNAi-mediated knockdown of Hox A1-like and Dnmt1 showed that the embryonic development was retarded and the hatching rate was decreased. Taken together, these data suggest that Hox A1-like and DNA methylation enhance the expression of ZnF 615, thereby affecting the development of B. mori embryos.

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Ruditapes philippinarum is an economically important bivalve with remarkable diversity in its shell coloration patterns. In this study, we sequenced the whole genome of the Manila clam and investigated the molecular basis of its adaptation to hypoxia, acidification, and parasite stress with transcriptome sequencing and an RNA sequence analysis of different tissues and developmental stages to clarify these major issues. A number of immune-related gene families are expanded in the R. philippinarum genome, such as TEP, C3, C1qDC, Hsp70, SABL, and lysozyme, which are potentially important for its stress resistance and adaptation to a coastal benthic life. The transcriptome analyses demonstrated the dynamic and orchestrated specific expression of numerous innate immune-related genes in response to experimental challenge with pathogens. These findings suggest that the expansion of immune- and stress-related genes may play vital roles in resistance to adverse environments and has a profound effect on the clam's adaptation to benthic life.

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We present a new genome assembly of the Manila clam Ruditapes philippinarum

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Analysis of gene family expansions and transcriptome characterization were conducted

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Tyr and mitf genes were potentially involved in shell color patterns of Manila clam

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Expansion of GPCRs and immune-related genes were found in R. philippinarum

Hox genes, evo-devo, and the case of the ftz gene

The discovery of the broad conservation of embryonic regulatory genes across animal phyla, launched by the cloning of homeotic genes in the 1980s, was a founding event in the field of evolutionary developmental biology (evo-devo). While it had long been known that fundamental cellular processes, commonly referred to as housekeeping functions, are shared by animals and plants across the planet-processes such as the storage of information in genomic DNA, transcription, translation and the machinery for these processes, universal codon usage, and metabolic enzymes-Hox genes were different: mutations in these genes caused "bizarre" homeotic transformations of insect body parts that were certainly interesting but were expected to be idiosyncratic. The isolation of the genes responsible for these bizarre phenotypes turned out to be highly conserved Hox genes that play roles in embryonic patterning throughout Metazoa. How Hox genes have changed to promote the development of diverse body plans remains a central issue of the field of evo-devo today. For this Memorial article series, I review events around the discovery of the broad evolutionary conservation of Hox genes and the impact of this discovery on the field of developmental biology. I highlight studies carried out in Walter Gehring's lab and by former lab members that have continued to push the field forward, raising new questions and forging new approaches to understand the evolution of developmental mechanisms.

Dynamic epigenetic control of highly conserved noncoding elements

Background

Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown.

Results

To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains.

Conclusion

HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

Current Status of Echinoderm Genome Analysis - What do we Know?

Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.

HOX genes in the sepiolid squid Euprymna scolopes: implications for the evolution of complex body plans

Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex central nervous system, and cognitive abilities unrivaled among the invertebrates. The aim of the current study is to define molecular parameters relevant to the developmental evolution of cephalopods by using the sepiolid squid Euprymna scolopes as a model system. Using PCR-based approaches, we identified one anterior, one paralog group 3, five central, and two posterior group Hox genes. The deduced homeodomain sequences of the E. scolopes Hox cluster genes are most similar to known annelid, brachiopod, and nemertean Hox gene homeodomain sequences. Our results are consistent with the presence of a single Hox gene cluster in cephalopods. Our data also corroborate the proposed existence of a differentiated Hox gene cluster in the last common ancestor of Bilaterians. Furthermore, our phylogenetic analysis and in particular the identification of Post-1 and Post-2 homologs support the Lophotrochozoan clade.

