The genes for human brain factor 1 and 2, members of the fork head gene family, are clustered on chromosome 14q

Paving Therapeutic Avenues for FOXG1 Syndrome: Untangling Genotypes and Phenotypes from a Molecular Perspective

Development of the central nervous system (CNS) depends on accurate spatiotemporal control of signaling pathways and transcriptional programs. Forkhead Box G1 (FOXG1) is one of the master regulators that play fundamental roles in forebrain development; from the timing of neurogenesis, to the patterning of the cerebral cortex. Mutations in the FOXG1 gene cause a rare neurodevelopmental disorder called FOXG1 syndrome, also known as congenital form of Rett syndrome. Patients presenting with FOXG1 syndrome manifest a spectrum of phenotypes, ranging from severe cognitive dysfunction and microcephaly to social withdrawal and communication deficits, with varying severities. To develop and improve therapeutic interventions, there has been considerable progress towards unravelling the multi-faceted functions of FOXG1 in the neurodevelopment and pathogenesis of FOXG1 syndrome. Moreover, recent advances in genome editing and stem cell technologies, as well as the increased yield of information from high throughput omics, have opened promising and important new avenues in FOXG1 research. In this review, we provide a summary of the clinical features and emerging molecular mechanisms underlying FOXG1 syndrome, and explore disease-modelling approaches in animals and human-based systems, to highlight the prospects of research and possible clinical interventions.

FOXG1 Gene and Its Related Phenotypes

FOXG1 is an important transcriptional repressor found in cell precursor of the ventricular region and in neurons in the early stage of differentiation during the development of the nervous epithelium in the cerebrum and optical formation. Mutations involving FOXG1 gene have been described first in subjects with congenital Rett syndrome. They can cause seizure, delayed psychomotor development, language disorders, and autism. FOXG1 deletions or intragenic mutations also determinate reduction in head circumference, structural defects in the corpus callosum, abnormal movements, especially choreiform, and intellectual retardation with no speech. Patients with duplications of 14q12 present infantile spasms and have subsequent intellectual disability with autistic features, head circumference in the normal range, and regular aspect of corpus callosum. Clinical characteristics of patients with FOXG1 variants include growth deficit after birth associated with microcephaly, facial dysmorphisms, important delay with no language, deficit in social interaction like autism, sleep disorders, stereotypes, including dyskinesia, and seizures. In these patients, it is not characteristic a history of loss of acquired skills.

Cognition and Evolution of Movement Disorders of FOXG1-Related Syndrome

FOXG1-related syndrome is a rare neurodevelopmental encephalopathy characterized by early onset hyperkinetic movement disorders, absent language, autistic features, epilepsy, and severe cognitive impairment. However, detailed evaluation of cognition and evolution of movement disorders over time have not been clearly described before. In this study, we performed whole-exome sequencing in a cohort with unknown severe encephalopathy and movement disorders, with/without autistic behaviors. We identified FOXG1 mutations in three patients. One of them had a novel mutation that has not been described before. The neuropsychological test by Mullen Scales of Early Learning (MSEL) showed severe psychomotor impairments in all patients. There were uneven cognitive abilities in terms of verbal and non-verbal cognitive domains in all of them, with approximately 2 months differences. Gross motor skills and expressive language were more severely affected than the other domains in all the patients. All individuals had early onset hyperkinetic movement disorders. The movement disorders in one of our patients changed from predominantly hyperkinetic in early childhood to more hypokinetic in adolescence with the development of dystonia. To the best of our knowledge, this evolution had never been described before. In conclusion, individuals with FOXG1-related syndrome may show clinical progression from hyperkinetic to hypokinetic features over time. There were also uneven cognitive abilities in verbal and non-verbal cognitive domains. The FOXG1 mutation should be considered in individuals with a history of hyperkinetic movements, microcephaly, and uneven cognitive abilities with characteristic brain images.

