bagpipe REGULATION Transcriptional Regulation Sloppy paired (Slp) and Even-skipped are involved in cell fate determination and segmentation in the Drosophila mesoderm. The primordia for heart, fat body, and visceral and somatic muscles arise in specificareas of each segment in the Drosophila mesoderm. The primordium ofthe somatic muscles, which expresses high levels of twist, a crucial factor of somaticmuscle determination, is lost in sloppy-paired mutants. The effect of slp on Twist levels is probably partly, but not completely mediated by wg. wg mutant embryos show a premature and ectopic decay of Twist, but not to the same degree as seen in slp embryos. Whereas patches of cells expressing high levels of Twist are initially established in wg mutant embryos, no Twist is seen in the trunk region of slp mutant embryos after stage 11. At the same time that twist expression is lost in slp mutants, the primordiumof the visceral muscles is expanded (Riechmann, 1997).Ectodermal Dpp is required for the maintenance of mesodermal tinman, which in turn activates bap expression in the eve domain. The visceral muscle and fat body primordiarequire even-skipped for their development and the mesoderm is thought to beunsegmented in even-skipped mutants. However, it has been found that even-skipped mutantsretain the segmental modulation of the expression of twist. Both the domain ofeven-skipped function and the level of twist expression are regulated by sloppy-paired, and eve serves reciprocally to regulate the slp domain.sloppy-paired thus controls segmental allocation of mesodermal cells to different fates (Riechmann, 1997). In strong tin mutants, bap expression is almost completely abolished in the middle body region, but continues in the stomodeal and proctodeal mesoderm. Schnurri, a zinc finger transcription factor, is the first identified downstream component of the signal transduction pathway used by DPP and its receptors. Absence of schnurri function blocks the expanded expression of bagpipe in the embryonic mesoderm caused by ectopic dpp expression, illustrating a possiblerequirement for shn function in regulating bagpipe, downstream of dpp (Staehling-Hampton, 1995).bagpipe expression in mesodermal tissue overlying foregut and hindgut, both considered to be ectodermal derivatives, is regulated by wingless and hedgehog activities in the underlying gut epithelium. The mesodermal layer of the fore- and hindgut is gradually assembled around the invaginating stomodeal and proctodeal tubes. bagpipe is strongly expressed in mesodermal cells on top of the proctodeum that will give rise later to the muscles of the hindgut. The expression domain then splits to give rise to two subdomains, one around the future small intestine and the other around the future rectum of the hindgut. Later bagpipe expression appears in a continuous expression domain. In both wg and hh mutants, bap expression is reduced or absent in the visceral mesoderm primordia of the developing hindgut. Similar results were obtained for the foregut (Hoch, 1996).In odd-paired mutants the visceral mesoderm is interrupted, evidently due to abnormal expression of bagpipe (Cimbora, 1995).Inactivation of either the secreted protein Wingless (Wg)or the forkhead domain transcription factor Sloppy Paired(Slp) has been shown to produce similar effects in thedeveloping Drosophila embryo. In the ectoderm, both geneproducts are required for the formation of the segmentalportions marked by naked cuticle. In the mesoderm, Wgand Slp activities are crucial for the suppression of bagpipe(bap), and hence visceral mesoderm formation, and thepromotion of somatic muscle and heart formation withinthe anterior portion of each parasegment. During these developmental processes, wg and slp act in a common pathway in which slp serves as adirect target of Wg signals that mediates Wg effects in bothgerm layers. Evidence has been found that the induction ofslp by Wg involves binding of the Wg effector Pangolin(Drosophila Lef-1/TCF) to multiple binding sites within aWg-responsive enhancer, located in 5' flankingregions of the slp1 gene. Based upon genetic andmolecular analysis, it is concluded that Wg signaling inducesstriped expression of Slp in the mesoderm. Mesodermal Slpis then sufficient to abrogate the induction of bagpipe byDpp/Tinman, which explains the periodic arrangement oftrunk visceral mesoderm primordia in wild type embryos.Conversely, mesodermal Slp is positively required,although not sufficient, for the specification of somaticmuscle and heart progenitors. It is proposed that Wg-inducedslp provides striped mesodermal domains with thecompetence to respond to subsequent slp-independent Wgsignals that induce somatic muscle and heart progenitors.It is also proposed that in wg-expressing ectodermal cells, slpis an integral component in an autocrine feedback loop ofWg signaling (Lee, 2000). In Drosophila, trunk visceral mesoderm, a derivative of dorsal mesoderm, gives rise to circular visceral muscles. It has been demonstrated that the trunk visceral mesoderm parasegment is subdivided into at least two domains by connectin expression, which is regulated by Hedgehog and Wingless emanating from the ectoderm. These findings have been extended by examining a greater number of visceral mesodermal genes, including hedgehog and branchless. Each visceral mesodermal parasegment appears to be divided in the A/P axis into five or six regions, based on differences in expression patterns of these genes. Ectodermal Hedgehog and Wingless differentially regulate the expression of these metameric targets in trunk visceral mesoderm. hedgehog expression in trunk visceral mesoderm is responsible for maintaining its own expression and con expression. hedgehog expressed in visceral mesoderm parasegment 3 may also be required for normal decapentaplegic expression in this region and normal gastric caecum development. branchless expressed in each trunk visceral mesodermal parasegment serves as a guide for the initial budding of tracheal visceral branches. The metameric pattern of trunk visceral mesoderm, organized in response to ectodermal instructive signals, is thus maintained at a later time via autoregulation, is required for midgut morphogenesis and exerts a feedback effect on trachea and ectodermal derivatives (Hosono, 2003). Metameric RNA expression of bnl, which encodes a ligand forBreathless FGF receptor, is first observed as 12 patches at mid stage 11. bnl RNAexpression becomes homogeneous and then diminished during stage 12. tin is a homeobox gene that is required for dorsal mesodermal development. At early stage 10, tin is expressed throughout thedorsal mesoderm from which VM is derived. Metameric Tin expression becomesevident by early stage 11. Tinexpression decreases during stage 12. Expression of bap, anotherhomeobox gene required for VM development, can be monitored by bap4.5#230; (bap-lacZ). Staining for Tin and bap-lacZ or bnl RNAindicates thattin, bap and bnl are co-expressed in VM-PS3-12 during stage11; in VM-PS2, only bnl is expressed. Stage 11-12 VM alsostains for Tin and VM-hh-lacZ. Tin andVM-hh-lacZ expression partially overlaps. VM-hh expressionin the anterior terminal region of VM-PSs indicates that eachtin/bnl/bap trio expression domain straddles the VM-PS boundary (Hosono, 2003). In summary, VM-PSs in thorax and abdomen, respectively, are subdivided into five or six regions with respect to differential expression ofVM-metameric genes at stages 11-12. Detailed