Position-specific and non-colinear expression of the planarian posterior (Abdominal-B-like) gene

Hox genes are pivotal molecules in the control of morphogenesis along the anterior-posterior (AP) axis in various bilaterians. Planarians are key animals for understanding the evolution of the bilaterian body plan. Furthermore, they are also known for their strong regeneration ability and are thought to use the Hox genes in the process of reconstruction of the AP axis. In the present paper, the identification and analysis of expression of two posterior (Abdominal-B-like) genes, DjAbd-Ba and DjAbd-Bb, is reported in the planarian Dugesia japonica. DjAbd-Ba is expressed in the entire tail region and its anterior boundary is the posterior pharyngeal region. In contrast, DjAbd-Bb is expressed in several types of cells throughout the body. During regeneration, the expression of DjAbd-Ba rapidly recovers a pattern similar to that in the normal worm. These findings suggest the possibility that DjAbd-Ba is involved in the specification of the tail region. The anterior boundary of the expression domain of the posterior gene DjAbd-Ba is anterior to the domains of the central genes Plox4-Dj and Plox5-Dj. These expression patterns of planarian Hox genes seem out of the rule of spatial colinearity and may reflect an ancestral feature of bilaterian Hox genes.

Molecular characterization of TgHBox4, a Drosophila Abd-B homolog found in the sea urchin Tripneustes gratilla

We have isolated and sequenced a cDNA clone that, as judged by the sequence of the homeobox region, encodes a sea urchin homolog of the homeobox containing the gene Abdominal-B of Drosophila. The total length of the cDNA is 3634 nucleotides and includes an open reading frame, which encodes a protein that is 32,321 Da. The N-terminal region of the homeodomain includes consensus sequences found in some of TgHBox4's Abdominal-B relatives. A genomic clone representing the 5' part of the message was also isolated. This clone and a previously isolated clone were found to represent the full-length cDNA sequence. We have also raised antibodies against a bacterially expressed portion of the TgHBox4 protein and used them to determine the location of TgHBox4 proteins during development. The protein displays ubiquitous expression early in development but becomes more restricted, to posterior regions, late in embryogenesis. Thus, in contrast to its Abd-B homologs in bilateral metazoans, TgHBox4 is probably not involved in pattern formation but may have a posterior-defining role late in embryogenesis.

Spatially restricted expression of PlOtp, a Paracentrotus lividus orthopedia-related homeobox gene, is correlated with oral ectodermal patterning and skeletal morphogenesis in late-cleavage sea urchin embryos

Several homeobox genes are expressed in the sea urchin embryo but their roles in development have yet to be elucidated. Of particular interest are homologues of homeobox genes that in mouse and Drosophila are involved in patterning the developing central nervous system (CNS). Here, we report the cloning of an orthopedia (Otp)-related gene from Paracentrotus lividus, PlOtp. Otp is a single copy zygotic gene that presents a unique and highly restricted expression pattern. Transcripts were first detected at the mid-gastrula stage in two pairs of oral ectoderm cells located in a ventrolateral position, overlying primary mesenchyme cell (PMC) clusters. Increases in both transcript abundance and the number of Otp-expressing cells were observed at prism and pluteus stages. Otp transcripts are symmetrically distributed in a few ectodermal cells of the oral field. Labelled cells were observed close to sites of active skeletal rod growth (tips of the budding oral and anal arms), and at the juxtaposition of stomodeum and foregut. Chemicals known to perturb PMC patterning along animal-vegetal and oral-aboral axes altered the pattern of Otp expression. Vegetalization by LiCl caused a shift in Otp-expressing cells toward the animal pole, adjacent to shifted PMC aggregates. Nickel treatment induced expression of the Otp gene in an increased number of ectodermal cells, which adopted a radialized pattern. Finally, ectopic expression of Otp mRNA affected patterning along the oral-aboral axis and caused skeletal abnormalities that resembled those exhibited by nickel-treated embryos. From these results, we conclude that the Otp homeodomain gene is involved in short-range cell signalling within the oral ectoderm for patterning the endoskeleton of the larva through epithelial-mesenchymal interactions.

Abdominal-B expression in a spider suggests a general role for Abdominal-B in specifying the genital structure

We have cloned an Abdominal-B (Abd-B) orthologue from the spider Cupiennius salei and have analysed its expression pattern during embryogenesis. An early expression domain is seen in the posterior part of the embryo, with an initial border in the third opisthosomal segment and later in the fifth opisthosomal segment. During mid-stage of germ band extension, two additional spots of expression appear in the posterior parts of the limb buds on the second opisthosomal segment. These coincide with the position of the future genital opening and Cs-Abd-B remains expressed in these regions until the openings are formed. In view of the fact that Abd-B and its orthologous genes are also required for specifying the genitalia in Drosophila and vertebrates, we suggest that this function may constitute an independent and ancestral role of Abd-B that can be separated from its role in specifying the posterior part of the body region.

