Do multigene families regulate vertebrate development?

PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches

The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications.

Understanding diabetic teratogenesis: where are we now and where are we going?

Maternal pregestational diabetes (type 1 or type 2) poses an increased risk for a broad spectrum of birth defects. To our knowledge, this problem first came to the attention of the Teratology Society at the 14th Annual Meeting in Vancouver, B.C. in 1974, with a presentation by Lewis Holmes, "Etiologic heterogeneity of neural tube defects". Although advances in the control of diabetes in the decades since the discovery of insulin in the 1920's have reduced the risk for birth defects during diabetic pregnancy, the increasing incidence of diabetes among women of childbearing years indicates that this cause of birth defects is a growing public health concern. Major advances in understanding how a disease of maternal fuel metabolism can interfere with embryogenesis of multiple organ systems have been made in recent years. In this review, we trace the history of the study of diabetic teratogenesis and discuss a model in which tissue-specific developmental control genes are regulated at specific times in embryonic development by glucose metabolism. The major function of such genes is to suppress apoptosis, perhaps to preserve proliferative capability, and inhibit premature senescence.

A homologue of the Drosophila female sterile homeotic (fsh) gene in the class II region of the human MHC

The RING3 gene maps in the class II region of the human major histocompatibility complex, at a CpG island distal of the HLA-DNA gene. RING3 cDNAs were obtained from a T cell cDNA library and the longest (4 kb) was sequenced. The sequence contained an open reading frame encoding a protein of 754 amino acids. A screen of protein databases revealed striking homology between the RING3 protein and the Drosophila female sterile homeotic gene (fsh) which is implicated in the establishment of segments in the early embryo. Partial sequence homology was also observed with some other proteins involved in cell cycle control (CCG1), cell division (ftsA) and regulation of cell growth (gamma interferons). This highly conserved gene may play an important role in human development. In addition, its location in the MHC class II region may be related to some HLA-associated diseases.

Spinal hemorrhages are associated with early neonatal motor function loss in human spina bifida aperta

BACKGROUND

In spina bifida aperta (SBA), leg movements caudal to the meningomyelocele are present in utero, but they disappear shortly after birth. It is unclear whether leg movements disappear by impact of the neuro-developmental malformation or by superimposed traumatic damage. If superimposed traumatic damage is involved, targeted fetal intervention could improve motor outcome.

AIM

To characterize neuromuscular pathology in association with perinatal motor function loss in SBA.

PATIENTS/METHODS

In fetal SBA (n=8; 16-40 weeks GA), the median time interval between ultrasound registrations of fetal motor behavior and post-mortem histology was 1 week. Histology was assessed cranial, at and caudal to the meningomyelocele and compared with findings in fetal controls (n=4).

RESULTS

Despite fetal movements caudal to the meningomyelocele (5/6), histology indicated muscle fiber alterations (6/6) that concurred with neuro-developmental and traumatic spinal defects [Neuro-developmental defects: spinal ependymal denudation (3/8), reduced amount of (caspase3-negative) lower motor neurons (LMNs; 8/8), aberrant spinal vascularization (8/8). Traumatic defects: gliosis (7/8), acute/fresh spinal hemorrhages near LMNs (8/8)].

CONCLUSION

In all delivered SBA patients, recent spinal hemorrhages were superimposed upon pre-existing defects. If early therapeutic strategies can prevent these superimposed secondary spinal hemorrhages, motor outcome may improve.

Neonatal loss of motor function in human spina bifida aperta

OBJECTIVE

In neonates with spina bifida aperta (SBA), leg movements innervated by spinal segments located caudal to the meningomyelocele are transiently present. This study in neonates with SBA aimed to determine whether the presence of leg movements indicates functional integrity of neuronal innervation and whether these leg movements disappear as a result of dysfunction of upper motor neurons (axons originating cranial to the meningomyelocele) and/or of lower motor neurons (located caudal to the meningomyelocele).

METHODS

Leg movements were investigated in neonates with SBA at postnatal day 1 (n = 18) and day 7 (n = 10). Upper and lower motor neuron dysfunction was assessed by neurologic examination (n = 18; disinhibition or inhibition of reflexes, respectively) and by electromyography (n = 12; absence or presence of denervation potentials, respectively).

RESULTS

Movements, related to spinal segments caudal to the meningomyelocele, were present in all neonates at postnatal day 1. At day 1, leg movements were associated with signs of both upper (10 of 18) and lower (17 of 18) motor neuron dysfunction caudal to the meningomyelocele. In 7 of 10 neonates restudied after the first postnatal week, leg movements had disappeared. The absence of leg movements coincided with loss of relevant reflexes, which had been present at day 1, indicating progression of lower motor neuron dysfunction.

CONCLUSIONS

We conclude that the presence of neonatal leg movements does not indicate integrity of functional lower motor neuron innervation by spinal segments caudal to the meningomyelocele. Present observations could explain why fetal surgery at the level of the meningomyelocele does not prevent loss of leg movements.