analysis of VM-hh, bnl, tinand bap expression in addition to con indicates that trunkvisceral mesodermal genes are classified into three distinct groups -- tin/bnl/bap, VM-hh and con -- and each VM-PSis subdivided into five or six regions, which become apparent during mid stage 11to stage 12 (Hosono, 2003). VM is presently considered to develop in two steps under the control ofectodermal Hh and Wg signals. First, by stage 10 (when four mesodermalprimordia have become specified), VM competent or bap expressionregions are promoted by hh but repressed by wg, via a directtargetor, slp. The second surge of hh and wg activity atstages 10-11 is responsible for subdividing VM-PSs into two regions:con positive and negative. These results indicate that the expression of four other VM-metameric genes, hh, tin, bnl and bap, is alsoregulated by the second surge of hh and wg activity atstages 10-11 (Hosono, 2003).In view of morphological changes in a VM competent region and considerationof these findings on VM gene regulation, the following model for VM-PS cellspecification is proposed. At stage 10 to early stage 11, anterior terminal cells of VM-PSs arepresumed to be situated near an ectodermal AP border, where they arecapable of continuously receiving Wg and Hh signals, and Wg confers competenceon these cells to express tin/bnl/bap. Wg and Hh are responsible forinducing VM-hh, and Hh, for con expression. In theanterior-most cells, con expression is reduced, which would beexpected in view of repression by high Wg signal. The different thresholds ofhh for con and VM-hh expression may explain why thecon area expands more posteriorly compared with that ofVM-hh. Posterior terminal VM cells, when formed, are situated farfrom Wg expressed on the ectodermal PS border. But as they migrateposteriorly and close to the posteriorly neighboring AP border by early stage11, they become capable of receiving Wg and acquire competence to expresstin/bnl/bap. Thus, thetin/bnl/bap domain would appear regulated by spatially and temporallydistinct Wg signals. The two-step induction of tin/bnl/bap expressionis supported by experiments using the wgts mutant, where,either posterior or anterior expression within one patch can be differentially turned off. Indeed, a stepwise activation oftin/bnl expression is seen in VM-PSs around stage 11. tinand bnl metameric expression became apparent almost simultaneously atmid-stage 11, and preliminary experiments have shown that neither tinnor bnl misexpression can induce the ectopic expression of anyother metameric genes examined here. Thus, tin and bnlexpression might be initiated in a mutually independent manner (Hosono, 2003). Targets of Activity tinman and bagpipe, two homeobox-containing genes, play important roles during the specification of the midgut visceral musculature from the mesoderm during Drosophila embryogenesis. Expression of tinman in the dorsal mesoderm activates the expression of the bagpipe gene in segmental subsets of those cells, which then become determined to form the midgut visceral mesoderm. Understanding how the bagpipe gene affects this specification requires the isolation andcharacterization of its downstream target genes. Using an enhancer trap line that expresses its marker in the midgut visceral mesoderm, a novel gene (vimar) has been cloned and characterized that is expressed embryonically in the midgut and hindgut visceral mesoderm, as well as in the CNS and PNS. The expression of this gene in the midgut visceral mesoderm initiates shortly after bagpipe expression and depends on bagpipe function. Maternal and zygotic transcripts are produced from this gene by alternative polyadenylation, and encode the same 634-amino acid protein. The Vimar protein contains 15 tandem copies of the Armadillo repeat, a protein interaction domain, and is similar to mammalian Smg guanine dissociation stimulator (GDS) protein, which stimulates the activity of a number of different p21 small G-proteins, including Rap1, K-Ras, RhoA and Rac1. The Smg GDS protein is composed almost entirely of 11 tandem copies of an Armadillo repeat. No detectable abnormalities with respect to the visceral mesoderm and gut constrictions are observed in vimar mutants. These results, together with the observed postembryonic lethality of vimar mutations, indicate that vimar is one of the bagpipe target genes that are required for normal development and differentiation of the midgut visceral mesoderm (Lo, 1998). The subdivision of the lateral mesoderm into a visceral (splanchnic) and a somatic layer is a crucial event during early mesodermdevelopment in both arthropod and vertebrate embryos. In Drosophila, this subdivision leads to the differential development of gutmusculature versus body wall musculature. biniou, the sole Drosophila representative of the FoxF subfamily of forkhead domain genes, has a key role in the development of the visceral mesoderm and the derived gut musculature. biniou expression is activated in the trunk visceral mesoderm primordia downstream of dpp, tinman, and bagpipe and is maintained in all types of developing gut muscles (Zaffran, 2001).bagpipe-expressing domains are defined by the intersecting dorsal activities of dpp/tin, which act positively, and segmentally modulated activities of wg/slp, which have repressing effects. bin alsorequires tin activity for normal expression in the trunk visceral mesoderm primordia. Whereas bap expression is virtually absent in these cells upon loss of tin activity, residual bin expression is observedin small clusters of cells. To test the possibility that residualexpression of bin in tin mutant embryos is due todirect inputs from Dpp, bin expression was examined in embryosin which dpp expression was induced ectopically in the entiremesoderm. Ectopic dpp in a wild-type background, which causestin expression to be expanded ventrally, resultsin an analogous expansion of the bin domains. Notably, ventral expansion of the bin domains is also observed upon ectopic dpp expression in the absence of tin activity, although the domains are narrow. Thus, Dpp is able to induce bin in the absence of tin, although tin activity is required for normal expression levels. The residual expression of bin in tin mutant embryos is unstable and not maintained in later stages of development (Zaffran, 2001).Similar to tin, bap activity is also required fornormal bin expression. This result is inagreement with the temporal sequence of bap and binexpression and with the observed expansion ofbin throughout most of the dorsal mesoderm upon ectopicbap expression in the mesoderm. These data suggestthat bin is furthest downstream within a mesoderm-intrinsic cascade of gene activation: twist -> tin -> bap -> bin.Moreover, bin itself is required for normal binexpression. Although bin expression initiates normally instage 10 bin mutant embryos, it disappears at early stage 11 in the trunk visceral mesoderm primordia of bin mutants,except for those in PS1 and 2. binexpression in these two parasegments is also less sensitive to the lossof tin and bap activity. Furthermore, theexpression of bin in foregut, hindgut, and caudal visceralmesoderm does not depend on any of the genes examined in the present study (Zaffran, 2001).Whereas the above data show that maintenance of bin expressionin most of the presumptive trunk visceral mesoderm requires positiveautoregulation, they do not establish whether this autoregulatory loopis direct or indirect. Of note, maintenance of bap during