FOXG1 Dose in Brain Development

Brain development is a highly regulated process that involves the precise spatio-temporal activation of cell signaling cues. Transcription factors play an integral role in this process by relaying information from external signaling cues to the genome. The transcription factor Forkhead box G1 (FOXG1) is expressed in the developing nervous system with a critical role in forebrain development. Altered dosage of FOXG1 due to deletions, duplications, or functional gain- or loss-of-function mutations, leads to a complex array of cellular effects with important consequences for human disease including neurodevelopmental disorders. Here, we review studies in multiple species and cell models where FOXG1 dose is altered. We argue against a linear, symmetrical relationship between FOXG1 dosage states, although FOXG1 levels at the right time and place need to be carefully regulated. Neurodevelopmental disease states caused by mutations in FOXG1 may therefore be regulated through different mechanisms.

FOXG1 syndrome: genotype-phenotype association in 83 patients with FOXG1 variants

PurposeThe study aimed at widening the clinical and genetic spectrum and assessing genotype-phenotype associations in FOXG1 syndrome due to FOXG1 variants.MethodsWe compiled 30 new and 53 reported patients with a heterozygous pathogenic or likely pathogenic variant in FOXG1. We grouped patients according to type and location of the variant. Statistical analysis of molecular and clinical data was performed using Fisher's exact test and a nonparametric multivariate test.ResultsAmong the 30 new patients, we identified 19 novel FOXG1 variants. Among the total group of 83 patients, there were 54 variants: 20 frameshift (37%), 17 missense (31%), 15 nonsense (28%), and 2 in-frame variants (4%). Frameshift and nonsense variants are distributed over all FOXG1 protein domains; missense variants cluster within the conserved forkhead domain. We found a higher phenotypic variability than previously described. Genotype-phenotype association revealed significant differences in psychomotor development and neurological features between FOXG1 genotype groups. More severe phenotypes were associated with truncating FOXG1 variants in the N-terminal domain and the forkhead domain (except conserved site 1) and milder phenotypes with missense variants in the forkhead conserved site 1.ConclusionsThese data may serve for improved interpretation of new FOXG1 sequence variants and well-founded genetic counseling.

FOXG1-Related Disorders: From Clinical Description to Molecular Genetics

Rett syndrome (RTT) is a severe neurodevelopmental disease that affects approximately 1 in 10,000 live female births and is often caused by mutations in the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2). Mutations in loci other than MECP2 have also been found in individuals that have been labeled as atypical RTT. Among them, a mutation in the gene forkhead box G1 (FOXG1) has been involved in the molecular aetiology of the congenital variant of RTT. The FOXG1 gene encodes a winged-helix transcriptional repressor essential for the development of the ventral telencephalon in embryonic forebrain. Later, FOXG1 continues to be expressed in neurogenetic zones of the postnatal brain. Although RTT affects quasi-exclusively girls, FOXG1 mutations have also been identified in male patients. As far as we know, about 12 point mutations and 13 cases with FOXG1 molecular abnormalities (including translocation, duplication and large deletion on the chromosome 14q12) have been described in the literature. Affected individuals with FOXG1 mutations have shown dysmorphic features and Rett-like clinical course, including normal perinatal period, postnatal microcephaly, seizures and severe mental retardation. Interestingly, the existing animal models of FOXG1 deficiency showed similar phenotype, suggesting that animal models may be a fascinating model to understand this human disease. Here, we describe the impacts of FOXG1 mutations and their associated phenotypes in human and mouse models.