Microarray analysis of Tbx2-directed gene expression: a possible role in osteogenesis

Tbx2 is a member of the developmentally important transcriptional regulatory T-box gene family, whose target genes have not been well characterized. In an attempt to identify genes that may be regulated by Tbx2, mouse cDNA microarrays were used to analyze differential gene expression profiles, comparing stably transfected NIH3T3 cells overexpressing Tbx2 and vector-transfected controls. Among 8734 genes, 107 genes were up-regulated by 2-fold or greater, and 66 genes were down-regulated by 2-fold or greater. Caveolin, pleiotrophin (osf-1), osteoblast-specific factor-2 (osf-2) and collagen type I alpha were among the genes upregulated in the Tbx2-overexpressing cells, whereas cadherin 3, tenascin C, and insulin-like growth factor binding protein 10/CYR61 (IBP10) were among the genes downregulated. Northern blot analysis confirmed the correlation of expression of several genes, including IBP10 and osf-2, in fibroblast NIH3T3 and rat osteosarcoma ROS17/2.8 cells differentially expressing Tbx2. In ROS17/2.8 cells transfected with antisense Tbx2, osf-2 was downregulated, whereas transfection of sense Tbx2 upregulated this gene. Interestingly, the expression of pleiotrophin (osf-1) and collagen I alpha with Tbx2 transfection showed an inverse regulatory correlation between NIH3T3 and ROS17/2.8 cells. Thus, Tbx2 can act as both a repressor and activator, and the cellular context can influence the effect on gene expression. Although the data do not address whether Tbx2 directly mediates the transcriptional effect, a number of candidate genes possess putative T-box gene regulatory elements. The results support the hypothesis that Tbx2 may be an important modulator of bone development. Further functional cluster analysis indicates that Tbx2 might also be involved in the regulation of cell cycle and cell adhesion.

Chromosomal localization, gene structure and transcription pattern of the ORFX gene, a homologue of the MHC-linked RING3 gene

We have mapped the human ORFX gene to chromosome 9q34 and determined its complete gene structure. Comparison with RING3, the human MHC-linked homologue on 6p21.3, shows the two gene structures to be highly conserved but with an approximate threefold expansion in the ORFX introns. RING3 and ORFX are found to be ubiquitously expressed in human adult and foetal tissues. Evidence suggests that the two genes may have arisen from an ancient duplication in a common ancestral chromosome.

Clustered organization and conservation of the Xiphophorus maculatus D locus, which includes two distinct gene sequences

Genomic organization and chromosomal localization of a previously uncharacterized D (Donor) locus in Xiphophorus and Poecilia species was investigated using fluorescence in situ hybridization (FISH) and Southern blot analysis. Part of this region is thought to be involved in the recombination event leading to formation of the Xmrk oncogene and it has recently been shown that this locus includes two different genes, one with high homology to a zinc finger protein of the Krüppel type, and the other an unknown gene with high similarity to a Caenorhabditis elegans gene. FISH to Xiphophorus chromosomes revealed that these two unrelated genes are closely linked and clustered at a unique chromosomal site. Southern blot hybridization patterns suggest that these genes exist in the genome as multiple copies. Furthermore, similar genomic organization profiles seem to prevail among other related fish. In particular, our FISH experiments reveal the existence of a conserved homologous chromosomal segment harboring the zinc finger protein sequence in several poeciliid fish.

Differences in origin and fate between the cranial and caudal spinal cord during normal and disturbed human development

Differences in histological appearance between the cranial and caudal parts of the spinal cord and associated axial organs were analyzed in 9- and 15-week-old human dysraphic fetuses and compared with normal fetuses. In human development the cranial part of the neural tube down to the lumbosacral level forms during primary neurulation, while its caudal part results from secondary neurulation. In the 9-week fetus with cervical spina bifida, the cranial spinal cord displayed a variety of morphological changes along the cranio-caudal axis. Spinal cord in the upper cervical region transformed into the area cerebrovasculosa, while the lower cervical and thoracic levels showed only disturbed differentiation of the cell layers and roof plate. The degree of the cranial spinal cord dysmorphogenesis correlated with anomalies of the underlying notochord and vertebral column. The caudal to lumbosacral region of the spinal cord appeared normal. In the case of the 15-week-old fetus with complete dysraphia, the area cerebrovasculosa was found along the whole extent of the cranial spinal cord, while more caudally, all axial organs showed a normal histological structure. Our findings confirmed a different origin for the cranial and caudal parts of the human spinal cord. The appearance of dysraphic disorders corresponded to the time of primary neurulation; therefore, they resulted in the faulty formation of the cranial spinal cord. Normally formed caudal spinal cord appears during secondary neurulation at later developmental stages.

Malformations of the heart, kidney, palate, and skeleton in alpha-MHC-Hoxb-7 transgenic mice

To begin to define the genetic network involved in cardiogenesis, we generated mice bearing the alpha-myosin heavy chain (MHC)-Hoxb-7 transgene. We hypothesized that using the cardiac-specific alpha-MHC promoter, we can direct ectopic expression of Hoxb-7 in the heart and perturb its normal development. Both whole mount in situ hybridization and northern analyses showed that this alpha-MHC promoter resulted in transgene expression in the developing heart. Severe ventricular septal defects (VSD) were found in several mutant mice. Interestingly, transgenic mice were observed to have other malformations as well, including cleft palate, renal anomalies, and skeletal abnormalities in the craniocervical and costosternal regions. The kidney defect consisted of double ureter and pelvis. In summary, we have shown that a dominant gain-of-function mutation of Hoxb-7 using the murine alpha-MHC promoter results in perturbation of the genetic circuitry underlying multiple developmental processes, including cardiogenesis. Misexpression of Hoxb-7 during heart development may be involved in the pathogenesis of VSD.

