Dm-Ftz
transcription factor - homeodomain - Antp class - pair rule gene - modulates Runt-dependent activation and repression of segment-polarity gene transcription
Please see the GBrowse view of Dmel\ftz or the JBrowse view of Dmel\ftz for information on other features
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Gene model reviewed during 5.50
1.9 (northern blot)
1.8 (northern blot)
There is only one protein coding transcript and one polypeptide associated with this gene
68 (kD observed)
413 (aa); 45 (kD predicted)
Phosphorylated at as many as 16 sites.
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\ftz using the Feature Mapper tool.
Comment: pair-rule pattern
Comment: anlage in statu nascendi
Comment: anlage in statu nascendi
Comment: anlage in statu nascendi
Comment: reference states 0-12 hr AEL
Expression was examined at four phases of embryonic stage 5. The striped pattern becomes visible in phase 1 (0-5'), all stripes except stripe 7 are expressed during phase 2 (5-17'), and their spacing and expression levels become largely uniform by phase 3 (17-30'). The stripes initially appear less clearly separated and more graded.
The ftz transcript is expressed in every even numbered parasegment in a pair-rule pattern of the blastoderm stage embryo. The stripes of ftz expression are broad at first, and later in development become more refined. At stage 10, neural expression is appearant in the ventral nerve cord. By stage 11, ftz transcript levels are diminished.
The ftz transcripts are first detected in stage 3 embryos uniformly distributed between 20 and 70% egg length. This pattern is then resolved into seven stripes of expression in even numbered parasegments and persists through germband retraction.
ftz transcripts are first detected at the 11th nuclear division in early embryos at which point they are distributed throughout the embryo. A striped pattern is first seen at the 13th nuclear division. At the cellular blastoderm stage, ftz transcripts can be clearly seen to localize in discrete patches between 15% and 65% egg length that are separated by unlabelled cells. Each labelled cluster is 3-5 cells wide and is separated by 3-5 cell-wide patches of unlabelled cells. ftz transcripts continue to be detected at gastrulation and in early germ band extended embryos. No ftz transcripts are observed after 4 hrs of development.
ftz transcripts are most abundant in RNA from 0-6hr embryos and are also detected in 6-12hr RNA. They are not detected in RNA from later embryonic stages, larvae, or pupae.
ftz transcripts peak in 2-4hr embryos but are detected at all two hour intervals from 0-2 to 10-12 hours of embryogenesis.
Comment: reference states 5-6 hr AEL
Comment: reference states 12-15 hr AEL
Comment: reference states 12-15 hr AEL
Comment: reference states 3-14 hr AEL
The position of run protein stripes was compared to that of other segmentation genes. The run protein stripes lie anterior to the ftz protein stripes but overlap them partially. Two rows of run expression are anterior to a two-row region of overlap with ftz followed by two rows of ftz expression and then a region of non-expression before the next run stripe.
ftz protein expression is more intense in the posterior stripes (parasegments 10, 12, and 14) compared to more anterior stripes.
Filtered fluorescence imaging (FFI) was used to visualize low level ftz protein expression. The order of stripe formation is the following: 1+2, 5+3, 4+6+7. The shape of the stripes changes during maturation. Stripes 3-7 have a graded D/V distribution with more protein ventrally tapering off toward the dorsal midline. Stripes 1 and 2 are less graded. The stripes narrow with time and are wider in intermediate stages than in their mature form. For example, stripes 6 and 7 arise from expression in a region ~15 nuclei wide. ftz protein is also observed in anterior and posterior portions of the embryo with FFI in the cellularizing embryo. The anterior region is 12 nuclei wide and extends from 75-84% egg length. The posterior band of staining lies adjacent to the pole cells. ftz protein is also detected transiently in the interband regions during cellularization.