The ring 14 syndrome: clinical and molecular definition

The ring 14 (r14) syndrome is a rare condition, whose precise clinical and genetic characterization is still lacking. We analyzed a total of 20 patients with r14 and another 9 patients with a linear 14q deletion. The ring was complete, with no apparent loss of chromosome material, in 6 cases; a terminal 14q deletion, varying in size from 0.65 to 5 Mb, was detected in the remaining 14 cases. Deleted ring chromosomes were 70% paternal and 30% maternal. UPD (14) was never detected. With respect to the linear 14q deletions, three were proximal, varying in size from 4 to 7.2 Mb, and six distal, varying in size from 4.8 to 20 Mb. The majority of the linear deletions were also of paternal origin, and UPD (14) was excluded in all cases. Clinically, the r14 syndrome was characterized by a recognizable phenotype, consisting of shortness of stature, a distinctive facial appearance, microcephaly, scoliosis, and ocular abnormalities, which included abnormal retinal pigmentation, strabismus, glaucoma, and abnormal macula. All patients except one had mental retardation. Drug-resistant epilepsy was another highly consistent finding. Aggressive and hyperactive behavior was noted in about half of the patients. Based on genotype-phenotype correlations, we could deduce that retinal abnormalities, epilepsy, microcephaly, and mental retardation map within the proximal 14q11.2-q12 region. Likewise, behavior disorders and scoliosis could be assigned to the 14q32 region.

Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation

Comparative analysis of orthologues from diverse vertebrates can be used to identify molecular signatures that are important for gene function and which may predict novel regulatory mechanisms or explain morphological diversity. The forkhead box G1 (FoxG1) transcription factor is potentially a strong candidate gene for determining forebrain size in vertebrates due to its role in the development of the telencephalon, where it promotes progenitor proliferation and suppresses premature neurogenesis. To investigate the role of FoxG1 in forebrain evolution, we cloned and analyzed the cDNA sequences for nine new FoxG1 orthologues, including six mammals and three reptiles, and show that there is an extended proline and glutamine region in the N-terminal domain that is specific to mammals. In contrast to some previous studies of other potential determinants of brain size, we find no evidence that the coding sequence of FoxG1 has evolved under positive selection in vertebrates. Previously published work has indicated that FOXG1 was duplicated in humans, and two forms, FOXG1A and FOXG1B, are present in the Entrez Gene database. We report that FOXG1 has not been duplicated in humans and that FOXG1A is likely to be an artifact. Our comparative analysis of FOXG1B and its orthologues has revealed a very high level of conservation in the 3' untranslated region (UTR). Using available computational tools, we find evidence for conserved recognition sites for the miR-9 and miR-33 microRNAs in the FoxG1 3' UTR and hypothesize that these brain-expressed microRNAs may regulate FoxG1 post-transcriptionally during forebrain development.

Comparative aspects of cerebral cortical development

This review aims to provide examples of how both comparative and genetic analyses contribute to our understanding of the rules for cortical development and evolution. Genetic studies have helped us to realize the evolutionary rules of telencephalic organization in vertebrates. The control of the establishment of conserved telencephalic subdivisions and the formation of boundaries between these subdivisions has been examined and the very specific alterations at the striatocortical junction have been revealed. Comparative studies and genetic analyses both demonstrate the differential origin and migratory pattern of the two basic neuron types of the cerebral cortex. GABAergic interneurons are mostly generated in the subpallium and a common mechanism governs their migration to the dorsal cortex in both mammals and sauropsids. The pyramidal neurons are generated within the cortical germinal zone and migrate radially, the earliest generated cell layers comprising preplate cells. Reelin-positive Cajal-Retzius cells are a general feature of all vertebrates studied so far; however, there is a considerable amplification of the Reelin signalling with cortical complexity, which might have contributed to the establishment of the basic mammalian pattern of cortical development. Based on numerous recent observations we shall present the argument that specialization of the mitotic compartments may constitute a major drive behind the evolution of the mammalian cortex. Comparative developmental studies have revealed distinct features in the early compartments of the developing macaque brain, drawing our attention to the limitations of some of the current model systems for understanding human developmental abnormalities of the cortex. Comparative and genetic aspects of cortical development both reveal the workings of evolution.