Preliminary evidence of phenytoin-induced alterations in embryonic gene expression in a mouse model

SWV mouse embryos collected on gestational days (GD) 9:12 and 10:00 following chronic in utero exposure to teratogenic concentrations of phenytoin were utilized for in situ transcription studies of gene expression. The substrate cDNA obtained from the frozen embryo sections was amplified into radiolabelled antisense RNA (RT/aRNA) and used as a probe to screen a panel of 20 cDNA clones representing genes that are important regulators of craniofacial and neural development. The magnitude of alteration in gene expression following phenytoin treatment was determined densitometrically by changes in the hybridization intensity of the aRNA probes to the cDNA clones immobilized to the slot blots. We found that both Wnt-1 and the calcium channel gene were developmentally regulated, as their level of expression decreased significantly between the two collection times. Phenytoin treatment produced a significant downregulation in the level of expression for 25% of the genes examined in the GD 9:12 embryos, including the growth factors TGF-beta and NT3, the proto-oncogene Wnt-1, the nicotinic receptor, and the voltage sensitive calcium channel gene. Additional changes in the coordinate expression of several of the growth and transcription factors were observed at both gestational timepoints. The application of RT/aRNA technology has extended our appreciation of the normal patterns of gene expression during craniofacial and neural development, and provided the first demonstration of multiple coordinate changes in transcription patterns following teratogenic insult.

Zinc, copper and selenium in reproduction

Of the nine biological trace elements, zinc, copper and selenium are important in reproduction in males and females. Zinc content is high in the adult testis, and the prostate has a higher concentration of zinc than any other organ of the body. Zinc deficiency first impairs angiotensin converting enzyme (ACE) activity, and this in turn leads to depletion of testosterone and inhibition of spermatogenesis. Defects in spermatozoa are frequently observed in the zinc-deficient rat. Zinc is thought to help to extend the functional life span of the ejaculated spermatozoa. Zinc deficiency in the female can lead to such problems as impaired synthesis/secretion of (FSH) and (LH), abnormal ovarian development, disruption of the estrous cycle, frequent abortion, a prolonged gestation period, teratogenicity, stillbirths, difficulty in parturition, pre-eclampsia, toxemia and low birth weights of infants. The level of testosterone in the male has been suggested to play a role in the severity of copper deficiency. Copper-deficient female rats are protected against mortality due to copper deficiency, and the protection has been suggested to be provided by estrogens, since estrogens alter the subcellular distribution of copper in the liver and increase plasma copper levels by inducing ceruloplasmin synthesis. The selenium content of male gonads increases during pubertal maturation. Selenium is localized in the mitochondrial capsule protein (MCP) of the midpiece. Maximal incorporation in MCP occurs at steps 7 and 12 of spermatogenesis and uptake decreases by step 15. Selenium deficiency in females results in infertility, abortions and retention of the placenta. The newborns from a selenium-deficient mother suffer from muscular weakness, but the concentration of selenium during pregnancy does not have any effect on the weight of the baby or length of pregnancy. The selenium requirements of a pregnant and lactating mother are increased as a result of selenium transport to the fetus via the placenta and to the infant via breast milk.

Recognition of regulatory regions in genomic sequences

For the functional interpretation of genomic sequences, effective algorithms have to be developed that will recognize regions of specific function and thus will suggest experiments for their verification. As a first step, relevant data have to be collected in an appropriate database from which suitable training sets can be extracted. In this paper, I discuss the requirements for a database that collects information about regulatory DNA sequences and describe the structure and contents of such a database (TRANSFAC). This compiled information will serve as a basis for comprehensive analysis of sites that regulate transcription, e.g., by statistical methods. It will thus facilitate the recognition of regulatory genomic sequence information and the assignment of the corresponding regulators. Moreover, it will provide all relevant data about the regulating proteins which will allow to trace back transcriptional control cascades to their origin.

Pax: genes for mice and men

The murine Pax family consists of nine genes containing a highly conserved sequence, the paired box. The expression of these genes is temporally and spatially restricted during development. Evidence gathered indicates that Pax genes are involved in the regionalization of the nervous system and in important inductive events leading to the formation of various organs. The demonstration that mutations in Pax-1, Pax-3 and Pax-6 are linked with various murine mutants (undulated, splotch and small eye) and human diseases (Waardenburg syndrome and aniridia) confirms the importance of these genes as essential morphoregulators. Recent observations also indicate that inappropriate expression of these genes can lead to the appearance of cancer.

Gene regulation in rodent hepatocytes during development, differentiation and disease

The expression of genes in the liver is mostly controlled at the transcriptional level and depends on the regulatory interactions between cis-acting sequences and trans-acting molecules. Proximal promoters and distant enhancers in combination with a number of hepatocyte-enriched DNA-binding proteins and general transcription factors interact specifically with these elements and control the expression of liver-specific genes. Hepatocyte-enriched regulatory proteins have been isolated from liver nuclear extracts, characterized, and their corresponding genes have been cloned. These include the hepatocyte nuclear factors 1, 3, 4 (HNF-1,3,4), some members of the CAAAT/enhancer binding protein (C/EBP) family, and D site binding protein (DBP). These factors belong to larger families and are able to form heterodimers, perhaps with the exception of the HNF-3 family, with other members of the same family. Interestingly, the majority of the genes encoding such proteins are themselves regulated at the transcriptional level, although both transcriptional and post-transcriptional events modulate their expression during development, hepatocyte differentiation and disease, suggesting that a transcriptional cascade may play a critical role in mammalian liver development and differentiation.