stage 11 (but not its initiation during stage 10) also requires bin activity. Therefore, it is possible that, at least during stage 11, bin and bap maintaineach other's expression through a cross-regulatory feedback loop (Zaffran, 2001). The NK homeobox gene bagpipe and the FoxF fork head domain gene biniou have been identified as essential regulators of visceralmesoderm development in Drosophila. Additional genetic and molecular information is presented on the functions of these two genes during visceralmesoderm morphogenesis and differentiation. Both genes are required for the activation of ß3Tub60D in the visceral mesoderm. A 254 bp derivative of a previously defined visceral mesoderm-specific enhancer element, vm1, from ß3Tub60D contains one specific in vitro binding site for Bagpipe and two such sites for Biniou. While the wild-type version of the 254 bp enhancer isable to drive significant levels of reporter gene expression within the entire trunk visceral mesoderm, mutation of either the Bagpipe or the Biniou bindingsites within this element results in a severe decrease of enhancer activity. Moreover, mutation of all three binding sites for Bagpipe and Biniou,respectively, results in the complete loss of enhancer activity. Together, these observations suggest that Bagpipe and Biniou serve as direct, partiallyredundant, and tissue-specific activators of the terminal differentiation gene ß3Tub60D in the visceral mesoderm (Zaffran, 2002). To test whether the expression of ßTub60D in the trunk visceral mesoderm depends on the activity of two known visceral mesoderm regulators, bap and bin, ßTub60D protein expression was examined in embryos that were mutant for the respective gene. In addition, the embryos carried a bap-lacZ transgene as an independent marker for the early visceral mesoderm which; in a wild-type background bap-lacZ is co-expressed with ß3 tubulin. In embryos lacking bap, ß3 tubulin expression is severely reduced in the visceral mesoderm and at early stage 12 only trace amounts remain detectable in this cell layer. Likewise, loss of bin activity also results in an almost complete loss of ß3 tubulin expression in the visceral mesoderm layer. These data show that the activities of both bap and bin are required for normal ß3-tubulin expression in the trunk visceral mesoderm (Zaffran, 2002).A visceral mesoderm-specific enhancer element from the ßTub60D gene, vm1, has been described that is contained in the reporter construct pWHß3-14 and consists of 515 bp of enhancer sequences from the first intron of this gene (+3154 to +3669). While two Ubx binding sites within this enhancer are involved in increasing enhancer activity within parasegments (PS) 6 and 7, bap and/or bin may act as direct regulator(s) of the broad basal activity of this enhancer in the entire trunk visceral mesoderm. To test this possibility a derivative of pWHß3-14, in which the Ubx sites were deleted (pWHß3-14/DeltaUbx1+2), was crossed into bap and bin mutant backgrounds. While in the wild-type background this enhancer derivative is driving significant (though anteroposteriorly graded) levels of ßgal expression in a continuous row of visceral mesoderm cells, in a bap null mutant background enhancer activity is completely lost in this tissue. Likewise, a strong reduction of enhancer activity driven by pWHß3-14/DeltaUbx1+2 is also observed in a bin null mutant background, although in this case some residual visceral mesoderm cells are still expressing low levels of the reporter gene (Zaffran, 2002).In order to clarify whether these genetic interactions reflect any direct interactions of the bap or bin products with vm1 enhancer sequences in vitro DNA-binding experiments were performed with the two proteins. DNaseI protection assays with bacterially expressed Bin fusion proteins revealed two strongly protected sequences, termed BIN-I and BIN-II, within vm1. Closer inspection of these sequences showed that BIN-I contains overlapping tandem copies and BIN-II a single copy of a canonical binding motif for fork head domain proteins. The specificities of these in vitro binding activities are further corroborated by the results from gel mobility shift experiments. In particular, these data show that both BIN-I and BIN-II oligonucleotides can compete for binding of Bin to vm1, whereas analogous oligonucleotides in which the canonical fork head domain binding sequence was mutated fail to compete (Zaffran, 2002).Bap fusion proteins also produce a strongly protected region in DNaseI footprinting experiments. The protected sequence contains an overlapping tandem repeat of a canonical NK-homeodomain binding motif, which has been shown to bind Tinman. Indeed, the footprints produced with Bap and Tin on this sequence are almost indistinguishable (Zaffran, 2002).In preparation for functional tests of the Bin and Bap binding sites in vivo, a shorter version of vm1, termed ß3-17, was generated that lacks 5' and 3' sequences that have been shown to be dispensable for driving basal levels of visceral mesoderm expression (+3252 to +3506). As predicted, ß3-17-driven ßgal expression occurs in a uniform pattern and at intermediate levels within the visceral mesoderm. Next the effects of mutant Bin and Bap binding sites on the in vivo activity of the ß3-17 enhancer element were tested. Mutation of either BIN-I (ß3-17 bin-Imt) or BIN-II ß3-17 (bin-IImt) results in a strong decrease of ß3-17 enhancer activity. Although it was expected that the activities of BIN-I and BIN-II may be partially redundant, simultaneous mutation of both binding sites did not result in a significant reduction of enhancer activity beyond the levels seen with mutations in either binding site alone, particularly BIN-II, (ß3-17 bin-I+IImt) (Zaffran, 2002).Mutation of the Bap binding site also results in a strong reduction but not a complete loss of enhancer activity within the visceral mesoderm. To determine whether the residual enhancer activity of the mutated elements is due to functional redundancy between the Bin or Bap binding sites the effects of mutations in all three binding sites were tested. Simultaneous disruption of all Bin and Bap binding sites within the ß3-17 enhancer element results in the complete loss of enhancer activity, thus confirming that Bin and Bap have partially redundant roles in activating the vm1 enhancer of ßTub60D (Zaffran, 2002).The residual enhancer activity upon mutation of Bin or Bap binding sites is largely observed in the middle portion of the visceral mesoderm, suggesting the influence of spatially restricted regulator(s). Indeed, the close spatial correlation between residual enhancer activity and Dpp-signaling activity as well as the presence of putative Smad binding sites within vm1(+3265: GGGCCG; +3289: CAGAC; +3431: CAGACGGCAGAC) suggests a role for direct inputs from Dpp in the regulation of vm1 enhancer activity. Thus, Smad complexes and Bap bound to vm1 sequences may act in a synergistic fashion, a situation that may be analogous to the synergistic activity of Smad and Tin during the induction of the Dpp-responsive enhancer of the tin gene. However, the fact that this effect is only observed with a weakened version of the enhancer indicates that the Dpp-input plays a minor role during the normal activation of the ßTub60D gene in the visceral mesoderm. Additional inputs, which may also be insignificant for ßTub60D regulation in the normal situation, could come from Wg and/or Hh and result in low levels of metameric expression