An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolution

During amphioxus development, the neural plate is bordered by cells expressing many genes with homologs involved in vertebrate neural crest induction. However, these amphioxus cells evidently lack additional genetic programs for the cell delaminations, migrations, and differentiations characterizing definitive vertebrate neural crest. We characterize an amphioxus winged helix/forkhead gene (AmphiFoxD) closely related to vertebrate FoxD genes. Phylogenetic analysis indicates that the AmphiFoxD is basal to vertebrate FoxD1, FoxD2, FoxD3, FoxD4, and FoxD5. One of these vertebrate genes (FoxD3) consistently marks neural crest during development. Early in amphioxus development, AmphiFoxD is expressed medially in the anterior neural plate as well as in axial (notochordal) and paraxial mesoderm; later, the gene is expressed in the somites, notochord, cerebral vesicle (diencephalon), and hindgut endoderm. However, there is never any expression in cells bordering the neural plate. We speculate that an AmphiFoxD homolog in the common ancestor of amphioxus and vertebrates was involved in histogenic processes in the mesoderm (evagination and delamination of the somites and notochord); then, in the early vertebrates, descendant paralogs of this gene began functioning in the presumptive neural crest bordering the neural plate to help make possible the delaminations and cell migrations that characterize definitive vertebrate neural crest.

Structural characterization of the mouse Foxf1a gene

Members in the superfamily of the forkhead/winged-helix transcription factors are known to play a critical role in the control of cell differentiation and tissue development. To understand the regulation and function of these genes, we have initially isolated and characterized the mouse Foxf1a gene, a novel forkhead gene predominantly expressed in the lung. The mouse gene consists of two exons with the forkhead domain contained in exon 1, and is located at band E1 on chromosome 8. Amino acid sequence of the mouse protein shares a high degree of homology to that of the corresponding human protein. The tissue specificity of expression of the mouse gene also resembles that found in the human gene. This gene is primarily expressed in the lung, and to a lesser extent in placenta and tissues in gastrointestinal tract. The transcription start site was mapped to 113 nucleotides upstream from the putative translation initiation site. The promoter of the mouse gene is highly GC rich and contains neither a CAAT nor a TATA box. A series of luciferase report constructs driven by the promoter and various deletions in the 5' flanking region of the gene were constructed and employed in transient transfection studies using a line of SV40 transformed mouse lymph node endothelial cells (SVEC4-10), which express the endogenous Foxf1a gene, and a line of mouse hepatoma cells (Hepa 1-6), in which Foxf1a is not expressed. To our surprise, these reporter genes are equally active in both cell lines. Further studies have shown that the proximal 5' flanking sequence and exon 1 of the endogenous gene are highly methylated in Hepa 1-6 cells but not in SVEC4-10 cells, suggesting that DNA methylation but not cell-specific transcription factor(s) regulates cell specificity of gene expression in these cultured cells.

Pleiotropic skeletal and ocular phenotypes of the mouse mutation congenital hydrocephalus (ch/Mf1) arise from a winged helix/forkhead transcriptionfactor gene

Congenital hydrocephalus is an etiologically diverse, poorly understood, but relatively common birth defect. Most human cases are sporadic with familial forms showing considerable phenotypic and etiologic heterogeneity. We have studied the autosomal recessive mouse mutation congenital hydrocephalus ( ch ) to identify candidate human hydrocephalus genes and their modifiers. ch mice have a congenital, lethal hydrocephalus in association with multiple developmental defects, notably skeletal defects, in tissues derived from the cephalic neural crest. We utilized positional cloning methods to map ch in the vicinity of D13Mit294 and confirm that the ch phenotype is caused by homozygosity for a nonsense mutation in a gene encoding a winged helix/forkhead transcription factor ( Mf1 ). Based on linked genetic markers, we performed detailed phenotypic characterization of mutant homozygotes and heterozygotes to demonstrate the pleiotropic effects of the mutant gene. Surprisingly, ch heterozygotes have the glaucoma-related distinct phenotype of multiple anterior segment defects resembling Axenfeld-Rieger anomaly. We also localized a second member of this gene family ( Hfh1 ), a candidate for other developmental defects, approximately 470 kb proximal to Mf1.