ftz protein is expressed in a segmentally repeated pattern in the embryonic CNS. Expression begins in a subset of neuronal precursor cells. It is eventually expressed in about 30 of the ~250 neurons in each hemisegment. Specific identified cells that express ftz protein include MP1, MP2, dMP2, vMP2, aCC, pCC, GMC1, RP1, RP2, and the glial precursor (GP). By stage 15, ftz protein is no longer detected in the nervous system.
ftz protein accumulation was assayed by western blot in embryos. An early peak of ftz protein is seen in 3-4 hr embryos. Protein levels subside and then rise to a second peak in 8-9hr embryos. Levels drop off again after 10 hours. No protein is detected after 14 hours. The pattern of protein distribution was determined by immunodetection. Between 3 and 5 hours of development, ftz protein is present in seven bands encircling the embryo. The order of appearance of the stripes is 2, 1+3, 5,6,7 (stripes are numbered from anterior to posterior). The bands are dynamic in width and position. Nuclei on the posterior edges of the stripes have a lower level of ftz protein. This is the region in which ftz protein expression is lost in stripes 1-5 when stripe narrowing occurs. Beginning at 5-6hr of development, staining becomes apparent in neuronal precursors in the CNS. A third stage of expression occurs in 12-15hr embryos. Expression is observed in the hindgut. Light staining is also observed in the proventriculus and in the dorsal posterior ectoderm.
At the cellular blastoderm stage of embryonic development ftz protein is expressed as a stripe in every even numbered parasegment.
ftz protein is first detected at the cellular blastoderm stage in a pattern of seven stripes, each about 4 nuclei wide, in the anterior-posterior axis. The most posterior stripe is wider, averaging 5 nuclei across. The space between stripes is about 4 nuclei across. The stripes become narrower at the beginning of gastrulation at which point they are about 3 nuclei across and the spaces between enlarge to about 5 cell nuclei. The staining in stripes can be followed nearly to the time of full germ band extension. The stripes disappear before the germ band is fully extended. In germ band extended embryos, ftz protein is observed in clusters of cells in the embryonic CNS. The staining is repeated bilaterally in 15 segmental units including the regions where the gnathocephalic segments are forming.
GBrowse - Visual display of RNA-Seq signals
View Dmel\ftz in GBrowse 23-48
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.
polyclonal
Source for identity of: ftz CG2047
DNA-protein interactions: genome-wide binding profile assayed for ftz protein in 2-3 hr embryos; see BDTNP1_TFBS_ftz collection report.
The LRALL motif is needed for the strong segmentation function of ftz.
Nucleotides 1374 to 1570 contains the minimal signal required for RNA localisation of ftz in the blastoderm and ovary.
Two RNA instability elements in the protein-coding region of ftz have been identified; the 63bp "FIE5-1" and 69bp "FIE5-2" elements. The function of both elements is position dependent; RNAs are destabilised when the elements are present within the coding region, but not when embedded in the 3' UTR. Each instability element is sufficient to destabilise a normally stable mRNA (RpLP2) but the destabilising activity is dependent on their position within the mRNA.
ftz may represent a category of LXXLL motif-dependant coactivators for nuclear receptors.
ttk accessory peptide N-terminal to the first zinc finger directly interacts with DNA, both in specific and nonspecific DNA-protein complexes.
Both positively and negatively regulated ftz target genes respond to ftz with the same kinetics as autoregulation. The rate limiting step is the time required for regulatory proteins to enter or be cleared from the nucleus. The matching of these processes is probably important for the rapid and synchronous progression of expression from one class of segmentation genes to the next.
In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes.
Mutants are isolated in an EMS mutagenesis screen to identify zygotic mutations affecting germ cell migration at discrete points during embryogenesis: mutants exhibit pair-rule pattern defects.
The AE1 enhancer element (which interacts with the ftz promoter in vivo) preferentially activates TATA-containing promoters when challenged with linked TATA-less promoters.
Analysis of Mmus\Hoxa7-Ecol\lacZ reporter constructs shows that the Mmus\Hoxa7 intron can function as an enhancer in Drosophila, and contains potential binding sites for cad and ftz.