with weakened enhancer constructs (Zaffran, 2002).Activation of the vm1 enhancer during stage 11 is restricted to the ventral row of visceral mesodermal cells, but is missing in the remaining cells of this tissue that also express Bap and Bin. Hence, the combination of Bap and Bin is required, but not sufficient for activating ßTub60D expression through vm1. Previous observations have shown that the region defined by deletion 3 (e3, +3439 to +3471), which neither contains Bap nor Bin binding sites, is also required for normal enhancer activity. Therefore, this sequence may be a target of an as yet unknown activity within the ventral row of visceral mesodermal cells that is required in combination with Bap and Bin to trigger vm1 activation. Recent reports have shown that these ventral cells are the equivalent of founder cells in the visceral mesoderm; these cells subsequently fuse with adjacent dorsal cells into binucleate syncytia. Similar to the expression of dpp in PS 7 of the visceral mesoderm, vm1-lacZ expression spreads throughout the visceral mesoderm only upon fusion of founders with fusion-competent cells (Zaffran, 2002).Combined with previous data, the current results define a continuous regulatory cascade of gene activation that initiates with the regulation of genes which pattern the early mesoderm; this process concludes with the activation of a terminal differentiation gene in the visceral mesoderm. Specifically, this pathway involves the activation of tin by twist, followed by the induction of dorsal mesodermal tin by dpp, then activation of bap by tin and dpp, activation of bin by bap and dpp, and finally activation of ßTub60D by the combined action of bap and bin. A second gene that is activated at the end of this cascade in the visceral mesoderm with a similar temporal, albeit more restricted spatial pattern as compared to ßTub60D, is dpp. In the case of dpp, a visceral mesoderm-specific enhancer requires only Bin, but not Bap, as a direct activator. Hence, genes controlling morphogenesis or differentiation of the visceral mesoderm differ in their requirement for either one or both of the ubiquitously distributed visceral mesoderm activators, Bap and Bin, as direct regulators. These differences may depend on the particular involvement of additional regulators, which in the case of dpp includes spatially-restricted activities such as Ubx, that may obviate a requirement for Bap in addition to Bin as a direct activator (Zaffran, 2002).Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network: Combinatorial action of Biniou and BagpipeSmooth muscle plays a prominent role in many fundamental processes and diseases, yet understanding of the transcriptional network regulating its development is very limited. The FoxF transcription factors are essential for visceral smooth muscle development in diverse species, although their direct regulatory role remains elusive. A transcriptional map of Biniou (a FoxF transcription factor) and Bagpipe (an Nkx factor) activity is presented as a first step to deciphering the developmental program regulating Drosophila visceral muscle development. A time course of chromatin immunoprecipitatation followed by microarray analysis (ChIP-on-chip) experiments and expression profiling of mutant embryos reveal a dynamic map of in vivo bound enhancers and direct target genes. While Biniou is broadly expressed, it regulates enhancers driving temporally and spatially restricted expression. In vivo reporter assays indicate that the timing of Biniou binding is a key trigger for the time span of enhancer activity. Although bagpipe and biniou mutants phenocopy each other, their regulatory potential is quite different. This network architecture was not apparent from genetic studies, and highlights Biniou as a universal regulator in all visceral muscle, regardless of its developmental origin or subsequent function. The regulatory connection of a number of Biniou target genes is conserved in mice, suggesting an ancient wiring of this developmental program (Jakobsen, 2007; full text of article). The dynamic enhancer binding of Biniou suggested that the timing of Biniou occupancy is important for the timing of enhancer activity. To assess this in vivo, a number of regions from each of the three temporal clusters were linked to a GFP reporter. The timing of enhancer activity was assayed in vivo by in situ hybridization in transgenic embryos, to avoid time delays due to GFP protein folding and protein perdurance. All regions examined drive expression in a subset of Biniou-expressing cells and recapitulate all or part of the target genes' expression. This study focused on their temporal activity (Jakobsen, 2007). The initiation of enhancer activity closely matches the first time point of Biniou binding for >90% of enhancers examined (10 of 11 CRMs). The early-bound enhancers (ttk, fd64a-e, lame duck (lmd), bap3) drive expression at stages 10-11, reflecting the binding of Biniou at these stages of development. Similarly, all four continuous-bound enhancers (HLH54F, otk, mib2, bap-FH) initiate expression at the first time period when Biniou binds. The two late-bound enhancers, in contrast, do not initiate expression at stages 10 or 11 of development, matching the lack of Biniou binding during these stages. Instead, the expression of the fd64a late enhancer initiates at stage 13, while the ken enhancer initiates VM expression at stage 14. This shift in the initiation of activity mirrors Biniou binding to these enhancers at stages 12-13 and 13-14, respectively. The only exception is the CG2330 enhancer, which initiates expression at stage 11, while Biniou enhancer binding was first detected at stage 13-14). As the expression of endogenous CG2330 does not initiate until stage 13, the apparent discrepancy in enhancer activity may simply reflect the exclusion of some regulatory motifs within the limits of the cloned region (Jakobsen, 2007). Remarkably, the duration of enhancer activity is also tightly correlated with the time span of Biniou binding in 10 out of 11 CRMs examined. This is particularly striking in the early-bound enhancers: When Biniou ceases to bind to these CRMs (lmd, ttk, fd64a early, and bap3), their ability to regulate expression is lost. The converse is also true. Continuous Biniou binding correlates with continuous enhancer activity, specifically for bap-FH, HLH54F, and otk. The exception is the mib2 enhancer. In the context of this module Biniou binding it is not sufficient to maintain enhancer activity in the VM at late developmental time points (Jakobsen, 2007). Taken together, these data indicate that the timing of Biniou enhancer binding is predictive for temporal enhancer activity in the large majority of cases (Jakobsen, 2007). All 11 Biniou target enhancers examined in vivo regulate expression in more restricted patterns than Biniou itself. Since Biniou has broad temporal and spatial expression, additional regulatory inputs must refine Biniou's activity in a combinatorial manner. To identify other factors that may impinge on these enhancers overrepresented motifs were sought within the Biniou-bound CRMs. This analysis identified significant enrichment of a number of TF motifs. Of particular interest is the differential enrichment of motifs for Biniou, Mef2, and Nkx family proteins, Bap and Tin, between the three temporal classes of enhancers (Jakobsen, 2007). Interestingly, the Bap motif is specifically enriched in the early-bound enhancers, and