- Tools
- Downloads
- Links
- Community
- About
- Help
FB2026_01
,
released March 12, 2026
transcription factor - homeodomain - maternally transcribed gene involved in anterior patterning of the Drosophila embryo - forms a concentration gradient to specify the fate map along the anterior-posterior axis of the embryo
Please see the JBrowse view of Dmel\bcd for information on other features
To submit a correction to a gene model please use the Contact FlyBase form
AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.
Gene model reviewed during 5.49
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.50
2.4 (unknown)
2.6, 1.6 (northern blot, sequence analsyis)
None of the polypeptides share 100% sequence identity.
494 (aa)
Both the cad protein
gradient and the hb transcript expression pattern are dependant upon the
homeodomain and the PEST domain of bcd protein. Deletions and mutations of
PEST sequences in the bcd coding region resulted in an inability to repress
cad expression in the anterior region of the embryo. Similar deltions result
is a loss of hb expression between 20 and 50% egg length in the anterior
expression domain. Thus, the deletional analysis of bcd protein domains
shows that the domain that is required for translational represssion of cad
is also required for transcriptional activation of hb.
Both the cad protein gradient and the hb transcript expression pattern are dependant upon the homeodomain and the PEST domain of bcd protein. Deletions and mutations of PEST sequences in the bcd coding region resulted in an inability to repress cad expression in the anterior region of the embryo. Similar deltions result is a loss of hb expression between 20 and 50% egg length in the anterior expression domain. Thus, the deletional analysis of bcd protein domains shows that the domain that is required for translational represssion of cad is also required for transcriptional activation of hb.
bcd protein is
expressed in yeast under the control of βestradiol in order to control the
amount of bcd protein produced. Cooperative binding to bcd response regions
on various lacZ reporter constructs was studied with transcription assays, in
vitro gel shift assays and foot print analysis. The bcd responsive region of
kni was used both in vitro and in vivo to ascertain the strength of bcd
binding sites.
bcd protein regulates the expression of cad through translational repression by binding to the cad 3''UTR at specific "bicoid binding regions" (BBR). Expression pattern analysis, UV crosslink assays and Schnieder cell co-transfection assays all conclude that the homeodomain of bcd protein is necessary and suffiecient for binding to the BBR of cad transcripts. bcd protein will supress translation of "BBR-containing"mRNAs.
The expression pattern of genes downstream of bcd were analysed after egg ligation at various egg lengths. It was observed that the bcd protein gradient, as well as the cad protein gradient were blocked by egg ligation, and thus, the expression of downstream gap genes were altered. The authors suggest that alteration of the bcd protein gradient, alters the hb expression profile and in turn, through regulation by hb, Kr and kni expression domains are altered, consequently altering the domains of pair-rule gene expression.
CAT assays with bcd protein expressed in Schneider cells show that bcd activates a promoter containing three copies of a bcd consensus sequence. Through studies both in vivo and in vitro it has been shown that the activation of transcription due to bcd is dependant upon the phosphorylation state of bcd protein. Phosphorylated bcd will not activate transcription, and the phosphorylation of bcd is dependant upon tor and Raf.
Antibodies recognize a doublet of proteins of 55kD and 57kD. The appearance of two bands is thought to be due to posttranslational modification because the 5aa difference between the two bcd proteins is not enough to account for the 2-3kD size difference.
One of several products generated by alternative splicing.
bcd protein is translated from in vitro transcribed bcd mRNA in wheat germ extract and rabit reticulocyte lysate and is expressed in Drosophila Scheider cells to yeild a 58 kD protein. Exchange of the bcd 5'' UTR for Xenopus beta-globin 5'' UTR yeilds higher protein levels in these translation systems.
The bcd protein was expressed and purified from embryos, Drosophila Schneider cells, and E. coli. The bcd protein produced by embryos and Schneider cells was 58kD, while the protein from E. coli was 53kD,indicating that the protein produced in Drosophila was highly phosphorylated. Indeed, when bcd protein isolated from Drosophila embryos or cells was incubated with phosphatase prior to elecrtophoresis, the protein was resolved at 53kD.