Histological features of axial structures during embryonic and fetal stages of human craniorachischisis

Histological characteristics of developing axial structures in human conceptuses with craniorachischisis were investigated during the embryonic and fetal periods and compared with normal samples. The morphological relationship of the notochord to the axial skeleton and neural tube was analyzed along cervical and thoracic vertebral segments using serial paraffin sections. The embryonic stage of malformed conceptuses disclosed a correlated affection of the notochord and vertebral column, as well as the overlying central nervous system. The degree of histological changes within the spinal cord depended on the level of the vertebral axis examined: completely unorganized nervous tissue was overlying cervical and upper thoracic vertebrae, while more caudally it resembled a normal spinal cord. During the fetal period the histological disturbances of all axial structures were more pronounced. Extensive notochordal branching was associated with the malformed formation and ossification of the vertebral column. At this stage we found no correlation of histological changes between the spinal cord and the mesodermally derived structures (notochord, vertebral column) along the cranio-caudal body extent, as neural tissue had completely transformed into area cerebrovasculosa. We speculate that our histological observations could be the result of primary affection of mesodermal structures during very early stages of development. Divergence in histological findings within axial structures between the embryonic and fetal periods support recent mutational investigations on animals.

Ectopic expression of Hox-2.3 induces craniofacial and skeletal malformations in transgenic mice

To better understand the role of the Hox-2.3 murine homeobox gene during development, a dominant gain-of-function mutation was generated. The developmental malformations that resulted when the chicken beta-actin promoter was used to direct widespread expression of the Hox-2.3 gene in transgenic mice included early postnatal death as well as craniofacial abnormalities, including open eyes and cleft palate. Ventricular septal defects were also observed in the hearts of three transgenic mice. Skeletal malformations were seen in the bones of the craniocervical transition, with the occipital, basisphenoid, and atlas bones deficient or misshapen. Interestingly, one mutant exhibited an extra pair of ribs as well as alterations in cervical vertebrae identities. Some of the malformations observed in Hox-2.3 gain-of-function mutants overlap with those seen in Hox-1.1 and Hox-2.2 misexpression mutants which suggests functional similarities between paralogous homeobox genes. The results of these experiments are consistent with a role for Hox-2.3 in specifying positional information during development.

PCR amplification of SRY-related gene sequences reveals evolutionary conservation of the SRY-box motif

SRY (sex-determining region of the Y chromosome) has recently been identified as a key regulatory gene in mammalian sex determination. The open reading frame of this gene contains an 80-amino-acid motif, the SRY-box, which shares a high degree of homology with a DNA-binding domain found in the high-mobility-group (HMG) proteins HMG1 and HMG2. The SRY box motif is highly conserved in several sequence-specific DNA-binding proteins that are known to act as transcription factors. Here we describe the use of degenerate PCR primers to identify SRY-related sequences containing the SRY-box motif from the genomic DNA of a variety of species. The results of this study suggest that in a diverse array of species SRY-related genes may serve as transcription factors that regulate a variety of developmental pathways, including sex determination.

Sources of behavioral deviation modeled by early color preferences in quail. II. Diathetic genes and the leftover variance "V(e)"

The sources of deviation from population-typical norms of variability were studied in relation to early approach preferences between colors in newly hatched Japanese quail chicks (Coturnix coturnix japonica). Subjects were drawn from an unselected genetic control line, two genetic lines that were artificially selected for extreme blue and red preferences, their hybrids, and a large set of backcross and assortatively derived generations. Large progressive increases were observed with selection in the leftover (V(e)) component of F1 variance and consistent additional variance increases in F2 hybrids. Backcross generations exhibited greater than expected expression of the blue and red preference genes. Discussion differentiates between diathetic and normative influences in preference deviations and relates the increased Ve to relaxed normative canalization of preference development by directional selection.

Conserved classes of homeodomains in Schistosoma mansoni, an early bilateral metazoan

Genes containing a homeobox can be divided into classes based on the distinctive peptide sequences of their diverged homeodomains. Many of these classes, including Antennapedia, engrailed and paired, are strongly conserved in higher multicellular animals, but have not previously been found in platyhelminths, the flatworms which represent the most primitive bilateral metazoans. We have screened cDNA libraries of the platyhelminth Schistosoma mansoni using a degenerate oligonucleotide derived from the third helix of the homeodomain, and have identified numerous schistosome homeobox-containing sequences, including members of the Antennapedia, engrailed and paired classes. The schistosome homeodomain sequences are more similar to the higher animals sequences in their respective classes than they are to each other, indicating that the establishment of these three distinctive classes is at least as ancient as the flatworms. Our data suggest that the ancestral functions of the Antennapedia, engrailed and paired classes involve fundamental features of all bilateral metazoan development. The putative full-length coding sequence of the S. mansoni en homologue is presented.