Probes labelled with digoxigenin, fluorescein and biotin allow detection of RNA of three different genes in three different colours.
The repression function of en::ftzEFE.hs is contributed by several domains, including the C-terminal region flanking the homeodomain and a conserved region found in the N-terminal repression domain.
ftz protein has broad DNA recognition properties in vitro that are likely to be important determinants of its distribution on DNA in vivo.
Most metazoan homeodomains share a preference for the TAAT motif, they can differ from each other in their preference for the bases immediately 3' to this core. This preference is determined, in part, by the identity of amino acid position 50. Because homeodomain sequences have been identified that possess at least 10 different amino acids at position 50 it is investigated whether multiple DNA binding specificities can be conferred by changing this position to a variety of amino acid side chains.
Four neuroblast molecular markers (svp, pros, en and ftz) have been used to demonstrate that some neuroblasts are homologous between insects (Drosophila and Schistocerca). They have similar position, time of formation and time of gene expression. Results suggest that evolution of the insect CNS has occurred in part through altering the neuroblast pattern and fate.
The ftz protein is specifically phosphorylated on serine and threonine residues at 3 to 4 hr after egg laying.
The sequence of the proximal part of the 'zebra' element of the ftz gene has been compared in a number of Drosophila species.
Protein-protein interactions and phosphorylation are two factors that play a major role in determining the specificity of action of the homeodomain containing protein ftz.
odd and nkd are required to restrict en expression. odd represses expression of ftz, an activator of en. nkd prevents activation of en by ftz without affecting ftz expression. In odd mutants the altered expression patterns of ftz, en and wg lead to the changes in positional identities of cells that causes mirror image duplications of the body pattern.
run and h act on ftz with opposing effect via a common 32 bp element, the fDE1. run acts via transcriptional activation and h acts via transcriptional repression. The fDE1 contains a binding site for a small family of orphan nuclear receptor proteins that are uniformly expressed in blastoderm embryos.
The expression pattern of ftz RNA during embryogenesis has been investigated.
Comparisons of early development to that in other insects have revealed conservation of some aspects of development, as well as differences that may explain variations in early patterning events.
In vivo crosslinking has been used to directly measure DNA binding of the homeodomain protein ftz. ftz protein binds at uniformly high levels throughout the length of their genetically identified target genes and at a lower, but significant level to genes ftz is not expected to regulate. Studies suggest that ftz and eve has similar DNA binding specificities in vivo.
In situ hybridisation using pre-embedded methods have been used to demonstrate that mitochondrial large ribosomal RNA is associated with polar granules in the pole plasm of cleavage embryos.
Transient expression assays using Ecol\CAT reporter gene constructs have been used to define the sequences responsible for the synergistic action of ftz and prd, these have been mapped to different regions of the two proteins. ftz protein has a synergistic effect on transcription of a target promoter in the presence of prd protein that is apparently entirely independent of binding of ftz protein to the promoter DNA. This synergism is dependent on the presence of homeodomain DNA binding sites in the promoter and does not occur at active promoters that are not regulated by homeodomain.
The highly complex pattern of ttk expression suggests specific functions for ttk late in development that are separate from the regulation of ftz. Ectopic ttk expression causes complete or near complete repression of ftz and significant repression of eve, odd, h and runt.
Biochemical studies led to the identification multiple DNA-binding proteins (including ftz-f1 and ttk) that regulate ftz gene expression through the proximal enhancer, to mediate stripe establishment and maintenance. DNaseI footprinting studies reveal the proximal enhancer contains a cluster of nuclear protein binding sites.
wg expression is aberrantly activated and regulated in pair rule mutant embryos.
DNA elements both 3' and 5' to the coding region that are important in proper regulation of expression are the most evolutionarily conserved regions in the vicinity of gene homologs.
The D.melanogaster ftz autoregulatory domain, AE, is a direct target for the ftz homeodomain gene product. Deletion analysis defines multiple elements redundantly involved in enhancer activity. Several of these elements are conserved in the AE homologs of D.virilis and D.hydei and in the developmentally regulated eve and Ubx genes. The AE homolog of D.virilis is functional in D.melanogaster.
