Embryonic canalization and its limits-A view from temperature.

Many animals are able to produce similar offspring over a range of environmental conditions. This property of the developmental process has been termed canalization-the channeling of developmental pathways to generate a stable outcome despite varying conditions. Temperature is one environmental parameter that has fundamental effects on cell physiology and biochemistry, yet developmental programs generally result in a stable phenotype under a range of temperatures. On the other hand, there are typically upper and lower temperature limits beyond which the developmental program is unable to produce normal offspring. This review summarizes data on how development is affected by temperature, particularly high temperature, in various animal species. It also brings together information on potential cell biological and developmental genetic factors that may be responsible for developmental stability in varying temperatures, and likely critical mechanisms that break down at high temperature. Also reviewed are possible means for studying temperature effects on embryogenesis and how to determine which factors are most critical at the high-temperature limits for normal development. Increased knowledge of these critical factors will point to the targets of selection under climate change, and more generally, how developmental robustness in varying environments is maintained.

Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis.

The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinalis cis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.

Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module.

The Ci-Dll-B gene is an early regulator of ectodermal development in the ascidian Ciona intestinalis (Imai et al., 2006). Ci-Dll-B is located in a convergently transcribed bigene cluster with a tandem duplicate, Ci-Dll-A. This clustered genomic arrangement is the same as those of the homologous vertebrate Dlx genes, which are also arranged in convergently transcribed bigene clusters. Sequence analysis of the C. intestinalis Dll-A-B cluster reveals a 378bp region upstream of Ci-Dll-B, termed B1, which is highly conserved with the corresponding region from the congener Ciona savignyi. The B1 element is necessary and sufficient to drive expression of a lacZ reporter gene in a pattern mimicking the endogenous expression of Ci-Dll-B at gastrula stages. This expression pattern which is specific to the entire animal hemisphere is activated preferentially in posterior, or b-lineage, cells by a central portion of B1. Expression in anterior, or a-lineage cells, can be activated by this central portion in combination with the distal part of B1. Anterior expression can also be activated by the central part of B1 plus both the proximal part of B1 and non-conserved sequence upstream of B1. Thus, cis-regulation of early Ci-Dll-B expression is activated by a required submodule in the center of B1, driving posterior expression, which works in combination with redundant submodules that respond to differentially localized anterior factors to produce the total animal hemisphere expression pattern. Interestingly, the intergenic region of the cluster, which is important for expression of the Dlx genes in vertebrates, does not have a specific activating function in the reporter genes tested, but acts as an attenuator in combination with upstream sequences.

Optimized conditions for transgenesis of the ascidian Ciona using square wave electroporation.

The protochordate Ciona has recently become an important model organism for the study of developmental gene regulation, in part because transient transgenic embryos can be produced rapidly and reliably using electroporation. Published methods are currently for the use of electroporation devices delivering exponentially decaying pulses. However, some workers have advocated the use of square wave electroporation devices for eukaryotic transgenics. This paper presents results of experiments to find optimal conditions for the use of square-wave electroporation in the ascidian Ciona. In the present analysis, a single pulse of 90 msec duration at 63-75 V/cm was found to give an optimal balance of a high proportion of cells transformed with the transgene, and a low level of abnormal development. Forty micrograms of DNA per electroporation is sufficient for effective visualization of reporter gene expression, although doses up to 100 µg provide higher proportions of transformed cells. In side-by-side comparison with exponential pulse electroporation, square wave pulses give similar penetrance of transgene expression, along with lower proportions of embryos with abnormal development at higher amounts of input DNA.

Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis.

The Pax6 gene has attracted intense research interest due to its apparently important role in the development of eyes and the central nervous system (CNS) in many animal groups. Pax6 is also of interest for comparative genomics since it has not been duplicated in tetrapods, making for a direct orthology between the Ciona intestinalis gene CiPax6 and Pax6 in mammals. CiPax6 has been shown to be expressed in the anterior brain, caudal nerve cord, and in parts of the brain associated with the photoreceptive ocellus. This information was extended here using in-situ hybridization, and shows that CiPax6 transcripts mark the lateral regions of the nerve cord, remarkably similar to Pax6 expression in the mouse. As a means of dissecting the cis-regulation of CiPax6 we tested 8 kb of sequence using transient reporter transgene assays. Three separate regions were found that work together to drive the overall CiPax6 expression pattern. A 211 bp sequence 2 kb upstream of the first exon was found to be a major enhancer driving expression in the sensory vesicle (the anterior portion of the ascidian brain). Other upstream sequences were shown to work with the sensory vesicle enhancer to drive expression in the remainder of the CNS. An "eye enhancer" was localized to the first intron, which controls specific expression in the central portion of the sensory vesicle, including photoreceptor cells. The fourth intron was found to repress ectopic expression of the reporter gene in middle portions of the embryonic brain. Aspects of this overall regulatory organization are similar to the organization of the Pax6 homologs in mice and Drosophila, particularly the presence of intronic elements driving expression in the eye, brain and nerve cord.