Rapid isolation of desired sequences from lone linker PCR amplified cDNA mixtures: application to identification and recovery of expressed sequences in cloned genomic DNA

A simple and efficient method for the rapid isolation of specific sequences from PCR-amplified cDNA mixtures has been developed. cDNA mixtures obtained using lone linker PCR (Ko et al. 1990) appeared to be highly representative even though the starting material, 100 ng-2 micrograms of total RNA, is much less than is required for making an ordinary cDNA library. With this method, cDNA mixtures were obtained from limited materials, including early mouse embryos and primordial germ cells. For selective enrichment of desired cDNAs, biotinylated probe was hybridized with the lone linker-linked cDNA in solution and the resulting probe-cDNA hybrid was captured by Streptavidin-coated magnetic beads. After appropriate washing, cDNA was released from the beads and subjected to amplification followed by cloning into a vector. Using genomic fragments isolated during chromosomal walking in the T/t complex of mouse Chromosome (Chr) 17, cDNAs encoding novel germ cell specific genes have been readily isolated by the above procedures. The method, termed random access retrieval of genetic information through PCR (RARGIP), will streamline the entire process from RNA to cDNA greatly. Its application potentials in various areas of molecular genetics will be discussed.

Isolation and mapping of EVX1, a human homeobox gene homologous to even-skipped, localized at the 5' end of HOX1 locus on chromosome 7

We isolated and mapped the human homeobox gene EVX1. This gene encodes a protein of 407 amino acid residues containing a homeodomain closely related to the Drosophila even-skipped (eve) segmentation gene of the pair-rule class. EVX1 belongs to a small family of vertebrate eve-related homeobox genes including human EVX1 and EVX2 genes, their murine homologs, Evx 1 and Evx 2, and the frog Xhox-3 gene. We previously reported that EVX2 is localized at the 5' end of the HOX4 locus on chromosome 2. We show here that EVX1 is localized at the 5' end of the HOX1 locus on chromosome 7, 48 kb upstream from the most 5' of the eleven HOX1 genes, namely HOX1J. Both EVX genes are transcribed in an opposite orientation as compared to that of adjacent HOX genes. Human HOX1 and HOX4 complex loci appear to be both closely linked to a homeobox gene of the EVX family.

A Xenopus multifinger protein, Xfin, is expressed in specialized cell types and is localized in the cytoplasm

Xfin is a member of a large family of Krüppel-type transcripts stored in the Xenopus egg, whose function is unknown. By using polyclonal antibodies raised against fusion proteins containing different portions of Xfin, we have identified the Xfin gene product and established its pattern of expression in some adult tissues and during oogenesis and embryogenesis. The corresponding mRNA localization has been studied by in situ hybridization on ovary and testis sections. The Xfin product is found in the cytoplasm, both during oogenesis and adulthood; in adult tissues, it is differentially expressed in a cell-type specific fashion. The expression of the protein in specialized cell types and its cytoplasmic localization may favour the hypothesis that it could be involved in cell differentiation events through protein-RNA interactions.

Molecular cloning, chromosomal assignment, and nucleotide sequence of the feline homeobox HOX3A

The feline homolog to the mammalian homeobox locus, HOX3A, was isolated by screening a domestic cat genomic library with the murine Hox-3.1 probe. The nucleotide sequence similarity of the feline homeobox was 96% to human HOX3A, 94% to mouse Hox-3.1, and 94% to rat R4. The deduced amino acid sequence (homeodomain) of this feline homeobox was identical to all homeodomains of these cognate genes. Using a panel of feline x rodent somatic cell hybrids, the HOX3A locus was assigned to feline chromosome B4. Human HOX3A and mouse Hox-3.1 have been mapped previously to human chromosome 12 and mouse chromosome 15, respectively, both of which share syntenic homology to feline chromosome B4. These data demonstrate evolutionary conservation of both HOX3A gene sequences and chromosomal location during mammalian evolution.

Lethal chromosomal deletions in the mouse, a model system for the study of development and regulation of postnatal gene expression

Mechanisms involved in the regulation of development and its genetic control are receiving ever-increasing attention in studies of mammalian developmental genetics. The potential success of such studies is strongly enhanced by the availability of suitable systems of analysis. Such a system was identified in a series of radiation-induced chromosomal deletions at and around the albino (c) locus of the mouse associated with cell type-specific effects on liver differentiation. Their detailed study has aided the analysis of possible mechanisms of cell type-specific gene expression. As summarized in this review, the experimental results strongly suggest that specific trans-acting developmental regulatory genes are concerned with the differentiation of hormone-inducible expression of a cluster of hepatocyte specific structural genes mapping in different parts of the genome.

Repeating developmental expression of G-Hox 7, a novel homeobox-containing gene in the chicken

Here we describe the isolation and characterization of a new chicken homeobox-containing gene, G-Hox 7, which is related to Drosophila msh. The deduced amino acid sequence of the cDNA shows greater than 96% homology to the homeo domain of other vertebrate msh-like genes. As for other species, the amino and carboxy termini of the protein are, however, greatly divergent when compared phylogenetically. In situ hybridization studies revealed the early and wide-spread expression of G-Hox 7 during chick development. This includes its expression in the primitive streak and extraembryonic cells undergoing epiboly, and its expression along the neural axis, including the forebrain. Expression was also observed in the neural crest, neural crest-derived facial and branchial structures, the otocyst, limb, and heart valves. This widespread and recurrent expression of the transcript suggests that the gene may play an essential role at multiple sites during the initiation of new developmental pathways.

