- Research article
- Open Access
cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers
BMC Genomics volume 16, Article number: 700 (2015)
One of the major challenges in developmental biology is to understand the regulatory events that generate neuronal diversity. During Drosophila embryonic neural lineage development, cellular temporal identity is established in part by a transcription factor (TF) regulatory network that mediates a cascade of cellular identity decisions. Two of the regulators essential to this network are the POU-domain TFs Nubbin and Pdm-2, encoded by adjacent genes collectively known as pdm. The focus of this study is the discovery and characterization of cis-regulatory DNA that governs their expression.
Phylogenetic footprinting analysis of a 125 kb genomic region that spans the pdm locus identified 116 conserved sequence clusters. To determine which of these regions function as cis-regulatory enhancers that regulate the dynamics of pdm gene expression, we tested each for in vivo enhancer activity during embryonic development and postembryonic neurogenesis. Our screen revealed 77 unique enhancers positioned throughout the noncoding region of the pdm locus. Many of these activated neural-specific gene expression during different developmental stages and many drove expression in overlapping patterns. Sequence comparisons of functionally related enhancers that activate overlapping expression patterns revealed that they share conserved elements that can be predictive of enhancer behavior. To facilitate data accessibility, the results of our analysis are catalogued in cisPatterns, an online database of the structure and function of these and other Drosophila enhancers.
These studies reveal a diversity of modular enhancers that most likely regulate pdm gene expression during embryonic and adult development, highlighting a high level of temporal and spatial expression specificity. In addition, we discovered clusters of functionally related enhancers throughout the pdm locus. A subset of these enhancers share conserved elements including sequences that correspond to known TF DNA binding sites. Although comparative analysis of the nubbin and pdm-2 encoding sequences indicate that these two genes most likely arose from a duplication event, we found only partial evidence of sequence duplication between their enhancers, suggesting that after the putative duplication their cis-regulatory DNA diverged at a higher rate than their coding sequences.
During Drosophila neuroblast (NB) lineage development, successive NB expression of the TF genes hunchback (hb) → Krüppel (Kr) → nubbin & pdm-2 (pdm) → castor (cas) is required for the birth order-dependent specification of neuronal identity [1, 2]. Recent studies indicate these genes are regulated by multiple modular enhancers located in their flanking genomic regions and/or within intronic sequences [3, 4]. For example, seven enhancers that regulate cas gene expression dynamics have been identified .
During the past two decades, functional analyses of many vertebrate and invertebrate enhancers have revealed that they are made up of multiple DNA-binding sites for different TFs, which collectively regulate enhancer activity, and that combinatorial protein-DNA and protein-protein interactions play an important role in specifying enhancer regulatory behavior . Phylogenetic comparative analyses of these enhancers have revealed a high degree of conservation within their sequences [7, 8]. For example, previous studies have shown that the hb  and cas  enhancers are each made up of a cluster of sequence blocks present in all drosophilids that we refer to as a conserved sequence cluster (CSC). These and other studies have shown that many of the noncoding CSCs function as autonomous cis-regulatory elements that control different spatial and temporal aspects of gene expression dynamics [7–9].
Located on the left arm of the 2nd chromosome, the adjacent pdm genes encode POU homeodomain TFs that are essential for neurogenesis [10–12] (Fig. 1a). The abundance of CSCs flanking the pdm genes and the dynamic nature of their expression [3, 10, 12] indicate that the pdm locus may contain multiple enhancers that regulate different or overlapping temporal and/or spatial aspects of their expression. Previous analysis of pdm gene regulation has identified three enhancers that recapitulate limited pdm expression in a subset of cells in the cellular blastoderm  and within the embryonic CNS [3, 9]. Given that these enhancers activate expression in only a subset of the tissues known to express the pdm genes, we set out to identify pdm locus enhancers that may regulate other aspects of pdm expression.