The author compared the sequences of several Drosophila melanogater genes and one human gene with consensus RNA Recognition Motifs (RRM) to bcd protein sequence and identified a putative RRM.
Interacts with Bin1; in vitro and yeast cells (PubMed:11455422). Interacts with bin3 (PubMed:10717484).
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\bcd using the Feature Mapper tool.
The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).
Comment: anlage in statu nascendi
Comment: reference states 0-2 hr AEL
Comment: 0-3.25 hr AEL
Comment: reference states 2-4 hr AEL
Comment: 0-3.25 hr AEL
bcd transcript expression was assayed at 20oC from embryonic time 0 to 7.25 hours. The authors stated that this was a temperature correction factor of 1.7, therefore, corresponding to 0-3.25 hours of development at 25oC. At time 0 prior to egg activation bcd transcript lacks a poly-A tail. Upon activation the transcript is rapidly poly-adenylated. Maximal polyadenylation corresponds to maximal translation of the bcd protein. At approximately 2 hours post activation at 25oC significant deadenylation is observed which leads to reduced translation of bcd protein and subsequent degradation of bcd transcript.
Following injection of the full length S35 labeled bcd transcript, the transcript becomes tightly localized to the anterior cortex of the embryo, reaching between 5-10% egg length.
bcd transcripts localize as an anterior cap in mature oocytes and are found in a characteristic patchy pattern in nurse cells.
bcd transcript accumulation occurs in 4 phases during oogenesis. Between stages S6 and S9, transcripts accumulate as a ring at the anterior end of the oocyte. In stages S9-S10a follicles, they localize to the apical region of nurse cells. As nurse cells contract in stages S10b-S11, all bcd transcripts localize to the cortex at the anterior end of the oocyte. Between stage S12 and egg deposition they become localized to a spherical dorsally located region at the anterior pole. The distribution of bcd transcripts in nurse cells and the oocyte is altered in exu and swa mutants. In early embryos, bcd transcripts are restricted to the anterior pole. exu and swa mutations lead to nearly uniform distribution of bcd RNA in the early embryo while stau mutations produce a gradient of expression at the anterior pole of the embryo.
During oogenesis bcd transcript is localized to the anterior edges of the oocyte and remains localized throughout oocyte development. bcd transcript is also detected surrounding the nurse cell nuclei. In early embryos bcd transcript is detected in an "anterior cap", with strong signal present in the most anterior part of the embryo. Lower levels of bcd transcript are detected in a gradient up to 80% egg length.
The bcd-XR transcript is expressed at very low levels through all stages of development.
Comment: reference states 0-3.25 hr AEL
Comment: 2-3 hr AEL
Although bcd protein is present in the cytoplasm, it is strongly concentrated in the nucleus.
bcd protein expression was assayed at 20oC from embryonic time 0 to 7.25 hours. The authors stated that this was a temperature correction factor of 1.7, therefore, corresponding to 0-3.25 hours of development at 25oC. bcd protein was detected throughout this period, but began to decrease after 2 hours of development at 25oC, the time at which bcd transcript deadenylation became pronounced.
The bcd protein isexpressed in a gradient from the anterior tip of the embryo reaching up to 30%egg length.
bcd protein is not detected in nanosbcd.3UTR embryos.
bcd protein is distributed in an exponential concentration gradient in the early embryo with a maximum at the anterior tip, reaching background levels in the posterior third of the embryo. None is detected in oocytes.
JBrowse - Visual display of RNA-Seq signals
View Dmel\bcd in JBrowse
3-44.2
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 JBrowse 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
DNA-protein interactions: genome-wide binding profile assayed for bcd protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).
A bcd mRNA concentration gradient is formed along the cortex of the embryo by nuclear cycle 10 or the beginning of syncytial blastoderm. The gradient falls off exponentially with distance from the anterior pole and persists unchanged during nuclear cycles 10-13. During the first third of nuclear cycle 14, bcd mRNA is transported to the apical nuclear periplasm where it is degraded rapidly. bcd mRNA and stau protein co-localise and form a similar gradient. Congruence of protein and mRNA gradients at all times implies that the bcd protein gradient may derive from the bcd mRNA gradient.