The mouse Fkh1/Mf1 gene: cDNA sequence, chromosomal localization and expression in adult tissues

The 'winged helix' or 'forkhead' transcription factor gene family is defined by a common 100-amino-acid DNA-binding motif. Here, we describe the chromosomal position, start site of transcription, sequence and adult expression pattern of the mouse Fkh1/Mf1 (Forkhead homologue 1/mesoderm/mesenchyme forkhead 1) gene. This gene contains one exon and encodes a protein of 553 amino acids that is highly related to the mouse MFH1 protein. The Fkh1/Mf1 mRNA is expressed widely in adult tissues. Linkage analysis showed that the Fkh1/Mf1 gene is localized to chromosome 13 at 17.02cM from the centromer, in close proximity to Bmp6 and Hfh1, another distinct member of the winged helix gene family.

Mouse HNF-3/fork head homolog-1-like gene: structure, chromosomal location, and expression in adult and embryonic kidney

Screening of a mouse kidney cDNA library with a HNF-3/fork head domain probe revealed cDNA Hfh-1L containing the highly conserved fork head DNA-binding domain. The Hfh1L cDNA shows 92.7% homology at the nucleic acid level with the fork head gene HFH-1 from rat. Southern blot analyses demonstrated that the Hfh-1L gene is highly conserved in a wide variety of species, including goldfish and frog. Sequencing the corresponding genomic clone, we found that the Hfh-1L gene is most likely intronless. By interspecific back-cross analysis, the Hfh-1L gene was localized to mouse chromosome 13. In order to analyze the expression pattern of Hfh-1L, we performed Northern blot analyses and revealed a 2.7-kb transcript in adult kidney and stomach. In situ hybridization experiments of adult mouse kidney showed Hfh-1L expression in the outer medulla of the kidney and the transitional epithelium. In light of the significance of a number of fork head genes in early embryonic development, the pattern of expression during murine embryogenesis was examined by reverse transcriptase-polymerase chain reaction (RT-PCR), and Hfh-1L transcripts were detected in mouse embryos at every stage tested from day 10.5 to 16.5 postconception (p.c.) and in the developing metanephros of 14.5- and 15.5-day p.c. embryos. This expression pattern suggests that the Hfh-1L gene is involved in the development of the kidney.

A human forkhead/winged-helix transcription factor expressed in developing pulmonary and renal epithelium

Members of the forkhead/winged-helix transcription factor family play crucial roles during vertebrate development. A human hepatocyte nuclear factor/forkhead homolog (HFH)-4 cDNA encoding a 421-amino acid protein was isolated from a human fetal lung cDNA library. By Southern blot analysis of human-rodent somatic cell hybrid genomic DNA, the human HFH-4 gene localizes to chromosome 17q23-qter. This is the locus of another forkhead/winged-helix gene, the interleukin enhancer binding factor gene. RNA blot analysis revealed a 2.5-kilobase human HFH-4 transcript in fetal lung, kidney, and brain as well as in adult reproductive tissues, lung, and brain. By in situ hybridization, HFH-4 expression is associated with differentiation of the proximal pulmonary epithelium, starting during the pseudoglandular stage of human lung development. During human renal morphogenesis, HFH-4 is expressed in the developing epithelial cells of the ureteric duct, glomerulus, and epithelial vesicles. The unique pattern of HFH-4 expression during human fetal development suggests a role for this forkhead/winged-helix factor during pulmonary and renal epithelial development.