Our phylogenetic footprint analysis of the 125 kb pdm locus using 12 drosophilids identified 116 CSCs (both coding and noncoding). Enhancer-reporter transgene analysis of these CSCs revealed 77 distinct cis-regulatory modules that activate reporter expression in different temporal and spatial subsets of the pdm expression domain. Although nubbin (nub) and pdm-2 most likely arose from a duplication event, we found little evidence of sequence collinearity between their noncoding sequences. However, cis-regulatory analysis of the CSCs flanking pdm shows that they each contain a diversity of functionally related enhancers. Comparative analysis of these enhancers revealed the presence of multiple conserved elements within them, and many of these correspond to consensus DNA-binding motifs for different TFs, including Hb [13, 14] and Cas . In addition, our analysis demonstrated clustering of functionally related enhancers, such as those that direct expression in the adult subesophageal ganglion (SOG), and we found that the functional relationship of the SOG enhancers can be inferred based on their shared conserved sequence elements. To increase the accessibility of the enhancer GAL4 transformant lines to the scientific community and enhance the description of the pdm locus cis-regulatory data, we have developed an online database that catalogues the pdm locus enhancers and highlights in vivo cis-regulatory activity in addition to their conserved sequences.
Sequence conservation analysis within the Dipteran pdm locus
In Drosophila, the pdm genes share a similar exon-intron gene structure and are positioned adjacently on the left arm of the 2nd chromosome at cytological map position 33F1 . Both paralogs have long and short isoforms, and each has five exons (Fig. 1a). Given the overall exon-intron organization of these genes and their homologous amino acid sequences, they most likely arose from a duplication event that occurred before Drosophila speciation, since all drosophilids contain both tandemly linked genes [12, 15]. The availability of genomic sequences from other Diptera, including 24 mosquito species, the Mediterranean fruit fly (Ceratitis capitata or medfly) and the housefly (Musca domestica), has allowed us to compare the Nub and Pdm-2 proteins in each of these species and determined their sequence relationship (Fig. 1b). Blastp alignment data reveals that the short isoforms of both Nub and Pdm-2 are present in both the housefly and medfly. In contrast, only a single Pdm ortholog is present in the mosquito, and comparative protein analysis indicates that its sequence aligns more closely to Nub (Fig. 1b). This indicates that either the mosquito lost one of the pdm genes or that the duplication occurred prior to the divergence of Drosophila from medfly and housefly (~100 million years ago)  but more recent than the divergence of Drosophila from mosquitos (~260 million years ago) . Sequence alignments also reveal a high degree of conservation between the Drosophila nub and pdm-2 3’ exons that code for their POU domain and homeodomain. In contrast, we were unable to align the 5’ exons of either the long or short pdm isoforms, indicating extensive sequence divergence within the N-terminal domains of these proteins. We also found a lack of detectable DNA sequence relationship between the nub and pdm-2 noncoding sequences (both conserved and less conserved sequences) using the pairwise sequence alignment tools Blastn  and cis-Decoder . Taken together, our findings reveal that the collinearity between the pdm genes is largely restricted to their POU domain and homeodomain coding sequences, whereas the remaining portions of the pdm genes have undergone significant divergence from one another.
As an initial step toward identifying cis-regulatory sequences that may control the dynamics of pdm gene expression, we surveyed the D. melanogaster pdm locus and its flanking sequences that span 125 kb positioned between a 7 kb transposable element ~29 kb upstream of the nub transcription start site and a chaperonin-encoding gene (CG5525) immediately downstream of pdm-2. We identified conserved sequences by phylogenetic footprinting using alignments of 12 Drosophila species, including D. melanogaster, D. simulans, D. sechellia, D. yakuba, D. erecta, D. ananassae, D. persimilis, D. pseudoobscura, D. willistoni, D. virilis, D. mojavensis and D. grimshaw. Our comparative analysis revealed multiple highly conserved sequence clusters that have undergone a cumulative evolutionary divergence of >150 million years . The comparative analysis identified 116 CSCs (both coding and noncoding) within the pdm locus (Figs. 2 and 3).
As indicated above, pairwise DNA alignments of flanking and intergenic pdm sequences did not show any evidence of collinearity. For example, the number of CSCs within the nub and pdm-2 introns differ. We identified 16 CSCs within the first intron of the nub long isoform transcript, and only 9 CSCs between the first and second exons of the pdm-2 long isoform. We also found that, unlike pdm-2, the most distal 5’ UTR of the nub long isoform is not well conserved among different Drosophila species. In particular, comparative analysis revealed that the nub 5’ UTR is conserved in the D. melanogaster, D. simulans, D. sechellia, D. yakuba, D. erecta, D. ananassae, D. persimilis, and D. pseudoobscura, but is not present in the distantly related species.