DNA-protein interactions: genome-wide binding profile assayed for bcd protein in 2-3 hr embryos; see BDTNP1_TFBS_bcd collection report.
Localisation of bcd mRNA in late oocytes is maintained by continual active transport on microtubules.
The bcd gene product contains separable protein domains for transcriptional and translational regulation of target genes.
exu protein is highly enriched in the sponge bodies, subcellular structures in nurse cells. Neither the accumulation of or level of exu protein is dependent on the amount of bcd mRNA present in the ovaries. Results propose that sponge bodies are structures that, by assembly and transport of included molecules or associated structures, are involved in localisation of mRNAs in oocytes.
Regulation of cad by bcd occurs at the level of translation and depends on both the bcd homeodomain and on cis-acting sequences in the 3' untranslated region (UTR) of the cad message. The bcd homeodomain can bind specifically to these cis-acting sequences in vitro. bcd regulates cad expression by blocking translational initiation.
In embryos lacking bcd activity, as a result of mutation, the cad gradient fails to form and cad becomes evenly distributed throughout the embryo. This suggests that bcd may act in the region specific control of cad mRNA translation. In vitro studies reveal that bcd binds through its homeodomain to cad mRNA and exerts translational control through a bcd-binding region (BBR) of cad mRNA.
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.
Regions of bcd that are important for protein-protein interaction and cooperative DNA binding are defined using coimmunoprecipitation analysis. The amino terminal half of bcd interacts with another bcd molecule, but the homeodomain alone fails to interact. Mutations that affect DNA binding do not adversely affect protein-protein interaction function.
Gene product is known to regulate Kr CD (cis acting control element) expression.
Several mutations have been isolated that fail to compensate for the fate change caused by the alteration in the bcd gradient.
In embryos from mothers with extra copies of bcd, the adjustment of the fate map involves inreased apoptosis in the anterior region, allowing the development of a normally proportioned larva.
Microtubules are necessary for the localisation of bcd RNA to the anterior oocyte margin during oogenesis.
The bcd product binds DNA cooperatively in vitro with an affinity that is ten fold higher for clustered than for single sites. The cooperativity maps to the homeodomain and flanking sequences. bcd acts as a translational repressor of cad, binding the 3' untranslated region of cad. The RNA binding activity maps to the homeobox.
The products of the Taf4 and Taf6 loci serve as coactivators to mediate transcriptional activation by the bcd and hb enhancer binding proteins. A quadruple complex containing Tbp, Taf1, Taf4 and Taf6 mediates transcriptional synergism by bcd and hb, whereas triple Tbp-Taf complexes lacking one or other coactivator failed to support synergistic activation. The concerted action of multiple regulators with different coactivators helps to establish the pattern and level of segmentation gene transcription during development.
Mutagenesis studies in combination with protein binding experiments and reconstituted transcription reactions identified two independent activation domains of bcd that target different coactivator subunits (Taf4 and Taf6). Both coactivators are required for bcd to recruit the Tbp-Taf complex to the promoter and direct synergistic activation of transcription. Contact between multiple activation domains for bcd and different targets within the TfIID complex can mediate transcriptional synergism.
Embryos with a reduced number of cells in the abdominal primordia have been used to determine whether they can regulate towards the normal during subsequent cell growth, no evidence was found for regulation of cell number.
bcd DNA binding specificity distinguishes among related binding sites by a base-specific contact between recognition helix residue 9 and base pair 7. DNA site specificity is necessary for bcd's action as a morphogen. bcd's ability to activate gene expression depends on the distance between its binding sites.
Among Drosophila species there is substantial conservation of components acting in bcd mRNA localization.
Fractionation procedure has been used to examine the cytoskeletal association of localised bcd RNA in egg chambers.
A PCR based assay has been used to determine whether the encoded mRNAs exhibit changes in poly(A) status upon translational activation.
The introduction of a membrane barrier across the embryo by ligation of the egg alters the bcd protein gradient.