Axial specification in higher vertebrates

The specification of the body axis in the embryo is reflected in the structure of the vertebral column. Expression patterns of Hox genes in the prevertebrae suggest their involvement in this specification process and in the maintenance of vertebral identities. A single, ectopically expressed Hox gene can reprogramme the rostral part of the vertebral column and induce phenotypic alterations interpretable as homeotic transformations.

Two members of an HNF1 homeoprotein family are expressed in human liver

HNF1 is a transcriptional activator, required for the liver-specific expression of a variety of genes, that binds to DNA as a dimer via the most diverged homeodomain known so far. We were interested to examine whether HNF1 is a unique homeoprotein example or whether it is the prototype of a new subfamily of homeodomain containing proteins. In this work we describe the isolation of a cDNA clone from a human liver library encoding a protein, highly homologous to HNF1 in three regions, including the homeo- and dimerization domains. We show that this protein can heterodimerize with human HNF1 in vitro. Sequence comparison of our clone with a rat variant HNF1 (vHNF1) clone, isolated in parallel in our laboratory from the dedifferentiated H5 hepatoma cell line, identified our cDNA as human vHNF1. vHNF1 is a nuclear protein recognizing the same binding site as HNF1 and previously thought to occur only in dedifferentiated hepatoma cells that fail to express most liver specific genes. Nevertheless, we show by Northern blot analysis that vHNF1 transcripts are present in differentiated human HepG2 hepatoma cells as well as in rat liver and that this transcript level is 10-20 fold lower than that of HNF1. We assigned the vHNF-1 gene to human chromosome 17 and murine chromosome 11. These chromosomal localizations differ from that of the HNF-1 gene indicating that both genes are not clustered on the genome.

Pattern formation during animal development

At the beginning of this century, embryologists defined the central problems of developmental biology that remain today. These questions include how differentiated cells arise and form tissues and organs and how pattern is generated. In short, how does an egg give rise to an adult? In recent years, the application of molecular biology to embryological problems has led to significant advances and recast old problems in molecular and cellular terms. Although not necessarily comprehensive, this idiosyncratic review is intended to highlight selected findings and indicate where there are important gaps in our knowledge for those less than familiar with developmental biology.

The paired box encodes a second DNA-binding domain in the paired homeo domain protein

The homeo box, which encodes the DNA-binding homeo domain, is a DNA sequence motif present in several Drosophila developmental genes; it has been used to identify many homologous genes involved in mammalian development. The paired box is another conserved sequence motif, first identified in the paired (prd) and gooseberry (gsb) Drosophila homeo domain genes. It encodes a 128-amino-acid domain, the paired domain, which has since been found in other fly and mouse gene products, in association with the homeo domain or in its absence. We show that the paired box of the prd gene encodes a DNA-binding activity, independent of the DNA-binding activity of the Paired (Prd) homeo domain and with a different sequence specificity. The amino-terminal region of the paired domain, including one of the three predicted alpha-helices, is necessary and sufficient for binding. We investigate the binding of the Prd protein to two sites in the even-skipped promoter, which are composed of overlapping sequences bound by the homeo domain and by the paired domain. We also show that a mutation in the paired box of Prd, corresponding to the mutation in the paired box of the mouse Pax-1 gene thought to cause the undulated skeletal phenotype, destroys the ability of the Prd protein to bind to the paired domain-specific site. This supports the view that the undulated phenotype results from the inactivation of the DNA-binding activity of the paired domain of Pax-1.

Balanced translocation 12/13 and situs abnormalities: homology of early pattern formation in man and lower organisms?

Studies in "lower" organisms have identified a set of homologous sequences expressed in oocytes and early embryos that is critical for pattern formation. Mutations in such genes may exhibit maternal effect--they cause abnormalities in the fetus only when present in the mother. We report on a mother and child with identical, apparently balanced translocations having the breakpoints 12q13.1 and 13p13. The fetus had multiple anomalies including bilateral trilobar lungs, complex heart defect, malrotation of the gut, and asplenia, while the mother was entirely normal. Several hypotheses are advanced to explain this variable expression including transection of a gene with maternal effect--lateral asymmetry in the fetus is influenced by the maternal genotype. This explanation would account for the higher transmission of congenital heart disease to offspring by affected females noted in several studies. The human counterparts of 2 loci (int-1 and HOX 3) involved in Drosophila early pattern formation are located near the translocation breakpoint 12q13.1. If one of these genes is responsible for situs abnormality, then university of positional code (but not of embryologic mechanism) is suggested for higher metazoans.

The M-twist gene of Mus is expressed in subsets of mesodermal cells and is closely related to the Xenopus X-twi and the Drosophila twist genes

The twist gene was characterized in Drosophila as being necessary at gastrulation for the establishment of the mesodermal germ layer. It codes for a nuclear DNA-binding protein that is probably a transcription factor. We have cloned and sequenced the M-twist gene of Mus musculus. The deduced proteins encoded by the Mus, Xenopus, and Drosophila twist cDNAs, respectively, show a high degree of similarity. Northern blot analyses and in situ hybridizations reveal that the 1.7-kb murine M-twist m-RNA is present at early stages, starting at 8 days post coitum, and is expressed the most at 9.5 days in the cephalic and branchial mesectoderm, in some derivatives of the mesodermal layer (sclerotoma and somatopleura), and in the limb buds.