Given the presence of the pdm genes in the medfly and housefly genomes, we explored whether some or all of the Drosophila CSCs could also be identified in these distant species. Submitting the D. melanogaster genomic sequences surrounding nub and pdm-2 to BLAST searches using the medfly and housefly genomes revealed sequences conserved in the three Dipteran species within several pdm locus CSCs (see Additional file 1: Figure S1) that were typically found within their longest conserved sequence blocks (CSBs). For example, we identified a 48 bp sequence within the pdm2-26 CSC that is conserved in all drosophilids, in addition to the medfly and housefly (see Additional file 2: Figure S2).
To distinguish between adjacent CSCs, we next compared the spacing variability between CSCs in different Drosophila species. Previous studies show that the length of flanking less-conserved DNA sequences between adjacent CSCs varies when compared to the same regions in other Drosophila species . These significant inter-clustal variations are due in part to species-specific insertions and/or deletions [8, 19]. In contrast, the sequence length of CSCs varies less among drosophilids. To measure the inter-clustal length differences, we identified the first and last conserved sequence in each CSC and measured the distance (in nucleotides) between CSCs in D. melanogaster and distant species of the melanogaster group (D. willistoni, D. virilis, D. mojavensis and/or D. grimshaw). Indeed, comparative genome analysis revealed significant inter-clustal variability between the pdm CSCs. For example, the inter-clustal distance between the CSCs nub-14 and nub-15 is 676 bp in D. melanogaster, whereas these CSCs are separated by 1458 bp in D. mojavensis (data not shown). To further confirm these observations, we added inter-clustal data from species closer to D. melanogaster and tested the statistical significance of the combined inter-clustal data using cluster analysis (see Methods). We predicted that closely related species would have similar inter-clustal values than more distantly related species. For example, inter-clustal spacing in D. melanogaster should more closely match spacing in D. erecta compared to D. mojavensis. We sampled the 24 CSCs upstream of the nub transcriptional start site in our analysis. Clustering and heatmap analysis of these CSCs (see Methods) revealed two majors species clusters: the Drosophila melanogaster group (D. melanogaster, D. yakuba, D. erecta, D. ananassae) and a cluster that included four outgroup species (D. persimilis, D. pseudoobscura, D. virilis, D. mojavensis) (Additional file 3: Figure S3). Notably, the outgroup species were clustered correctly based on their known phylogeny, which includes the Sophophora subgenus (D. persimilis, D. pseudoobscura) and the Drosophila subgenus (D. virilis, D. mojavensis) [20, 21].
Enhancer transgene analysis reveals a wide array of cis-regulatory elements spanning the pdm locus
The pdm genes are expressed during multiple stages of development. For example, previous studies have shown that nub expression is relatively high in multiple tissues during embryogenesis and is steadily reduced in the larvae and adult, whereas pdm-2 transcripts are detectable during embryonic and larval development [10–12]. Recent analysis of the level of expression of each of the isoforms of nub and pdm-2 confirmed that RNA coding for the short and long isoforms are present both in the embryo and larvae . Both of these genes are also active during multiple phases of CNS development [3, 11, 12, 23], and loss of either pdm gene function disrupts neurogenesis . For example, in pdm null mutants, cas expression is delayed  and U5 motor neurons fail to form . In contrast, prolonged misexpression of Pdm-2 is sufficient to activate cas and to produce the U5 motor neurons . In addition to CNS development [3, 11], the nub and pdm-2 genes are also expressed in wing imaginal discs  and the larval hindgut , respectively.