High temperature limits on developmental canalization in the ascidian Ciona intestinalis.

The normal embryogenesis of marine animals is typically confined to a species-specific range of temperatures. Within that temperature range development results in a consistent, or canalized, phenotype, whereas above and below the range abnormal phenotypes are produced. This study reveals a high temperature threshold, occurring over a 1-2 °C range, for normal embryonic development in C. intestinalis. Above that threshold the prevalence of morphological abnormalities increases significantly, beginning with cleavage and gastrula stages, and becoming more pronounced as embryogenesis proceeds. However, even in highly morphologically abnormal temperature disrupted (TD) embryos, muscle, endoderm, notochord, epidermis, and sensory pigment cells are recognizable, as evidenced by histochemical markers or morphology. On the other hand, morphogenesis of the notochord and other structures is dependent on precise cell movement and shape changes after the gastrula stage, which are disrupted above the high temperature threshold. These findings suggest that morphogenetic processes may be more sensitive to high temperature than cell type specification events. They also point to avenues for investigation of the limiting factors to developmental canalization in marine invertebrates.

Whole-mount in situ hybridization of small invertebrate embryos using laboratory mini-columns.

To facilitate the handling of small invertebrate embryos during whole-mount in situ hybridization, a method of solution exchange using laboratory mini-columns was developed. This protocol speeds time-consuming aspiration of buffers, and avoids accidental loss of the embryos, by gently pushing solutions through the column using air pressure from a syringe after each incubation. The next buffer is then added using a pipettor. Embryos are retained on a filter within the column. As many columns as desired may be processed in parallel for different probes or stages.

Proteomic responses to elevated ocean temperature in ovaries of the ascidian Ciona intestinalis.

Ciona intestinalis, a common sea squirt, exhibits lower reproductive success at the upper extreme of the water temperatures it experiences in coastal New England. In order to understand the changes in protein expression associated with elevated temperatures, and possible response to global temperature change, we reared C. intestinalis from embryos to adults at 18°C (a temperature at which they reproduce normally at our collection site in Rhode Island) and 22°C (the upper end of the local temperature range). We then dissected ovaries from animals at each temperature, extracted protein, and measured proteomic levels using shotgun mass spectrometry (LC-MS/MS). 1532 proteins were detected at a 1% false discovery rate present in both temperature groups by our LC-MS/MS method. 62 of those proteins are considered up- or down-regulated according to our statistical criteria. Principal component analysis shows a clear distinction in protein expression pattern between the control (18°C) group and high temperature (22°C) group. Similar to previous studies, cytoskeletal and chaperone proteins are upregulated in the high temperature group. Unexpectedly, we find evidence that proteolysis is downregulated at the higher temperature. We propose a working model for the high temperature response in C. intestinalis ovaries whereby increased temperature induces upregulation of signal transduction pathways involving PTPN11 and CrkL, and activating coordinated changes in the proteome especially in large lipid transport proteins, cellular stress responses, cytoskeleton, and downregulation of energy metabolism.

The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia.

Fanconi anemia (FA) is a human genetic disease characterized by congenital defects, bone marrow failure, and increased cancer risk. FA is associated with mutation in one of 24 genes. The protein products of these genes function cooperatively in the FA pathway to orchestrate the repair of DNA interstrand cross-links. Few model organisms exist for the study of FA. Seeking a model organism with a simpler version of the FA pathway, we searched the genome of the simple chordate Ciona intestinalis for homologs of the human FA-associated proteins. BLAST searches, sequence alignments, hydropathy comparisons, maximum likelihood phylogenetic analysis, and structural modeling were used to infer the likelihood of homology between C. intestinalis and human FA proteins. Our analysis indicates that C. intestinalis indeed has a simpler and potentially functional FA pathway. The C. intestinalis genome was searched for candidates for homology to 24 human FA and FA-associated proteins. Support was found for the existence of homologs for 13 of these 24 human genes in C. intestinalis. Members of each of the three commonly recognized FA gene functional groups were found. In group I, we identified homologs of FANCE, FANCL, FANCM, and UBE2T/FANCT. Both members of group II, FANCD2 and FANCI, have homologs in C. intestinalis. In group III, we found evidence for homologs of FANCJ, FANCO, FANCQ/ERCC4, FANCR/RAD51, and FANCS/BRCA1, as well as the FA-associated proteins ERCC1 and FAN1. Evidence was very weak for the existence of homologs in C. intestinalis for any other recognized FA genes. This work supports the notion that C. intestinalis, as a close relative of vertebrates, but having a much reduced complement of FA genes, offers a means of studying the function of certain FA proteins in a simpler pathway than that of vertebrate cells.