Specific DNA binding is an important but not sufficient determinant of the functional specificity of ftz in vivo. Binding of ftz to homeodomain binding site BS2 of en has been studied: specificity mutations only partially reduce enhancer activity as compared to null mutations of this site.
The induction of a ftz-specific ribozyme mimics the effects of known ftz mutations. Expression of the ftz ribozyme at the blastoderm stage caused ftz-like morphological defects in the resulting first instar larval cuticles: the second thoracic segment and the odd-numbered abdominal segments are completely deleted in the most severely affected cuticles. Expression during development of the central nervous system affects the morphology and/or migration of neurons.
Expression analysed in CNS study of neuroblasts and ganglion mother cells, using a ftz-lacZ fusion gene.
Distamycin and the ftz homeodomain peptide compete for their DNA binding sites. This demonstrates that minor groove binders can compete with the binding of proteins in the major groove, providing an experimental indication for the influence of biological activities exerted by DNA ligands binding in the minor groove.
Mutational analysis of the helix-turn-helix motif has revealed a set of class-specific DNA backbone contacting residues, particularly Arg28 and Arg43 that are required for efficient target site recognition and full ftz activity both in vivo and in vitro.
Post cellularization ftz expression is repressed by ectopic eve expression, precellularization ectopic eve expression stimulates ftz expression.
Footprint analysis and tests in transformed embryos of Ubx-lacZ fusions bearing mutated footprinted regions suggest that ftz protein acts directly as a transcriptional activator of Ubx.
In csw- embryos hb remains as a posterior cap and the seventh ftz stripe expands posteriorly, both due to lack of hkb repressing activity.
Mutant analysis shows that wild type ftz function is required to set up expression of ac and sc in row D of the embryonic proneural cluster.
Pattern of hh expression in ftz mutants studied.
Apical localization of pair-rule transcripts restricts lateral protein diffusion allowing pair-rule proteins to define sharp boundaries and precise spatial domains.
The DNA binding properties of the ftz homeodomain have been studied in vitro.
Nuclear extracts prepared from developmentally staged embryos were transcriptionally active for several non-muscle genes: Tm2 non-muscle promoter, Act5C, ftz, Adh and en.
Mutations in zygotic pair rule gene ftz interact with RpII140wimp. Ecol\lacZ reporter gene constructs demonstrate that mutations of ftz interact with RpII140wimp.
The activator and repressor functions sufficient to generate a stripe pattern of transcription are encoded in the ftz promoter.
Deletions and subfragments of the ftz scaffold attached region have been analysed in yeast and Drosophila to define the sequences involved in scaffold association.
Germline transformation of ftz:lacZ promoter fusion genes demonstrate that the ftz promoter can be divided into three functional subunits (Hiromi, Cell 43: 603): an enhancer element, an element that influences neural expression and a region that is sufficient for the generation of the seven stripe pattern.
ftz mutants exhibit pattern deletions that correspond to even numbered segments.
Mutants show a deletion of all even numbered parasegments. Temperature sensitive alleles demonstrate that ftz is required for cell viability and pattern formation between 1--4 hours of embryogenesis.
In saturation mutagenesis of a protein a background of nonsense mutations can complicate genetic analysis of the resulting mutations. Methods are proposed for elimination of those molecules containing stop codons at the target codon from the pool. Application of these methods should ensure that all changes are missense mutations, thereby simplifying genetic analysis.
ftz protein distribution is altered in mutant cad embryos: stripes 2, 3 and 4 are abnormally spaced and reduced, posterior stripes stain stronger than anterior stripes.
DNAse I footprinting of ftz binding sites near the two Antp promoters identifies a consensus sequence including ATTA, as does the consensus sequence for en, eve and bcd binding sites. DNA bending is proposed as an explanation for the presence of a shared motif between proteins with divergent recognition helices. The ATTA would not directly contact amino acid side chains of the recognition helix, but would be necessary for bending the DNA around the homeodomain, perhaps facilitating protein-DNA contacts.