In its anterior domain (labral primordia) cnc is activated by bicoid and torso maternal pathways.
An artificial bcd responder gene composed of three bcd consensus binding sites driving Ecol\lacZ expression is activated by bcd and repressed by tor. This repression does not require tll or hkb. Phosphorylation resulting from the tor signal transduction pathway down-regulates transcriptional activation by the bcd morphogen. The normal phosphorylation changes that affect bcd during development do not occur in tor mutant embryos.
Bicoid sequences were used to mislocalise nanos in experiments that determined that localisation of nanos RNA controls embryonic polarity.
The 3' untranslated region of bcd contains a conserved motif involved in mRNA localization.
bcd is responsible for the activation of tll transcription at the anterior pole in terminal mutant embryos and plays a critical role in the formation of the tll stripe.
The gene products of bcd, hb, Kr and gt all bind within the 480bp region that is necessary and sufficient for the expression of eve stripe 2. Activation depends on cooperative interactions between hb and bcd. Forming the posterior border of the stripe involves a delicate balance between Kr repressor and bcd activator.
Apical localization of pair-rule transcripts restricts lateral protein diffusion allowing pair-rule proteins to define sharp boundaries and precise spatial domains.
bcd is involved in the pathway that leads to the activation of Sxl in the anterior region. Embryos carrying four doses of maternal bcd show an expansion of the anterior fate map. If the embryos also lack run activity the anterior domain of Sxl expression extends posteriorly so causing the central domain of Sxl expression to shrink.
The bcd gradient can only activate the hb gene in the anterior part of the embryo. The anterior domain of gt expression is most likely directly controlled by bcd.
The interaction of the bcd homeodomain with mutated bcd binding sites has been studied using assays in yeast. Base pair 7 on the bcd recognition helix is important for bcd binding, base pairs 8 and 9 influence recognition.
gt may be a target for the bcd morphogen in the embryo.
bcd mRNA localization requires the function of at least three genes, the exu gene acts earliest in the pathway. exu acts in initiating bcd mRNA localization but does not play a persistent role in that process.
Mutations in maternal anterior class gene bcd interact with RpII140wimp.
Microtubules are required for establishing and maintaining the position of bcd mRNA in nurse cells and the oocyte. When microtubule inhibitors are removed from the egg chamber bcd mRNA is relocalized. Taxol treatment results in the localization of bcd mRNA at ectopic positions in the oocyte.
The eve stripe 2 is lost in bcd- embryos.
bcd nos response elements (NREs) confer nos sensitivity on maternal hb mRNA.
The effects of an altered nucleocytoplasmic ratio on transcripts that normally undergo changes in transcript pattern in cell cycle 14 is studied. A delay in the degradation of the bcd maternal message is correlated with a decrease in nuclear density and a change in the cell cycle program.
The bcd mRNA leader sequence is not required for transcript localization nor for the translational block of bcd mRNA during oogenesis. The concentration gradient, not the existence of different forms of bcd protein, is responsible for specifying subregions of the embryo.
bcd mutants exhibit deletion of the head and thorax, the acron is transformed to the telson.
Mature follicles are immunologically stained for asymmetric distribution of ecdysteroid-related antigen. During late oogenesis localisation of the antigen changes dramatically suggesting the antigen plays a role in early embryogenesis and, perhaps, in pattern formation.
Maternal effect mutations disrupt the anteroposterior or dorsoventral pattern of the early embryo. Examination of an allelic series of hypomorphic alleles reveals a graded requirement for bcd activity along the anteroposterior axis. Deletion of anterior head structures is associated with all bcd mutations, further posterior deletions depend on the severity of the mutation. Analysis of a temperature sensitive allele demonstrates the time of bcd function is from pole cell formation to the cellular blastoderm.
bcd gene function is not required for vas protein localization.
bcd genes from several Drosophila species were isolated and analyzed to define more precisely the cis-acting bcd mRNA localization signal. Each has the potential to form an extensive, stereotypical secondary structure. These results suggest that the cis-acting element responsible for anterior localization of bcd mRNA is, or is part of, the secondary structure.