Hox-type and non-Hox homeobox gene sequences in genomic DNA of the sea urchin Holopneustes purpurescens

As a preliminary step in an analysis of Hox gene expression and radial body plan specification in sea urchin development, we amplified partial homeobox sequences in H. purpurescens by PCR using degenerate primers. The primers, HoxE and HoxF (Pendleton et al., 1993), spanned a highly conserved region of 82 nucleotides encompassing amino acids 21-47 of the homeodomain. Seven Hox-type homeobox sequences and two non-Hox homeobox sequences were identified. The seven Hox-type sequences were placed provisionally in Hox paralogous groups, one in paralogous group 3, three in paralogous groups 6-8 and three in paralogous groups 9 13. The non-Hox sequences had similarities with Xlox and Gbx homeobox genes.

A PCR survey of hox genes in the sea star, Asterina minor

The sea star, Asterina minor, was surveyed for Hox genes using the method of PCR and subsequent sequence determination. Seven different Hox-type homeobox fragments and homeobox fragments of two other types, the Gbx-type and the Xlox-type, were identified. The results of comparative analysis with known homeobox sequences suggest that the sea star has only one Hox gene cluster including two genes of the anterior group, four genes of the medial group, and one gene of the posterior group. The existence of a gene of the cognate group 1 has not been known in echinoderm species. Each of the other fragments indicated a definite relationship with one of sea urchin homeoboxes. The hypothetical cluster in the sea star is consistent with the results published for another class of echinoderm, sea urchins, in the putative number of cluster. The present result provides strong evidence that a single Hox cluster is common to echinoderms and its structure in the anterior region is more similar to other deuterostomes than previously thought.

SpHbox7, a new Abd-B class homeobox gene from the sea urchin Strongylocentrotus purpuratus: insights into the evolution of hox gene expression and function

Hox genes, by virtue of their key functions in axial patterning, have long been thought to be pivotal players in the evolution of developmental mechanisms. Despite their potential importance in evolution, there is little information about Hox genes in animal groups that are most closely related to ancestral Chordates. Accordingly, we have taken the step of analyzing Hox gene expression and function in the sea urchin embryo, whose simple bilateral body plan is thought to resemble that of a stem organism in the Chordate lineage. Here we describe the isolation, sequences analysis and spatiotemporal expression pattern of a sea urchin (Strongylocentrotus purpuratus) Abd-B-like gene, designated SpHbox7. We show that this gene is one of at least two Abd-B-like genes in the S. purpuratus genome, a result that argues against the simple hypothesis that Hox gene duplications occurred only during the evolution of the chordates. SpHbox7 transcripts are first detectable in midblastula stage embryos, increase in amount during gastrulation, decline slightly by the pluteus stage, and are not detectable in any tissue of the adult. Whole mount in situ hybridization and antibody staining with an SpHbox7-specific antibody reveal that both SpHbox7 mRNA and protein are present throughout the embryo in the blastula. Subsequently, they are localized in the invaginating archenteron, secondary mesenchyme, and oral ectoderm. By the pluteus larva stage, SpHbox7 protein and mRNA are present in the gut, larval arms, and portions of the oral ectoderm. This complex and dynamic expression pattern suggests that SpHbox7 has a role in the patterning of the gut, the mesoderm, and the oral surface.

Homeobox-containing gene transiently expressed in a spatially restricted pattern in the early sea urchin embryo

In the sea urchin embryo, the lineage founder cells whose polyclonal progenies will give rise to five different territories are segregated at the sixth division. To investigate the mechanisms by which the fates of embryonic cells are first established, we looked for temporal and spatial expression of homeobox genes in the very early cleavage embryos. We report evidence that PlHbox12, a paired homeobox-containing gene, is expressed in the embryo from the 4-cell stage. The abundance of the transcripts reaches its maximum when the embryo has been divided into the five polyclonal territories--namely at the 64-cell stage--and it abruptly declines at later stages of development. Blastomere dissociation experiments indicate that maximal expression of PlHbox12 is dependent on intercellular interactions, thus suggesting that signal transduction mechanisms are responsible for its transcriptional activation in the early cleavage embryo. Spatial expression of PlHbox12 was determined by whole-mount in situ hybridization. PlHbox12 transcripts in embryos at the fourth, fifth, and sixth divisions seem to be restricted to the conditionally specified ectodermal lineages. These results suggest a possible role of the PlHbox12 gene in the early events of cell specification of the presumptive ectodermal territories.