Zinc finger protein gene complexes on mouse chromosomes 8 and 11

Two murine homologs of the Drosophila Krüppel gene, a member of the gap class of developmental control genes that encode a protein with zinc fingers, were mapped to mouse chromosomes 8 and 11 by using somatic cell hybrids and an interspecific backcross. Surprisingly, both genes were closely linked to two previously mapped, Krüppel-related zinc finger protein genes, suggesting that they are part of gene complexes.

Oct-6: a POU transcription factor expressed in embryonal stem cells and in the developing brain

A family of octamer binding proteins is expressed during mouse development. Oct-4 and Oct-6 have been identified as two octamer binding proteins present in embryonal stem cells. Here we report the complementary DNA cloning and characterization of the mouse Oct-6 gene. The protein of 448 amino acids contains a glycine/alanine-rich amino terminal region, a histidine-rich sequence with homology to a region of kininogen associated with clotting, a POU domain and a short proline/histidine-rich carboxy terminal region. Expression of Oct-6 in HeLa cells is sufficient for transcriptional activation from the octamer motif, identifying Oct-6 as a transcription factor. The Oct-6 expression is downregulated upon embryonic stem cell differentiation increasing again during brain development. Expression in brain is present in certain areas of telencephalon, mesencephalon and brain stem with abundant expression in the cortex anlagen and in the developing colliculi. Thus Oct-6 is a new octamer binding transcription factor specifically regulated during mouse development.

Cloning of human hepatic nuclear factor 1 (HNF1) and chromosomal localization of its gene in man and mouse

HNF1 is a transcription factor that is required for hepatocyte-specific expression of several genes, including albumin and fibrinogen. Rat HNF1-encoding cDNAs have recently been cloned, revealing that this factor is a distant member of the homeoprotein family. We have now isolated HNF1 clones from a human liver cDNA library by using a rat HNF1 cDNA-derived probe. The longest clone, HCL20, contains a sequence corresponding to the intact rat HNF1-coding region followed by a 3' nontranslated region and a poly(A) tail, hence representing an almost full-length HNF1 cDNA. Alignment of the human and rat sequences shows that HNF1 is highly conserved between the two species. The HNF1 gene was mapped by in situ hybridization and by RFLP analysis of interspecific mouse backcrosses to chromosomes 12q24.3 and 5F in human and mouse, respectively, establishing a new segmental homology between these two chromosomes.

Identification of positive and negative regulatory elements governing cell-type-specific expression of the neural cell adhesion molecule gene

The neural cell adhesion molecule (NCAM) is one of the most prevalent cell adhesion molecules in vertebrates. Its expression is subject to complex cell-type- and developmental-stage-dependent regulation. To study this regulation at the level of transcription, we analyzed the promoter region of the mouse NCAM gene. The NCAM promoter did not contain a typical TATA box. Transcription started at several sites that were used indiscriminately by different cell types, implying that the different NCAM isoforms are expressed from a single promoter. Sequences responsible for both promotion and inhibition of transcription resided within 840 base pairs upstream of the main transcriptional start site. The sequence from positions -645 to -37 relative to the translation initiation site directed high levels of expression in NCAM-expressing N2A cells. The same fragment was six times less active but still significantly active in L cells, but this activity was repressed by inclusion of an additional upstream segment. We mapped eight domains of interactions with nuclear proteins within the 840-base-pair region. The segment with maximum promoter activity contained two adjacent footprints, the occupation of which appeared to be mutually exclusive. One of them corresponded to an Sp1-factor-binding consensus site, the other one bound a factor with nuclear factor I activity. The single protected domain in the fragment harboring a repressor activity consisted of a GGA repeat resembling negative regulatory elements in other promoters. Three adjacent binding sites occupied an A + T-rich segment and contained ATTA motifs also found in the recognition elements of homeodomain proteins. These results show that negative and positive elements interact to regulate the tissue-specific patterns of expression of the NCAM gene and indicate that a factor related to nuclear factor I is involved in its transcriptional control.

Identification of positive and negative regulatory elements governing cell-type-specific expression of the neural cell adhesion molecule gene

The neural cell adhesion molecule (NCAM) is one of the most prevalent cell adhesion molecules in vertebrates. Its expression is subject to complex cell-type- and developmental-stage-dependent regulation. To study this regulation at the level of transcription, we analyzed the promoter region of the mouse NCAM gene. The NCAM promoter did not contain a typical TATA box. Transcription started at several sites that were used indiscriminately by different cell types, implying that the different NCAM isoforms are expressed from a single promoter. Sequences responsible for both promotion and inhibition of transcription resided within 840 base pairs upstream of the main transcriptional start site. The sequence from positions -645 to -37 relative to the translation initiation site directed high levels of expression in NCAM-expressing N2A cells. The same fragment was six times less active but still significantly active in L cells, but this activity was repressed by inclusion of an additional upstream segment. We mapped eight domains of interactions with nuclear proteins within the 840-base-pair region. The segment with maximum promoter activity contained two adjacent footprints, the occupation of which appeared to be mutually exclusive. One of them corresponded to an Sp1-factor-binding consensus site, the other one bound a factor with nuclear factor I activity. The single protected domain in the fragment harboring a repressor activity consisted of a GGA repeat resembling negative regulatory elements in other promoters. Three adjacent binding sites occupied an A + T-rich segment and contained ATTA motifs also found in the recognition elements of homeodomain proteins. These results show that negative and positive elements interact to regulate the tissue-specific patterns of expression of the NCAM gene and indicate that a factor related to nuclear factor I is involved in its transcriptional control.