To identify neural enhancers within the pdm locus that activate reporter gene expression, we tested each CSC for enhancer activity during embryonic, larval, and adult neurogenesis using enhancer-reporter transgenes that were integrated into the same location on the 3rd chromosome (see Methods) . Our screen identified 77 enhancers positioned throughout the nub and pdm-2 noncoding sequences that generated robust reporter expression with no expression pattern variability detected among independently derived transformant lines for each of the enhancers. Reporter-gene expression patterns demonstrated that they are active either inside and/or outside of the nervous system during stages of embryonic and postembryonic development. A summary of their cis-regulatory activities is shown in Fig. 3 and Additional file 4: Table S1. Although a subset of these enhancers directed overlapping expression patterns, the majority activated reporter expression in unique temporal and spatial domains (Additional file 4: Table S1 and see cisPatterns). We also observed that many of the enhancers activated expression during multiple developmental temporal windows (Fig. 3). For example, we found that 42 enhancers drove expression in ≥ 2 developmental stages, and 13 enhancers were active in embryos, larvae and adults (Fig. 3). In particular, the nub-53 enhancer directed expression in embryonic ventral nerve cord (VNC) cells, larval brain and VNC, and throughout the adult brain including within the central brain and optic lobe (Fig. 4a). In addition, the nub-54 enhancer regulated expression in lateral PNS cells in the embryo, in medial brain lobe larval neurons, and in the putative nodular neurons in the adult brain (Fig. 4b). The pdm2-15 enhancer directed expression in the embryonic procephalon, embryonic and postembryonic VNC, and adult lateral horn (Fig. 4c). The pdm2-37a enhancer drove expression in the embryonic clypeolabrum, salivary gland, and subesophageal ganglion, in addition to expression in the postembryonic CNS (Fig. 4d). Further studies using cell-specific markers are required to definitively identify the cell types that activate the enhancers.
To show in greater detail the cis-regulatory dynamics of these enhancers, we generated a web-based database that contains enhancer data collected from this survey of the pdm locus and from our previous studies. The website, titled cisPatterns (http://cispatterns.ninds.nih.gov), provides access to over 100 Drosophila cis-regulatory enhancers (see Methods). Information available includes images of embryonic, larval and adult expression patterns, sequence conservation, base pair length, genomic location, and keywords to facilitate searches. An online guide describes various options for viewing information. All of the GAL4 driver lines shown in cisPatterns are freely available to the research community.
Embryonic expression of enhancer-reporter transgenes
Among the cis-regulatory elements identified, we detected 41 CSCs that directed reporter expression during embryogenesis (Fig. 3 and Additional file 4: Table S1). Activity data for these enhancers is also shown at the cisPatterns database. Twenty-two of these enhancers activated neural expression, including the NB enhancers nub-46 and pdm2-34 (Fig. 5d, h, respectively). NBs were identified based on their large diameters and their position within the developing CNS. While nub-46 and pdm2-34 are the only enhancers that regulated expression in VNC NBs, we identified five additional enhancers that activated transgene reporter expression in cephalic lobe embryonic NBs. At stage 11, nub-41 directed expression in a subset of NBs in the lateral region of the cephalic lobe (Fig. 5b). Similar to nub-41, nub-44 also drove expression in a subset of lateral cephalic lobe NBs (Fig. 5c). However, nub-44 regulatory activity was restricted to approximately a small subset of neural precursors per developing brain lobe at stage 9. pdm2-7b also regulated a very specific NB expression in the cephalic lobes at stage 10 (Fig. 5e). pdm2-25 drove expression in posterior and medial cephalic lobe NBs at stage 13 (Fig. 5f). pdm2-31a directed expression in a subset of lateral and medial NBs at stage 12 (Fig. 5g). It is worth noting that the cephalic lobe NB enhancers do not appear to have overlapping regulatory activity, suggesting that these enhancers may regulate different NB sublineages during embryonic neurogenesis.
We also identified enhancers that activated expression in putative postmitotic neurons in the VNC and cephalic lobe. For example, nub-12 was sufficient for expression in small-diameter daughters cells of NBs located in the procephalon and VNC at stage 13 (Fig. 5a). This observation is in agreement with studies that implicate a role for nub during asymmetric division of ganglion mother cells [27, 28].