not in the continuous- or late-bound group. Tin motifs are also enriched in the early-bound group. This is in agreement with the transient expression of both TFs in the trunk VM during early stages development, and suggests that one or both of these TFs could impart some of the specificity for Biniou transient binding to these enhancers (Jakobsen, 2007). The Mef2 motif is highly enriched in both early- and continuous-bound enhancers, but not in late VM enhancers. This was surprising since Mef2 regulates muscle differentiation genes and is therefore expected to coregulate late-bound enhancers. To substantiate this further, in vivo bound Mef2 enhancers were compared with the Biniou-bound enhancer regions at the same stages of development. In agreement with the motif enrichment, there is substantial combinatorial binding of Biniou and Mef2 on the early-bound and continuous-bound enhancers: 65.1% and 50.4%, respectively. In contrast, only 20.1% of the late Biniou-bound enhancers are cobound by Mef2. The same trend holds true in the other direction: There is no significant Biniou binding to many enhancers regulated by Mef2 at late developmental stages (e.g., the Mef2-bound enhancers for the contractile proteins Mhc, Mlc1, and Mlc2). This indicates that the VM may have two largely independent differentiation programs, one governed by Mef2 regulating more general muscle contractile proteins, and a second more VM-specific program driven by Biniou (Jakobsen, 2007). Biniou consensus motifs are overrepresented in all three classes of temporal enhancers, providing global confirmation of the specificity of the ChIP-bound regions. Biniou motifs are particularly highly enriched in the continuous-bound and late-bound enhancers. This highlights a prominent role for Biniou in regulating enhancer activity at late stages of VM development. The inability of Biniou to bind to the late enhancers at early stages of development implies a mechanism that either blocks Biniou binding to these CRMs early in development or enhances Biniou's binding later in development. This could be mediated by many different mechanisms. Binding of the C. elegans FoxA TF, PHA-4, to early versus late pharyngeal muscle enhancers is primarily determined by the presence of high or low affinity binding sites, respectively (Gaudet, 2002). No apparent differences were detected in the Biniou motif between the early- and late-bound VM enhancers, and therefore a combinatorial model is favored with as-yet-unidentified cofactors. This is strongly supported by the restricted expression of all Biniou-bound CRMs examined, necessitating extensive combinatorial regulation to limit their activity (Jakobsen, 2007). The specific enrichment of Bagpipe motifs in Biniou early-bound CRMs, in addition to the similarity of bagpipe and biniou mutant phenotypes, implies a potential for combinatorial regulation by these two TFs during the stages of VM specification. Since Biniou is downstream from Bagpipe, it has been very difficult to differentiate between a direct regulatory role by Bagpipe versus an indirect requirement via Biniou using genetic studies. To investigate the molecular function of bagpipe and its potential occupancy on Biniou-bound CRMs, ChIP-on-chip experiments were performed using anti-Bagpipe antibodies. This experiment identified 80 Bagpipe-bound genomic regions, using the same criteria as the Biniou experiments (Jakobsen, 2007). A number of genomic regions are exclusively bound by Bagpipe, with no detectable Biniou binding at stages 10-11 of development. For example, the Bagpipe-bound region within the intron of CG8503: This enhancer is sufficient to drive transient expression in the trunk VM at stages 10-11, reflecting the transient expression of bagpipe in this tissue. Other Bagpipe-bound enhancer regions contain low levels of Biniou binding. The slp1 enhancer is within this class. This region drives expression in the foregut VM, recapitulating the endogenous gene's expression. Together these enhancers demonstrate that Bagpipe provides a direct regulatory role within the VM developmental program, independently of Biniou (Jakobsen, 2007). In contrast, 51% of Bagpipe enhancers are cobound by Biniou at the same stage of development. This extensive combinatorial binding provides the first evidence of global coregulation by these TFs during early stages of VM specification. These cobound enhancers suggests that transient Biniou occupancy on early group enhancers, may in part be due to cobinding with Bagpipe, which is transiently expressed at these stages. To investigate this, the temporal profile of Biniou binding to the 80 Bagpipe-bound CRMs was examined using K-means clustering. Two distinct classes of Biniou-Bagpipe-cobound CRMs were apparent: Group 1 enhancers are cobound at stages 10-11 and remain continuously bound by Biniou at later developmental time points. This indicates that Biniou does not require the presence of Bagpipe to bind to the trunk VM enhancers among this class. In contrast, Group 2 enhancers are cobound by Biniou and Bagpipe at stages 10-11 of development, but are largely not bound by Biniou later in development. In the context of these early enhancers, Bagpipe binding may be the temporal cue dictating transient Biniou binding. Many of these CRMs are likely to be cooperatively regulated by both TFs (Jakobsen, 2007). In summary, this study used two complementary genomic approaches to systematically dissect the transcriptional program driving VM development in vivo: a time course of ChIP-on-chip experiments and expression profiling of mutant embryos performed during consecutive stages of embryogenesis. This global view revealed the following insights into the underlying cis-regulatory network (Jakobsen, 2007): (1) Biniou binds to enhancers in a temporally regulated manner. Since Biniou is expressed from VM specification until the end of development, this demonstrates that additional regulatory inputs are necessary to restrict Biniou activity. For the early-bound enhancers, some temporal specificity likely stems from combinatorial binding with Bagpipe. However, other TFs are also likely to be involved (Jakobsen, 2007). (2) Biniou-bound CRMs drive expression in diverse subtypes of VM. This restricted spatial expression again necessitates combinatorial regulation with additional factors. It is proposed that much of this spatial specificity is conferred through Biniou-mediated feed-forward regulation: Biniou regulates a large group of spatially restricted TFs and components of cell signaling pathways that likely target different subsets of these CRMs. Such feed-forward regulation is a prevalent feature in many developmental networks (Jakobsen, 2007). (3) The timing of Biniou enhancer occupancy is tightly correlated with the time span of enhancer activity. This is surprising given the extensive combinatorial binding necessary to produce restricted spatio-temporal expression of Biniou CRMs and suggests Biniou recruitment is the key trigger for enhancer activity. Taken together, these data indicate that Biniou provides VM enhancers with the competence to be expressed within the VM at the appropriate stage, and that these modules integrate extensive inputs from additional factors to restrict Biniou activity (Jakobsen, 2007). (4) Although bagpipe and biniou mutants phenocopy each other, their regulatory role within the underlying network is very different. The majority of Bagpipes regulation occurs via combinatorial binding to