Cloning and characterization of freac-9 (FKHL17), a novel kidney-expressed human forkhead gene that maps to chromosome 1p32-p34

We describe the cloning of a near full-length cDNA of 4258 nucleotides encoding freac-9 (HGMW-approved symbol FKHL17), a novel human forkhead gene. The 5' untranslated region is unusual since it is very long, 2127 nucleotides, and contains 15 upstream AUG codons. Hybridization to a panel consisting of RNA derived from 50 different tissues showed that freac-9 is transcribed exclusively in the kidney. The kidney-derived cell lines COS-7 and 293 are shown to express freac-9. A combination of fluorescence in situ hybridization and somatic cell hybrids localizes freac-9 to the chromosomal region of 1p32-p34. The conceptual translation product predicts a protein of 372 amino acids with an N-terminal domain rich in acidic amino acids and with a high likelihood of forming an amphipatic helix, a DNA binding forkhead domain, and a C-terminal region that has a high probability of forming an amphipatic beta-sheet. The amino acid sequence of the DNA binding forkhead motif of FREAC-9 is identical to that of another forkhead protein, FREAC-4, whereas 12 substitutions are present at the nucleotide level. There are no similarities in regions outside of the DNA binding domains of FREAC-9 and FREAC-4 and since freac-4 maps to a different chromosome (5q12-q13) it is likely that an evolutionary selection has acted to maintain identical DNA binding domains between these two kidney expressed transcription factors.

Structural characterization of the mouse Hfh4 gene, a developmentally regulated forkhead family member

Hepatocyte nuclear factor-3/forkhead homologue 4 (HFH-4) is a forkhead/winged-helix transcription factor family member that has a unique temporal and spatial pattern of gene expression in the developing and adult lung, choroid plexus, testis, and oviduct. To characterize HFH-4 further, mouse genomic clones were isolated and analyzed. The Hfh4 gene is encoded on a 5.5-kb region located on the distal end of mouse chromosome 11 and consists of two exons and one intron. Unlike most forkhead genes, the DNA binding domain is divided between two exons, and the intron position corresponds precisely to the site of gene translocations involving two known human forkhead homologues. Multiple putative transcription start sites are identified in a G+C-rich sequence that does not contain TATA or CAAT boxes. Within 2.1 kb of 5' flanking sequence are three identical E boxes and multiple putative transcription factor binding sites. Transfection of plasmids containing Hfh4 5' flanking sequence linked to a reporter gene results in promoter activity in lung epithelial cells but not in epithelial-like fibrosarcoma cells, suggesting that this 5' flanking sequence can function as a promoter with the proper cell-type specificity.

A 1.2-megabase BAC/PAC contig spanning the 14q13 breakpoint of t(2; 14) in a mirror-image polydactyly patient

We previously assigned a 14q13 breakpoint of t(2; 14) in a patient with mirror-image polydactyly to a segment between two loci, AFM200ZH4 and D14S306, within a genetic distance of 0.6 cM. In the present study, we constructed a 1.2-Mb high-resolution physical map with a contig composed of 16 bacterial artificial chromosomes (BACs) and 6 P1-derived artificial chromosomes (PACs) at a region around the breakpoint, extending from D14S75 to D14S728 loci. Thirty-four novel sequence-tagged sites (STSs) were also characterized at this region. Of nine ESTs that had been mapped between D14S75 and D14S288, T99065 was confirmed to be in two BAC clones, B102 and B319. This BAC/PAC contig with STSs is useful for further genomic sequencing, for construction of a transcription map, and for the isolation of the putative gene for mirror-image polydactyly.