Non-overlapping expression patterns of the clustered Dll-A/B genes in the ascidian Ciona intestinalis.

The Ci-Dll-A and Ci-Dll-B genes of Ciona intestinalis are arranged in a convergently transcribed gene cluster. This genomic arrangement is similar to that of the multiple bigene clusters of the Dlx homologs in vertebrates. Analysis of whole genome sequences showed that linkage to the Hox cluster is conserved with the vertebrate clusters. Phylogenetic analysis supports gene trees consistent with homology of the ascidian and vertebrate Dlx clusters, and in combination with the apparent conservation of genomic arrangement, it is concluded that the ascidian cluster is most likely homologous with the vertebrate clusters. Using whole-mount in situ hybridization, Ci-Dll-B transcripts were detected in all ectodermal lineages through gastrulation. Expression is radically downregulated in the neurula with detectable expression disappearing around the time that Ci-Dll-A expression appears in the anterior ectoderm. By the late tailbud stage Ci-Dll-Atranscripts were detected in the bilateral atrial primordia and persisted in the atrial rudiments to the larval stage, suggesting a role in development of these neural placode-like structures. This non-overlapping expression contradicts a common pattern seen in clustered genes, where as adjacent paralogs have largely overlapping expression domains. Enhancer sharing is often proposed as an explanation for the overlapping expression of gene cluster members. For this case of non-overlapping expression a model is proposed in which repressors acting at different stages override one or more shared enhancers. The enhancer sharing prevents breakup of the cluster while the independent temporal suppressors hide the presence of the shared enhancers.

The role of gene duplication in the evolution and function of the vertebrate Dlx/distal-less bigene clusters.

The Dlx gene family controls developmental patterning principally in the pharyngeal and cranial regions. We review the structure and function of these genes in the vertebrates and relate these properties to their evolution. We particularly focus on the Dlx3-7 bigene cluster which we postulate to be more derived phylogenetically and functionally than the other two bigene clusters, Dlx1-2 and Dlx5-6. We stress the transcriptional control of the Dlx3-7 bigene cluster, and postulate its control by Dlx1-2.

Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus.

The sea lamprey Petromyzon marinus is among the most primitive of extant vertebrates. We are interested in the organization of its Hox gene clusters, because, as a close relative of the gnathostomes, this information would help to infer Hox cluster organization at the base of the gnathostome radiation. We have partially mapped the P. marinus Hox clusters using phage, cosmid, and P1 artificial chromosome libraries. Complete homeobox sequences were obtained for the 22 Hox genes recovered in the genomic library screens and analyzed for cognate group identity. We estimate that the clusters are somewhat larger than those of mammals (roughly 140 kbp vs. 105 kbp) but much smaller than the single Hox cluster of the cephalochordate amphioxus (at more than 260 kb). We never obtained more than three genes from any single cognate group from the genomic library screens, although it is unlikely that our screen was exhaustive, and therefore conclude that P. marinus has a total of either three or four Hox clusters. We also identify four highly conserved non-coding sequence motifs shared with higher vertebrates in a genomic comparison of Hox 10 genes.

Genomic structure and functional control of the Dlx3-7 bigene cluster.

The Dlx genes are involved in early vertebrate morphogenesis, notably of the head. The six Dlx genes of mammals are arranged in three convergently transcribed bigene clusters. In this study, we examine the regulation of the Dlx3-7 cluster of the mouse. We obtained and sequenced human and mouse P1 clones covering the entire Dlx3-7 cluster. Comparative analysis of the human and mouse sequences revealed several highly conserved noncoding regions within 30 kb of the Dlx3-7-coding regions. These conserved elements were located both 5' of the coding exons of each gene and in the intergenic region 3' of the exons, suggesting that some enhancers might be shared between genes. We also found that the protein sequence of Dlx7 is evolving more rapidly than that of Dlx3. We conducted a functional study of the 79-kb mouse genomic clone to locate cis-element activity able to reproduce the endogenous expression pattern by using transgenic mice. We inserted a lacZ reporter gene into the first exon of the Dlx3 gene by using homologous recombination in yeast. Strong lacZ expression in embryonic (E) stage E9.5 and E10.5 mouse embryos was found in the limb buds and first and second visceral arches, consistent with the endogenous Dlx3 expression pattern. This result shows that the 79-kb region contains the major cis-elements required to direct the endogenous expression of Dlx3 at stage E10.5. To test for enhancer location, we divided the construct in the mid-intergenic region and injected the Dlx3 gene portion. This shortened fragment lacking Dlx7-flanking sequences is able to drive expression in the limb buds but not in the visceral arches. This observation is consistent with a cis-regulatory enhancer-sharing model within the Dlx bigene cluster.