Biniou-Bagpipe CRMs to regulate a shared set of target genes. From a limited number of enhancers assayed in vitro, Bagpipes contribution to enhancer activity is mainly cooperative, with little regulatory potential by itself. In contrast, Biniou targets an additional large group of CRMs during VM specification, and can regulate their activity independently of Bagpipe. This underlying nature of Biniou and Bagpipes regulatory potential was not apparent from genetic studies due to the severity of their mutant phenotypes (Jakobsen, 2007). (5) Biniou provides regulatory input at all stages of VM development, not just specification. Moreover, the temporal regulation of target genes at either early or late stages reflects developmental progression. For example, 17% of target genes regulated late in development are involved in the formation or function of the neuromuscular junction, compared with 4% of continuously regulated targets and 0% of early targets. This reflects the requirement of neuronal stimulation for gut muscle contraction at the end of embryogenesis. These results also revealed a new role for Biniou as a direct regulator of the transcriptional program within the foregut and hindgut VM (Jakobsen, 2007). (6) The underlying cis-regulatory circuitry between Biniou and its target genes is at least partially conserved from flies to mice. Four genes that are directly regulated by Biniou in flies require FoxF function for their expression in mice. Due to the limited number of characterized FoxF direct target genes in vertebrates, it is currently too early to determine if VM development represents an ancient trans-bilaterian kernel (Jacobsen, 2006). Taken together, these data indicate that Biniou serves as a universal regulator of VM: The broad expression of Biniou in all VM subtypes and its extensive occupancy on VM enhancers strongly suggests that Biniou provides all VM cells, regardless of their origin or ultimate cell fate, with their VM identity (Jakobsen, 2007).Principlesof microRNA-target recognition: Targeting of bagpipe 3'UTR by microRNAsMicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression inplants and animals. Although their biological importance has become clear, howthey recognize and regulate target genes remains less well understood. Thisstudy systematically evaluates the minimal requirements for functionalmiRNA-target duplexes in vivo and classes of target sites with differentfunctional properties are distinguished. Target sites can be grouped into twobroad categories. 5' dominant sites have sufficient complementarity to the miRNA5' end to function with little or no support from pairing to the miRNA 3' end.Indeed, sites with 3' pairing below the random noise level are functional givena strong 5' end. In contrast, 3' compensatory sites have insufficient 5' pairingand require strong 3' pairing for function. Examples and genome-wide statisticalsupport is presented to show that both classes of sites are used in biologicallyrelevant genes. Evidence is provided that an average miRNA has approximately 100target sites, indicating that miRNAs regulate a large fraction of protein-codinggenes and that miRNA 3' ends are key determinants of target specificity withinmiRNA families (Brennecke, 2005).To improve understanding of the minimal requirements for a functionalmiRNA target site, use was made of a simple in vivo assay in theDrosophila wing imaginal disc. A miRNA was expressed in a stripe ofcells in the central region of the disc and its ability to repress theexpression of a ubiquitously transcribed enhanced green fluorescent protein(EGFP) transgene containing a single target site in its 3' UTR was assessed. The degreeof repression was evaluated by comparing EGFP levels in miRNA-expressing andadjacent non-expressing cells. Expression of the miRNA strongly reduced EGFPexpression from transgenes containing a single functional target site (Brennecke, 2005).In a first series of experiments it was asked which part of the RNA duplex is mostimportant for target regulation. A set of transgenic flies was prepared, each ofwhich contained a different target site for miR-7 in the 3' UTRof the EGFP reporter construct. The starting site resembled the strongestbantam miRNA site in its biological target hidand conferred strong regulationwhen present in a single copy in the 3' UTR of the reporter gene. The effects were tested ofintroducing single nucleotide changes in the target site to produce mismatchesat different positions in the duplex with the miRNA (note that the target sitemismatches were the only variable in these experiments). The efficientrepression mediated by the starting site was not affected by a mismatch atpositions 1, 9, or 10, but any mismatch in positions 2 to 8 strongly reduced themagnitude of target regulation. Two simultaneous mismatches introduced into the3' region had only a small effect on target repression, increasingreporter activity from 10% to 30%. To exclude the possibility that thesefindings were specific for the tested miRNA sequence or duplex structure, the experiment was repeated with miR-278 and a different duplex structure.The results were similar, except that pairing of position 8 was not importantfor regulation in this case. Moreover, some of the mismatches in positions2-7 still allowedrepression of EGFP expression up to 50%. Taken together, these observationssupport previous suggestions that extensive base-pairing to the 5' end ofthe miRNA is important for target site function (Brennecke, 2005).Next the minimal 5' sequence complementarity necessary to confer target regulation was determined.The core of 5' sequence complementarity essential for targetsite recognition is referred to as the 'seed'. All possible 6mer, 5mer, and 4merseeds complementary to the first eight nucleotides of the miRNA were tested inthe context of a site that allowed strong base-pairing to the 3' end ofthe miRNA. The seed wasseparated from a region of complete 3' end pairing by a constant centralbulge. 5mer and 6mer seeds beginning at positions 1 or 2 are functional.Surprisingly, as few as four base-pairs in positions 2-5 confersefficient target regulation under these conditions, whereas bases 1-4 arecompletely ineffective. 4mer, 5mer, or 6mer seeds beginning at position 3 areless effective. These results suggest that a functional seed requires acontinuous helix of at least 4 or 5 nucleotides and that there is some positiondependence to the pairing, since sites that produce comparable pairing energiesdiffer in their ability to function. These experiments also indicatethat extensive 3' pairing of up to 17 nucleotides in the absence of theminimal 5' element is not sufficient to confer regulation. Consequently,target searches based primarily on optimizing the extent of base-pairing or thetotal, and ranking miRNA target sitesaccording to overall complementarity or free energy of duplex formation mightnot reflect their biological activity (Brennecke, 2005).To determine the minimal lengths of 5' seed matches that are sufficient toconfer regulation alone, single sites were tested that pair with eight, seven, orsix consecutive bases to the miRNA's 5' end, but that do not pair toits 3' end. Surprisingly, a single 8mer seed (miRNA positions 1-8) is sufficient toconfer strong regulation by the miRNA. A single 7mer seed (positions 2-8)is also functional, although less effective. The magnitude of regulation for8mer and 7mer seeds is strongly increased when two copies of the site areintroduced in the