Deletion analysis of the ftz upstream element defines several independent regulatory units, including at least two independent enhancers. The enhancers are autoregulated independently by the wild type ftz gene product and contain multiple binding sites for purified ftz homeodomain. Results suggest that the ftz gene product is one of the trans-acting factors that acts directly to positively regulate transcription of the ftz gene.
The role of segment polarity genes in arm protein accumulation has been investigated.
ftz transcription is activated in each parasegment through the "zebra stripe" promoter region and is then inhibited selectively in the odd numbered parasegments by repressors that bind directly to elements within this promoter region.
Injection of protein synthesis inhibitors into early embryos induces expression of ftz mRNA in virtually all regions of the embryo.
A transient expression assay has been employed to investigate the potential of homeobox genes to function as transcriptional activators.
Heat shock constructs have been used to distinguish between two models that try to explain the generation of embryonic pattern: the "cell identity" and parasegmental models.
Novel ftz protein expression has been detected in very early embryos (before the cellular blastoderm stage) using a sensitive immunocytochemical staining technique.
ftz protein is phosphorylated at multiple sites, and at different subsets of these sites during different stages of development.
Genetic analysis demonstrates that ftz is not required for efficient homeotic gene expression in the visceral mesoderm.
Cotransfection assays have been used to demonstrate that the homeodomain proteins encoded by ftz can specifically activate transcription of certain promoters by acting upon a common sequence to modulate gene transcription.
ftz protein expression has been studied.
The ftz enhancer-like upstream element (USE) has been sequenced, and the binding sites for embryonic nuclear proteins within this region have been determined by in vitro DNAase I footprinting.
The expression of ftz has been used as a positional marker to investigate the relationship between the dorsoventral and anteroposterior axes in the embryo.
The pattern of ftz RNA and protein expression in blastoderm embryos with disrupted cellularisation has been studied.
ftz protein expression has been analysed in various mutants that disrupt segmentation.
The DNA sequences of the homeobox region of 11 Drosophila genes, including ftz, have been compared.
ftz transcript localization was compared to prd transcript localization.
Null loss-of-function mutations result in embryonic lethality. Animals survive to the end of embryogenesis and exhibit a pair-rule mutant phenotype in the cuticle. This same phenotype is observable in animals at the beginning of segmentation of the germ band. Prior to deposition of cuticle, ftz- animals have two rather than three mouth (gnathocephalic) segments and five as compared to ten trunk metameres. The material deleted is derived from the even-numbered parasegments, ps2 through ps12. Similar metameric deletions/fusions are seen in the neuromeres of the ventral nerve cord of the CNS. Temperature-sensitive alleles of the gene have shown that the temperature-critical period for viability and phenotype falls between 1 and 4 hours of embryogenesis with the mid-point of 2.5 hours at the blastoderm stage. The recovery of clones of ftz- cells created by X-ray-induced somatic exchange after cellular blastoderm have demonstrated that ftz+ activity is not necessary for normal cuticular morphogenesis subsequent to this point in development. In addition to these recessive null and hypomorphic alleles there are two classes of dominant gain-of-function lesions at the ftz locus. The first, ftz-Regulator of postbithorax-like, causes a variable transformation of the posterior haltere into posterior wing. The second, ftz-Ultra-abdominal-like, is associated with a patchy transformation of the adult first abdominal segment toward third abdominal identity. The former (ftzRpl) lesion also shows a recessive loss-of-function phenotype while the latter class (ftzUal) has no discernible embryonic phenotype and is homozygous viable. The fact that these dominant alleles produce mutant phenotypes that mimic lesions in the BXC has been interpreted as demonstrating a regulatory link between the segment enumeration genes and the homeotics.
The name of the locus derives from the phenotype and is Japanese for 'segment' (fushi) 'deficient' (tarazu).