The HOX-5 and surfeit gene clusters are linked in the proximal portion of mouse chromosome 2

Using an interspecies backcross, we have mapped the HOX-5 and surfeit (surf) gene clusters within the proximal portion of mouse chromosome 2. While the HOX-5 cluster of homeobox-containing genes has been localized to chromosome 2, bands C3-E1, by in situ hybridization, its more precise position relative to the genes and cloned markers of chromosome 2 was not known. Surfeit, a tight cluster of at least six highly conserved "housekeeping" genes, has not been previously mapped in mouse, but has been localized to human chromosome 9q, a region of the human genome with strong homology to proximal mouse chromosome 2. The data presented here place HOX-5 in the vicinity of the closely linked set of developmental mutations rachiterata, lethargic, and fidget and place surf close to the proto-oncogene Abl, near the centromere of chromosome 2.

How gene families evolve

Theories and facts of gene family evolution are reviewed. Concerted evolution is commonly observed for gene families which originated a long time ago, however there are many different types of multigene families, from uniform to diverse. The rate of homogenization by unequal crossing-over, gene conversion, etc. has been evolutionarily adjusted for each gene family. When new functions are needed by organisms, gene families may evolve into superfamilies, in which no further concerted evolution takes place, and each member of the family may acquire an indispensable function. The homeobox-containing gene family is a most exciting example of such superfamily.

Structure, expression and chromosomal localization of Zfp-1, a murine zinc finger protein gene

Zinc finger proteins (Zfp) are encoded by a large family of genes present in many organisms including yeast and human. Some of them are transcriptional activators and bind specifically to DNA by zinc mediated folded structures commonly known as zinc fingers. The Drosophila Krüppel (Kr) is a segmentation gene and encodes a zinc finger protein. Using a probe from the finger domain of Kr, we have isolated a structurally related gene Zfp-1 from the mouse. In this paper, we report the complete nucleotide sequence of two cDNA clones and the amino acid sequence deduced from them. The putative Zfp-1 protein contains in addition to 7 zinc fingers, two helix-turn-helix motifs. During murine embryogenesis, the Zfp-1 was found to express at a peak level in day 12 embryos. The ubiquitously expressed Zfp-1 gene is located in the 16q region on mouse chromosome 8, between the uvomorulin and the tyrosine amino transferase genes.

A single amino acid can determine the DNA binding specificity of homeodomain proteins

Many Drosophila developmental genes contain a DNA binding domain encoded by the homeobox. This homeodomain contains a region distantly homologous to the helix-turn-helix motif present in several prokaryotic DNA binding proteins. We investigated the nature of homeodomain-DNA interactions by making a series of mutations in the helix-turn-helix motif of the Drosophila homeodomain protein Paired (Prd). This protein does not recognize sequences bound by the homeodomain proteins Fushi tarazu (Ftz) or Bicoid (Bcd). We show that changing a single amino acid at the C-terminus of the recognition helix is both necessary and sufficient to confer the DNA binding specificity of either Ftz or Bcd on Prd. This simple rule indicates that the amino acids that determine the specificity of homeodomains are different from those mediating protein-DNA contacts in prokaryotic proteins. We further show that Prd contains two DNA binding activities. The Prd homeodomain is responsible for one of them while the other is not dependent on the recognition helix.

The liver-specific transcription factor LF-B1 contains a highly diverged homeobox DNA binding domain

The nuclear protein LF-B1 (also referred to as HNF-1) is a transcription activator required for the expression of several liver-specific genes. LF-B1 has been purified to homogeneity from rat liver nuclear extracts. The sequence of the protein has been partially determined and, subsequently, overlapping cDNA clones containing the entire open reading frame of LF-B1 were isolated. The full-length cDNA encodes a 628 amino acid protein and directs the synthesis in vitro of a protein capable of binding DNA with the same specificity as LF-B1. The cDNA was recombined into a vaccinia virus vector and active LF-B1 was obtained from infected HeLa cells. Addition of the vaccinia recombinant protein to rat spleen extracts results in activation of transcription of an LF-B1-dependent promoter. The DNA binding domain of LF-B1 is located in the amino-terminal part of the protein and displays distant structural similarity to the homeobox domain. The distribution of LF-B1 mRNA is restricted to liver, which correlates with the tissue-specific expression of its target genes.

Interference with function of a homeobox gene in Xenopus embryos produces malformations of the anterior spinal cord

XIHbox 1 is expressed in a narrow band across the cervical region of Xenopus embryos. The gene produces two related proteins: "long" and "short" XIHbox 1 homeodomain proteins. Injection of antibodies to the long XIHbox 1 protein into 1-cell embryos caused a phenotype in which the anterior spinal cord was morphologically transformed into a hindbrain-like structure. This alteration was restricted to the region normally expressing long XIHbox 1 protein. Injection of long protein mRNA disrupted segmentation and tissue organization without inhibiting cell proliferation. Injection of short protein mRNA into 1-cell embryos produced spinal cord malformations similar, but not identical, to those caused by the antibodies, suggesting antagonistic roles for long and short XIHbox 1 proteins. We immunostained tadpoles carrying extended hindbrains for N-CAM and consistently found defective organization of spinal nerves over the affected region.