UTR. In contrast, 6mer seeds show no regulation, even whenpresent in two copies. Comparable results have been reported for two copiesof an 8mer site with limited 3' pairing capacity in a cell-based assay. These results do not support a requirement for a central bulge (Brennecke, 2005). From these experiments it is concluded that (1) complementarity ofseven or more bases to the 5' end miRNA is sufficient to conferregulation, even if the target 3' UTR contains only a single site; (2)sites with weaker 5' complementarity require compensatory pairing to the3' end of the miRNA in order to confer regulation, and (3) extensivepairing to the 3' end of the miRNA is not sufficient to confer regulationon its own without a minimal element of 5' complementarity (Brennecke, 2005).Whilerecognizing that there is a continuum of base-pairing quality between miRNAs andtarget sites, the experiments presented here suggest that sites that dependcritically on pairing to the miRNA 5' end (5' dominant sites) can bedistinguished from those that cannot function without strong pairing to themiRNA 3' end (3' compensatory sites). The 3' compensatorygroup includes seed matches of four to six base-pairs and seeds of seven oreight bases that contain G:U base-pairs, single nucleotide bulges, ormismatches (Brennecke, 2005).It is useful to distinguish two subgroups of5' dominant sites: those with good pairing to both 5' and 3'ends of the miRNA (canonical sites) and those with good 5' pairing butwith little or no 3' pairing (seed sites). Seed sites are considered to bethose where there is no evidence for pairing of the miRNA 3' end to nearbysequences that is better than would be expected at random. Thepossibility cannot be excluded that some sites identified as seed sites might be supported byadditional long-range 3' pairing. Computationally, this is always possibleif long enough loops in the UTR sequence are allowed. Whether long loops arefunctional in vivo remains to be determined (Brennecke, 2005).Canonical sites have strongseed matches supported by strong base-pairing to the 3' end of the miRNA.Canonical sites can thus be seen as an extension of the seed type (with enhanced3' pairing in addition to a sufficient 5' seed) or as an extensionof the 3' compensatory type (with improved 5' seed quality inaddition to sufficient 3' pairing). Individually, canonical sites arelikely to be more effective than other site types because of their higherpairing energy, and may function in one copy. Due to their lower pairingenergies, seed sites are expected to be more effective when present in more thanone copy (Brennecke, 2005).Most currently identified miRNA target sites arecanonical. For example, the hairy 3' UTR contains a single sitefor miR-7, with a 9mer seed and a stretch of 3' complementarity.This site has been shown to be functional in vivo , and it is strikingly conserved inthe seed match and in the extent of complementarity to the 3' end ofmiR-7 in all six orthologous 3' UTRs (Brennecke, 2005).Although seed siteshave not been previously identified as functional miRNA target sites, there issome evidence that they exist in vivo. For example, the Bearded (Brd)3' UTR contains three sequence elements, known as Brd boxes, that arecomplementary to the 5' region of miR-4 and miR-79. Brd boxes have been shown torepress expression of a reporter gene in vivo, presumably via miRNAs;expression of a Brd 3' UTR reporter is elevated indicer-1 mutant cells, which are unable to produce any miRNAs. All three Brd box target sitesconsist of 7mer seeds with little or no base-pairing to the 3' end ofeither miR-4 or miR-79. The alignment ofBrd 3' UTRs shows that there is little conservation in themiR-4 or miR-79 target sites outside the seed sequence, nor isthere conservation of pairing to either miRNA 3' end. This suggests thatthe sequences that could pair to the 3' end of the miRNAs are notimportant for regulation as they do not appear to be under selective pressure.This makes it unlikely that a yet unidentified Brd box miRNA could form acanonical site complex (Brennecke, 2005).The 3' UTR of the HOX gene Sex combsreduced (Scr) provides a good example of a 3' compensatory site.Scr contains a single site for miR-10 with a 5mer seed and acontinuous 11-base-pair complementarity to the miRNA 3' end.The miR-10 transcript isencoded within the same HOX cluster downstream of Scr, a situation thatresembles the relationship between miR-iab-5p andUltrabithorax in flies and miR-196/HoxB8in mice. The predictedpairing between miR-10 and Scr is perfectly conserved in allsix drosophilid genomes, with the only sequence differences occurring in theunpaired loop region. The site is also conserved in the 3' UTR of theScr genes in the mosquito, Anopheles gambiae, the flourbeetle, Tribolium castaneum, and the silk moth, Bombyx mori.Conservation of such a high degree of 3' complementarity over hundreds ofmillions of years of evolution suggests that this is likely to be a functionalmiR-10 target site. Extensive 5' and 3' sequenceconservation is also seen for other 3' compensatory sites, e.g., the twolet-7 sites in lin-41 or the miR-2 sites ingrim and sickle (Brennecke, 2005).Several families ofmiRNAs have been identified whose members have common 5' sequences butdiffer in their 3' ends. In view of the evidence that 5' ends ofmiRNA are functionally important, and in some cases sufficient, it can be expected that members of miRNA families may haveredundant or partially redundant functions. According to this model, 5'dominant canonical and seed sites should respond to all members of a given miRNAfamily, whereas 3' compensatory sites should differ in their sensitivityto different miRNA family members depending on the degree of 3'complementarity. This is being tested using the wing disc assay with 3' UTRreporter transgenes and overexpression constructs for various miRNA familymembers (Brennecke, 2005).miR-4 and miR-79 share a common 5'sequence that is complementary to a single 8mer seed site in thebagpipe 3' UTR. The 3' ends ofthe miRNAs differ. miR-4 is predicted to have 3' pairing atapproximately 50% of the maximally possible level (10.8 kcal/mol),whereas the level of 3' pairing for miR-79 is approximately25% maximum (6.1 kcal/mol), which is below the average level expectedfor random matches. Both miRNAs repressed expression of thebagpipe 3' UTR reporter, regardless of the 3'complementarity. Thisindicates that both types of site are functional in vivo and suggests thatbagpipe is a target for both miRNAs in this family (Brennecke, 2005).To test whether miRNA family members can also havenon-overlapping targets, 3' UTR reporters were used of the pro-apoptoticgenes grim and sickle, two recently identified miRNA targets. Both genes contain K boxesin their 3' UTRs that are complementary to the 5' ends of themiR-2, miR-6, and miR-11 miRNA family. These miRNAs share residues2-8 but differ considerably in their 3' regions. The site in the grim3' UTR is predicted to form a 6mer seed match with all three miRNAs, but only miR-2shows the extensive 3' complementarity that would be needed fora 3' compensatory site with a 6mer seed to function (19.1 kcal/mol,63% maximum 3' pairing, versus 10.9 kcal/mol, 46% maximum,for miR-11 and 8.7 kcal/mol, 37% maximum, formiR-6). Indeed, only miR-2 is able to regulate thegrim 3' UTR reporter, whereas miR-6 and miR-11are non-functional (Brennecke, 2005).The sickle 3' UTR contains two Kboxes and provides an opportunity to test whether weak sites can