The human hepatocyte nuclear factor 3/fork head gene FKHL13: genomic structure and pattern of expression

We describe the isolation and characterization of the cDNA for FKHL13, the human homologue of the mouse hepatocyte nuclear factor 3/fork head homologue 4 (HFH-4) gene, a member of the HNF-3/fork head (also called winged helix) gene family. Members of this gene family contain a conserved DNA binding region of approx. 110 amino acids and are thought to play an important role in cell-specific differentiation. Previous analysis of the mouse and rat HFH-4 cDNAs revealed a distinct pattern of expression for this gene, suggesting that the gene plays an important role in the differentiation of lung and oviduct/ampulla epithelial cells and testicular spermatids. Analysis of the human FKHL13 gene confirmed this pattern of expression. We also found expression in adult human brain cortex, which we were able to confirm for the mouse. The expression pattern of FKHL13/HFH-4, confined to cilia/flagella-producing cells, leads us to believe that the gene plays an important role in the regulation of axonemal structural proteins. We show that the human gene for FKHL13 lies on chromosome 17 (comparison with the chromosomal location of the mouse gene strongly suggests 17q22-q25) and that the gene, which is approx. 6 kb, contains a single intron disrupting the fork head DNA binding domain. Such a disruption of a functional unit provides strong evidence for the theory of intron insertion during gene evolution. The expression of the gene is probably controlled by the CpG island, which is located in the promoter region of the gene. We also demonstrate that the FKHL13 gene is highly conserved among a wide variety of species, including birds.

The novel human HNF-3/fork head-like 5 gene: chromosomal localization and expression pattern

Analysis of cDNA clones, isolated from a human fetal brain cDNA library, that hybridized with the rat HNF-3 alpha fork head homolog domain revealed the 3.6-kb HFKL5 cDNA. The transcript of HFKL5 is 4.4 kb long and represents a novel member of the HNF-3/fork head transcription factor family. Comparison of the amino acid sequence of the fork head domain reveals a relatively low level of homology to other members of this family of genes, the closest related sequence being rat HFH7 with 68% homology. The HFKL5 cDNA codes for a putative 500-amino-acid protein. Southern analysis revealed that the HFKL5 gene homolog is present as a single copy in the human genome. Zoo Southern analysis showed strong evolutionary conservation of HFKL5 among mammalian and possibly avian species. Expression of HFKL5 in neurons is restricted to the fully differentiated neurons in fetal and adult brain as well as in the parasympathic ganglia of the small intestine. We also observed expression in lymphocytes, kidney tubule cells, and a subset of hepatocytes. The HFKL5 gene homolog was mapped to chromosome 22q13-qter by cell panel hybridization.

Transcription factor genes and the developing eye: a genetic perspective

We review the current knowledge of transcription factors in mammallan eye development. The 14 transcription factors presently known to be required for eye formation are examined in some detail, incorporating data from both humans and rodents. Aspects of the biochemistry, expression patterns, genetics, mutant phenotypes, and biological insights acquired from the examination of loss-of-function mutations are summarized. The other 32 tissue-restricted transcription factors that are currently known to be expressed in the developing or mature mammallan eye are tabulated, together with the timing and site of their ocular expression; the requirement for most of these genes in the eye is unknown. Contributions to mammallan eye development from the study of the genetics of the Drosophila eye are discussed briefly. Identification of the entire cohort of transcription factors required for eye development is an essential first step towards understanding the mechanisms underlying eye morphogenesis and differentiation, and the molecular basis of inherited eye abnormalities in humans.

Clustered arrangement of winged helix genes fkh-6 and MFH-1: possible implications for mesoderm development

The ‘winged helix’ or ‘forkhead’ transcription factor gene family is defined by a common 100 amino acid DNA binding domain which is a variant of the helix-turn-helix motif. Here we describe the structure and expression of the mouse fkh-6 and MFH-1 genes. Both genes are expressed in embryonic mesoderm from the headfold stage onward. Transcripts for both genes are localised mainly to mesenchymal tissues, fkh-6 mRNA is enriched in the mesenchyme of the gut, lung, tongue and head, whereas MFH-1 is expressed in somitic mesoderm, in the endocardium and blood vessels as well as the condensing mesenchyme of the bones and kidney and in head mesenchyme. Both genes are located within a 10 kb region (in mouse chromosome 8 at 5.26 +/− 2.56 cM telomeric to Actsk1. The close physical linkage of these two winged helix genes is conserved in man, where the two genes map to chromosome 16q22-24. This tandem arrangement suggests the common use of regulatory mechanisms. The fkh-6/MFH-1 locus maps close to the mouse mutation amputated, which is characterised by abnormal development of somitic and facial mesoderm. Based on the expression patterns we suggest that a mutation in MFH-1, not fkh-6 is the possible cause for the amputated phenotype.