Promoter analysis meets pattern formation: transcriptional regulatory genes in sea urchin embryogenesis

Analyses of spatial and temporal gene control mechanisms in the sea urchin embryo have identified several important trans-regulatory factors, including some that are related to known developmental control genes of the fly and mouse. Recent advances in gene perturbation technologies, including the use of antisense oligonucleotides to target mRNAs in early-stage embryos, as well as the injection of mRNAs into zygotes to express genes ectopically, have made it possible to test the functions of such factors directly.

Identification of an antennapedia-like homeobox gene in the ascidians Styela clava and S. plicata

Homeobox genes from the urochordates Styela clava (AHox2) and S. plicata (AHox3) were cloned and analyzed. The two genes are homologous and Antennapedia-like. The homeobox regions have 87% identity at the nucleotide level and are identical at the amino-acid level. No introns are present in the homeobox region of AHox3, and AHox3 is represented at a low copy number per haploid genome. AHox2 and AHox3 represent the second type of homeobox gene found in this evolutionarily and developmentally important group of organisms.

Expression of homeobox-containing genes in the sea urchin (Parancentrotus lividus) embryo

Two homeobox-containing genes that belong to different homeodomain classes have been isolated from a sea urchin genomic library. One, PlHbox11, is the sea urchin homologue of the human and mouse Hox B3 gene, the other, PlHbox12, shows about 55% identity with paired class genes. Expression profile analysis of the two sea urchin Hbox genes suggests that they play different roles during embryogenesis. In fact, PlHbox11 transcripts are rare and are detected only in the pluteus larva and in the Aristotle's lantern and intestine of the adult. The PlHbox12 gene is, on the contrary, transiently expressed in the very early embryo already at the four cell stage; it accumulates at the 64 cell stage and disappears at later stages of development. In situ hybridization experiments to 16 and 32 cell stage whole mount embryos showed localization of the PlHbox12 mRNA to part of the mesomere-macromere region of the early cleavage embryo. These observations suggest a possible role of this gene in early events of cell specification.

The Antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution

The developmental control genes containing an Antennapedia-type homeobox are clustered in insects and vertebrates. The evolution of these genes was studied by the construction of evolutionary trees and by statistical geometry in sequence space. The comparative analysis of the homeobox sequences reveals the subdivision of the Antennapedia-type homeobox genes into three classes early in metazoan evolution. This observation suggests an important function of these genes even in the most primitive metazoans. Subsequent duplication events generated a cluster of at least five homeobox genes in the last common ancestor of insects and vertebrates. These genes later independently gave rise to the 13 groups of paralogous genes in vertebrates and to the 11 Antennapedia-type genes in the Drosophila complexes.

Problems and paradigms: Hoemeobox genes in vertebrate evolution

A wide range of anatomical features are shared by all vertebrates, but absent in our closest invertebrate relatives. The origin of vertebrate embryogenesis must have involved the evolution of new regulatory pathways to control the development of new features, but how did this occur? Mutations affecting regulatory genes, including those containing homeobox sequences, may have been important: for example, perhaps gene duplications allowed recruitment of genes to new roles. Here I ask whether comparative data on the genomic organization and expression patterns of homeobox genes support this hypothesis. I propose a model in which duplications of particular homeobox genes, followed by the acquisition of gene-specific secondary expression domains, allowed the evolution of the neural crest, extensive organogenesis and craniofacial morphogenesis. Specific details of the model are amenable to testing by extension of this comparative approach to molecular embryology.

Stage- and adult tissue-specific expression of a homeobox gene in embryo and adult Parechinus angulosus sea urchins

We report the isolation of a gene (PaHbox6), encoding a homeobox-containing protein of the South African sea urchin, Parechinus angulosus. Sequencing identified an Antennapedia-class gene encoding a homeobox that is the homologue of the Hawaiian sea urchin Tripneustes gratilla homeobox gene. Extensive restriction-fragment length polymorphism surrounds the gene. RNase-protection analyses revealed expression of PaHbox6 in mesenchyme blastula embryos at maximal levels of 44 +/- 8 transcripts/embryo. Four adult tissues examined (testes, ovary, intestines, Aristotle's lantern) showed expression of PaHbox6, though at greatly differing levels, with testes highest at eleven transcripts/10 pg RNA. Two transcripts of 5.2 and 5.7 kb were identified in adult tissue.