functionsynergistically. The first site is similar to the grim 3' UTR inthat it contains a 6mer seed for all three miRNAs but extensive 3'complementarity only to miR-2. The second site contains a 7mer seed formiR-2 and miR-6 but only a 6mer seed for miR-11. miR-2 stronglydownregulates the sickle reporter, miR-6 has moderate activity(presumably via the 7mer seed site), and miR-11 has nearly no activity,even though the miRNAs were overexpressed. The fact that a site is targeted byat least one miRNA argues that it is accessible (e.g., miR-2 is able toregulate both UTR reporters), and that the absence of regulation for otherfamily members is due to the duplex structure. These results are in line withwhat would be expected based on the predicted functionality of the individualsites, and indicate that the model of target site functionality can be extendedto UTRs with multiple sites. Weak sites that do not function alone also do notfunction when they are combined (Brennecke, 2005).To show that endogenous miRNA levelsregulate all three 3' UTR reporters, EGFP expression was compared inwild-type cells and dicer-1 mutant cells, which are unable to producemiRNAs. dicer-1clones did not affect a control reporter lacking miRNA binding sites, but showedelevated expression of a reporter containing the 3' UTR of the previouslyidentified bantam miRNA target hid. Similarly, all 3' UTRreporters above were upregulated in dicer-1 mutant cells, indicatingthat bagpipe, sickle, and grim are subject to repression bymiRNAs expressed in the wing disc. Taken together, these experiments indicatethat transcripts with 5' dominant canonical and seed sites are likely tobe regulated by all members of a miRNA family. However, transcripts with3' compensatory sites can discriminate between miRNA family members (Brennecke, 2005).Experimental tests such asthose presented in this study and the observed evolutionary conservation suggest thatall three types of target sites are likely to be used in vivo. To gainadditional evidence the occurrence of each site type was examined in allDrosophila 3' UTRs. Use was made of the D.pseudoobscura genome, the second assembled drosophilid genome, to determinethe degree of site conservation for the three different site classes in analignment of orthologous 3' UTRs. From the 78 known DrosophilamiRNAs, a set of 49 miRNAs with non-redundant 5' sequences was chosen. Whether sequences complementary to the miRNA 5' endsare better conserved than would be expected for random sequences was tested. For eachmiRNA, a cohort of ten randomly shuffled variants was constructed. To avoid abias for the number of possible target matches, the shuffled variants wererequired to produce a number of sequence matches comparable (15%) tothe original miRNAs for D. melanogaster 3' UTRs. 7mer and 8merseeds complementary to real miRNA 5' ends were significantly betterconserved than those complementary to the shuffled variants. Conserved 8mer seeds for real miRNAsoccur on average 2.8 times as often as seeds complementary to the shuffledmiRNAs. For 7mer seeds thissignal was 2:1, whereas 6mer, 5mer, and 4mer seeds did not show betterconservation than expected for random sequences. To assess the validity of thesesignals and to control for the random shuffling of miRNAs, thisprocedure was repeated with 'mutant' miRNAs in which two residues in the 5'region were changed. There was no difference between the mutant test miRNAs andtheir shuffled variants.This indicates that a substantial fraction of the conserved 7mer and 8mer seedscomplementary to real miRNAs identify biologically relevant target sites (Brennecke, 2005). Protein InteractionsDrosophila Groucho, like its vertebrate Transducin-like Enhancer-of-split homologues, is a corepressor that silences gene expression in numerous developmental settings. Groucho itself does not bind DNA but is recruited to target promoters by associating with a large number of DNA-binding negative transcriptional regulators. These repressors tether Groucho via short conserved polypeptide sequences, of which two have been defined: (1) WRPW and related tetrapeptide motifs have been well characterized in several repressors; (2) a motif termed Engrailed homology 1 (eh1) has been found predominantly in homeodomain-containing transcription factors. A yeast two-hybrid screen is described that uncovered physical interactions between Groucho and transcription factors, containing eh1 motifs, with different types of DNA-binding domains. One of these, the zinc finger protein Odd-skipped, requires its eh1-like sequence for repressing specific target genes in segmentation (Goldstein, 2005). The eh1 Gro recruitment domain was originally defined as a heptapeptide motif that is conserved in members of the En family of homeodomain proteins and their vertebrate homologues. More recently, eh1-dependent binding to Gro has also been demonstrated in vitro for various other Drosophila and mammalian proteins, nearly all of which contain homeodomains. Given that Bowl and Odd, two non-homeodomain ZnF transcription factors, contain this motif and interact with Gro, the possibility was explored that eh1 motifs are prevalent among additional non-homeodomain transcription factor families. Indeed, an unbiased yeast screen for Gro-interacting proteins selected two additional transcriptional regulators that contain eh1-like motifs, namely, Sloppy-paired (Slp; Forkhead related) and Dorsocross (Doc; T box). Alignment of the eh1-like sequences of Bowl, Odd, Slp, and Doc with those of En and Gsc revealed three conserved amino acids: phenylalanine-x-isoleucine-x-x-isoleucine (Phe-x-Ile-x-x-Ile, where x is any amino acid). Subsequent database searches for presumptive Drosophila transcription factors containing this minimal peptide sequence identified a wide range of potential negative regulators belonging to different superfamilies as classified by their distinct DNA-binding domain types. Remarkably, eh1-related motifs have been preserved in many human homologues of these fly proteins, indicating that the ability to bind Gro/TLE has been evolutionarily conserved in human transcriptional regulators and that this sequence may have been widely adopted throughout the proteome as a Gro recruitment domain (Goldstein, 2005). Several representatives, corresponding to different transcription factor families, were tested for the ability to bind Gro in biochemical assays. Where possible, full-length expressed sequence tags encoding these proteins were obtained; otherwise, single exons containing the eh1-like sequence were PCR amplified from genomic DNA. Each polypeptide was assessed for the ability to pull down radiolabeled Gro in vitro. GST-tagged Slp and Doc (amino acids 254 to 391) readily retain Gro, as do Eyes absent (Eya) and the homeodomain proteins Ventral nervous system defective (Vnd, 1 to 465), Bagpipe (Bap, 1 to 129), BarH1, and Empty spiracles (Ems, 1 to 360), as well as the orphan nuclear hormone receptor DHR96. To confirm that these interactions rely on intact eh1-related sequences, the eh1 motif of one of these, BarH1, was mutated by substituting glutamic acid for Phe at position 1, finding that its binding to Gro is reduced by >60% (Goldstein, 2005). bagpipe: Biological Overview Evolutionary Homologs Developmental Biology Effects of Mutation ReferencesHome page: The Interactive Fly 1997 Thomas B. Brody, Ph.D.The Interactive Fly resides on theSociety for Developmental Biology's Web server.
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