Five years on the wings of fork head

Since its discovery five years ago the conserved family of fork head/HNF-3-related transcription factors has gained increasing importance for the analysis of gene regulatory mechanisms during embryonic development and in differentiated cells. Different members of this family, which is defined by a conserved 110 amino acid residues encompassing DNA binding domain of winged helix structure, serve as regulatory keys in embryogenesis, in tumorigenesis or in the maintenance of differentiated cell states. The purpose of this review is to summarize the accumulating amount of data on structure, expression and function of fork head/HNF-3-related transcription factors.

Expression of the winged helix genes fkh-4 and fkh-5 defines domains in the central nervous system

The 'winged helix' or 'forkhead' transcription factor gene family is defined by a common 100 amino acid DNA binding domain which is a variant of the helix-turn-helix motif. Here we describe the structure and expression of the mouse fkh-4 and fkh-5 genes. The two genes encode proteins of 427 and 324 amino acids, respectively, with highly similar winged helix domains. Both genes are expressed in adjacent domains in the developing diencephalon from the headfold stage onward. Linkage analysis localised fkh-5 to chromosome 9 at 34.5 centiMorgans (cM) and fkh-4 to chromosome 19 at 10.5 cM. The potential relationship of the two genes to the mouse mutations staggerer and small thymus (for fkh-5) and muscle deficient (for fkh-4) is discussed.

Reverse transcriptase: mediator of genomic plasticity

Reverse transcription has been an important mediator of genomic change. This influence dates back more than three billion years, when the RNA genome was converted into the DNA genome. While the current cellular role(s) of reverse transcriptase are not yet completely understood, it has become clear over the last few years that this enzyme is still responsible for generating significant genomic change and that its activities are one of the driving forces of evolution. Reverse transcriptase generates, for example, extra gene copies (retrogenes), using as a template mature messenger RNAs. Such retrogenes do not always end up as nonfunctional pseudogenes but form, after reinsertion into the genome, new unions with resident promoter elements that may alter the gene's temporal and/or spatial expression levels. More frequently, reverse transcriptase produces copies of nonmessenger RNAs, such as small nuclear or cytoplasmic RNAs. Extremely high copy numbers can be generated by this process. The resulting reinserted DNA copies are therefore referred to as short interspersed repetitive elements (SINEs). SINEs have long been considered selfish DNA, littering the genome via exponential propagation but not contributing to the host's fitness. Many SINEs, however, can give rise to novel genes encoding small RNAs, and are the migrant carriers of numerous control elements and sequence motifs that can equip resident genes with novel regulatory elements [Brosius J. and Gould S.J., Proc Natl Acad Sci USA 89, 10706-10710, 1992]. Retrosequences, such as SINEs and portions of retroelements (e.g., long terminal repeats, LTRs), are capable of donating sequence motifs for nucleosome positioning, DNA methylation, transcriptional enhancers and silencers, poly(A) addition sequences, determinants of RNA stability or transport, splice sites, and even amino acid codons for incorporation into open reading frames as novel protein domains. Retroposition can therefore be considered as a major pacemaker for evolution (including speciation). Retroposons, with their unique properties and actions, form the molecular basis of important evolutionary concepts, such as exaptation [Gould S.J. and Vrba E., Paleobiology 8, 4-15, 1982] and punctuated equilibrium [Elredge N. and Gould S.J. in Schopf T.J.M. (ed). Models in Paleobiology. Freeman, Cooper, San Francisco, 1972, pp. 82-115].