Detection of homeobox genes in development and evolution

The homeobox genes encode a family of DNA-binding regulatory proteins whose function and genomic organization make them an important model system for the study of development and differentiation. Oligonucleotide primers corresponding to highly conserved regions of Antennapediaclass homeodomains were designed to detect and identify homeobox sequences in populations of DNA or RNA by means of the polymerase chain reaction (PCR). Here we present a survey of sequences detected by PCR using an initial set of primers (HoxA and HoxB) based on an early nucleotide consensus for vertebrate Antennapedia-class homeodomains. Several novel sequences are reported from both mouse genomic DNA and RNA from the developing mouse telencephalon. Forebrain-derived clones are similar to the chicken CHox7, Drosophila H2.0, and mouse Hlx genes. PCR also proved to be a rapid method for identifying homeobox sequences from diverse metazoan species. Cloning of three Antennapedia-related sequences from cnidarians provides evidence of ancient roles for homeobox genes early in metazoan evolution.

Activation of the L1 late H2B histone gene in blastula-stage sea urchin embryos by Antennapedia-class homeoprotein

The L1 late H2B histone gene of the sea urchin Strongylocentrotus purpuratus is transcriptionally activated in late blastula stage embryos by a mechanism that depends on an enhancer element located 3' of the gene (Zhao et al., 1990). A protein factor, designated H2B abp 1, binds this element at a site that resembles the consensus recognition sequence of Antennapedia-class homeodomain proteins. We demonstrate here that Antennapedia (Antp) and Hbox4 proteins, members of the Antennapedia class of homeoproteins from Drosophila and sea urchin respectively, bind the L1 H2B abp 1 site, and that the Drosophila Antp protein acts through this site to trans-activate the L1 H2B gene, in vivo. In addition, RNA gel blot analysis demonstrated that Hbox4 transcripts accumulate in developing embryos with a time course that closely resembles that of H2B adp 1 DNA binding activity and the activity and the transcription rate of the L1 late H2B gene. Finally, we show that antibody prepared against the sea urchin Hbox4 protein, a member of the Abd-B subclass of the Antennapedia class, specifically inhibits binding of the H2B abp 1 factor to the L1 H2B enhancer, suggesting that H2B abp 1 is encoded by Hbox4 or a closely related gene.

Activation of a late H2B histone gene in blastula-stage sea urchin embryos by an unusual enhancer element located 3' of the gene

In the sea urchin embryo, late histone genes are transcribed at low levels during cleavage and blastula formation and at substantially higher levels in later stages of embryogenesis. To investigate the molecular basis of the stage-specific expression of a late H2B histone gene, we injected mutant genes lacking portions of 5'- and 3'-flanking regions into Lytechinus pictus embryos and monitored their expression by RNase protection. A 200-bp region located 489 bp downstream of the mRNA 3' terminus was necessary for the increase in transcription of the late H2B gene at the mid-blastula stage of development. DNase I and methylation interference footprint analyses located only one factor-binding site in this region, and gel mobility shift experiments showed that the DNA-binding activity of this factor (designated H2B abp 1) paralleled the transcriptional activity of the L1 H2B gene. Additional mutagenesis and microinjection experiments located the activator element to a 32-bp DNA segment that includes the H2B abp 1-binding site. These experiments also showed that the 32-bp fragment functions independently of position and orientation and therefore has the hallmarks of an enhancer. That this fragment contains most or all of the L1 H2B gene transcription-stimulatory activity makes it unusual among enhancerlike elements, which generally consist of several clustered factor-binding sites that act additively or cooperatively to affect transcription. The nucleotide sequence of the L1 H2B enhancer element suggests that the trans-acting factor that interacts with it is a member of the antennapedia or engrailed class of homeodomain proteins.