The bcd gene of D.pseudoobscura.pseudoobscura has been cloned and sequenced for use as a tool for identifying important functional domains within the transcription unit.
Double abdomen induction in bcd is more efficient by genetic methods, within bcd mutant embryos, than removal of anterior cytoplasm.
Multiple steps are involved in the localization of bcd RNA at the anterior pole of the oocyte.
In bcd embryos the anterior anlagen are missing while the posterior pattern is enlarged and spread to the anterior.
Increases or decreases in bcd protein levels in a given region of the embryo cause a corresponding posterior or anterior shift of anterior anlagen in the embryo.
The bcd gene product is a 55kD protein translated soon after egg deposition. The distribution of protein in wild type embryos can be explained by models involving local source, diffusion and dispersed decay. Protein is detectable at up to 30% egg length explaining how long range effects can be observed in bcd- embryos.
Maternal-effect lethal mutations showing defective head and thorax development. Females homozygous for strong alleles produce embryos in which head and thorax are replaced by duplicated telson, including anal plates, tuft, spiracles, and filzkorper; however, no pole cells formed at the anterior end. Deletions and fusions of anterior abdominal segments and occasionally anterior abdominal segments in reversed polarity are also observed. Strong alleles amorphic based on phenotypic similarities of embryos produced by homozygous and hemizygous females. Weak alleles result in pattern defects in heads of embryos; lack only labral derivatives (median tooth, dorsal bridge); intermediate weak genotypes produce reduced head but retain normal thoracic development; intermediate strong produce further reduction of head, deletion of second and third and reduction of first thoracic dentical belts; thoracic segments fused. Partial rescue of embryonic phenotype effected by injection of cytoplasm (5% of volume) from the anterior ends of unfertilized wild-type eggs into the anterior pole of newly fertilized eggs of bcd mothers; injection into ectopic sites stimulates differentiation of anterior structures at site of injection; efficiency proportional to number of bcd+ alleles carried by cytoplasm donor. Phenocopies result from leakage of 5% of egg volume from anterior perforation of normal embryos. The distance of the head fold at gastrulation is proportional to the number of bcd+ alleles in the maternal genotype. bcd mRNA appears as a flattened disc plastered to the anterior extremity of early embryos; by the time of pole cell migration it has become localized to the clear cytoplasm at the periphery, forming a cap over the anterior end of the egg and is distributed in a steeply decreasing gradient such that 90% of the RNA is in the anterior 18% of egg length; by nuclear cycle 14 the RNA begins to disappear and becomes undetectable by midway through cellularization. bcd protein on the other hand forms a shallower gradient in which 57% of protein is in the anterior 18% of egg length and the gradient doesn't reach baseline until the posterior 30% of egg length; the gradient forms from two to four hours after oviposition in both fertilized and unfertilized eggs and except during mitosis is concentrated in nuclei; diffusion postulated to account for the establishment of the protein gradient following translation from anteriorly anchored RNA. Protein levels decrease during cellularization, although some nuclear staining persists until the end of germ-band elongation. bcd transcript first detectable in the ovaries of bcd females; forms a ring around the anterior margin of the developing oocyte in stages 5 and 6; in stages 9 and 10 nurse-cell accumulation observed to be localized toward the periphery of the cyst; by stage 12 the nurse cells have emptied their contents into the oocyte and the bcd transcript appears as an anterior cap (St. Johnston, Driever, Berleth, Richstein and Nusslein-Volhard, 1989). No evidence of translation of bcd protein during oogenesis. Formation of the bcd gradient is regulated by three maternally active genes exu, swa and stau; exu appears necessary for nurse cell accumulation; swa is required for anterior localization of bcd mRNA in the oocyte; and stau appears to be involved in RNA localization in the embryo. A defect in any of these functions results in little or no gradient of bcd activity. bcd in turn appears to control the activity of anterior gene activity; specifically the anterior pattern of hb expression is not observed and is replaced by a mirror-image posterior hb stripe in bcd- embryos (Tautz, 1988; Schroder, Tautz, Seifertz and Jackle, 1988).
Source for identity of: bcd CG1034