Activation of a late H2B histone gene in blastula-stage sea urchin embryos by an unusual enhancer element located 3' of the gene

In the sea urchin embryo, late histone genes are transcribed at low levels during cleavage and blastula formation and at substantially higher levels in later stages of embryogenesis. To investigate the molecular basis of the stage-specific expression of a late H2B histone gene, we injected mutant genes lacking portions of 5'- and 3'-flanking regions into Lytechinus pictus embryos and monitored their expression by RNase protection. A 200-bp region located 489 bp downstream of the mRNA 3' terminus was necessary for the increase in transcription of the late H2B gene at the mid-blastula stage of development. DNase I and methylation interference footprint analyses located only one factor-binding site in this region, and gel mobility shift experiments showed that the DNA-binding activity of this factor (designated H2B abp 1) paralleled the transcriptional activity of the L1 H2B gene. Additional mutagenesis and microinjection experiments located the activator element to a 32-bp DNA segment that includes the H2B abp 1-binding site. These experiments also showed that the 32-bp fragment functions independently of position and orientation and therefore has the hallmarks of an enhancer. That this fragment contains most or all of the L1 H2B gene transcription-stimulatory activity makes it unusual among enhancerlike elements, which generally consist of several clustered factor-binding sites that act additively or cooperatively to affect transcription. The nucleotide sequence of the L1 H2B enhancer element suggests that the trans-acting factor that interacts with it is a member of the antennapedia or engrailed class of homeodomain proteins.

Functions of maternal mRNA in early development

In this review, the types of mRNAs found in oocytes and eggs of several animal species, particularly Drosophila, marine invertebrates, frogs, and mice, are described. The roles that proteins derived from these mRNAs play in early development are discussed, and connections between maternally inherited information and embryonic pattern are sought. Comparisons between genetically identified maternally expressed genes in Drosophila and maternal mRNAs biochemically characterized in other species are made when possible. Regulation of the meiotic and early embryonic cell cycles is reviewed, and translational control of maternal mRNA following maturation and/or fertilization is discussed with regard to specific mRNAs.

Characterization and expression of two sea urchin homeobox gene sequences

We describe two homeobox sequences, TgHbox5 and TgHbox6, isolated from the Hawaiian sea urchin Tripneustes gratilla using a Drosophila Sex combs reduced probe. Sequence analysis shows that the encoded TgHbox5 homeodomain shares only 30-52% amino acid identity with homeodomains encoded by previously characterized genes, establishing that it is a divergent homeobox that is not in any known class of homeoboxes. TgHbox5 is expressed in the embryo as two major developmentally regulated transcripts. one at 5.0 kilobase (kb) appearing by blastula stage and the other at 2.7 kb appearing at pluteus stage. Multiple transcripts from TgHbox5 are present at a much lower level in adult tissues and are predominantly expressed in small and large intestines. The TgHbox6 homeobox is an Antenna-pedia-class homeobox, which appears not to be expressed during embryogenesis but produces abundant 3.6 and 3.2 kb transcripts in the six adult tissues examined.

Progressively restricted expression of a homeo box gene within the aboral ectoderm of developing sea urchin embryos

A homeo box-containing gene, Hbox1 is expressed in an unusual and highly conserved spatial pattern in embryos of two different species of sea urchin, Tripneustes gratilla and Strongylocentrotus purpuratus. Hybridization in situ shows that this mRNA accumulates initially throughout the aboral ectoderm; however, between blastula and pluteus stages, the region containing Hbox1 mRNA retracts gradually until only a small area around the vertex is labeled in pluteus larvae. Aboral ectoderm appears cytologically uniform and also accumulates uniform levels of other tissue-specific mRNAs. Therefore, the Hbox1 pattern reveals a previously unsuspected heterogeneity of aboral ectoderm cells and a polarity within this tissue. In S. purpuratus, the Hbox1 gene product probably is not involved in initial specification of cell fate, as this message does not achieve a significant fraction of its peak abundance until almost hatching blastula stage, well after the time aboral ectoderm cells have initiated a tissue-specific program of gene expression. RNA blot and RNase protection analyses revealed low levels of Hbox1 mRNA in all adult tissues examined. However, this message was not detectable in mature eggs, suggesting that the Hbox1 gene does not have a maternal function. In addition to highly conserved spatial and temporal patterns of expression, the homeo box genes of these two urchin species also are conserved highly in sequences outside the homeo domain, despite the divergence of these two species (30-45 my). Two notable features of the protein shared with several vertebrate homeo proteins are a short conserved sequence encoded by an exon upstream of that encoding the homeo domain and a large region of high serine and proline content.