We also found that enhancer activity was consistent with the temporal order of Pdm and Cas expression during NB lineage development (Fig. 6). For example, we observed the staggered onset of the initial nub-46 enhancer activity followed by Cas expression in the developing CNS (Fig. 6). nub-46 regulated expression in a subset of VNC NB lineages, whereas Cas was restricted to a separate group of NBs located at the VNC midline (Fig. 6a’, a”). In agreement with the transient overlap of Nub and Cas expression , co-localization of nub-46 enhancer activity and Cas in NBs was observed during late developmental time points (Fig. 6b–d). While the costaining of nub-46 enhancer activity and Cas shows correct temporal expression, additional work is needed to characterize the temporal window of the other NB enhancers.
Enhancer-reporter transgene analysis during larval CNS development
We utilized the GAL4/UAS system [29, 30] to test the cis-regulatory potential of the CSCs during postembryonic nervous system development. To better distinguish between different cell types including NBs, GMCs and neurons, we used a membrane-bound GFP (mCD8-GFP) reporter. Our survey revealed 46 enhancers that drove expression in the larval brain and/or imaginal discs (Fig. 3). Many of the larval enhancers regulated expression in brain and VNC neurons. The following describes a subset of pdm enhancers that direct neuronal expression during larval CNS development and that highlight the dynamic nature of pdm cis-regulatory function. It is also worth noting that these enhancers are silent during embryonic neurogenesis. Expression pattern data for all 46 identified larval enhancers is provided in Additional file 4: Table S1 and shown at cisPatterns.
pdm2-17 regulated expression in the larval brain and VNC neurons. Enhancer activity was restricted to a narrower subset of neurons (Fig. 7a). For example, pdm2-17 directed expression in posterior and medial anterior central brain neurons. In the VNC, enhancer activity was present in neurons with axonal projections that extend laterally to the midline, transverse, and continue longitudinally between the ventromedial and dorsomedial VNC tracts. Two pairs of these neurons are located in the third thoracic (t3) and first through fourth abdominal segments (a1-a4). Although not positively identified, their morphology and position is consistent with crustacean cardioacceleratory peptide (CCAP) neurons, which are laterally positioned in the VNC thoracic and abdominal segments . These observations are also in agreement with previous studies on serotonergic lineage specification showing that pdm is expressed in neurons throughout the larval VNC . However, additional work using specific cell markers is required to definitively determine their neuronal identity. pdm2-19 drove expression in many brain and VNC neurons during larval neurogenesis (Fig. 7b). Unlike the pdm2-17 pattern, GFP expression was detected in neurons within the medial and lateral central brain, as well as many neurons throughout the VNC. Notably, we did not detect any enhancer activity in the optic lobe. pdm2-35 drove expression along the midline of the larval brain and VNC (Fig. 7c). Reporter expression was restricted to a single neuron in each anterior medial brain lobe, a pair of symmetric neurons in the medial thoracic 1 (t1) and thoracic 2 (t2) segments, and a subset of midline neurons in the lower abdominal VNC. pdm2-39 is located ~3.5 kb downstream of pdm2-35 and also drove expression in midline neurons (Fig. 7d). Further, we observed enhancer activity in dorsolateral neurons in the fifth through seventh abdominal (a5-a7) segments. Their axonal projections cross and then ascend the midline of the VNC. pdm2-40a is immediately adjacent to pdm2-39 but regulated expression in a different subset of VNC neurons (Fig. 7e). The expression pattern was made up of bilateral pairs of neurons located in the lateral t3, medial a1, lateral a2-a4 and lateral a7 segments. Given their location and morphology, the lateral a2-a4 cells may be serotonergic neurons. Consistent with this prediction is that lateral serotonergic neurons express pdm during larval neurogenesis .
We also identified enhancers that activated reporter expression in imaginal discs. These enhancers (nub-19, nub-31, nub-32b, nub-36, and nub-41) were active in different imaginal discs (described in Additional file 4: Table S1 and shown at cisPatterns). The identification of disc enhancers is in agreement with previous studies that have detected Nub expression in wing discs via immunostaining [25, 33]. Of the five disc enhancers, nub-31 drove expression in a subset of cells occupying the dorsal anterior region of the leg imaginal disc  (Fig. 7f). nub-36 directed weak expression in the leg imaginal disc (Fig. 7g). Specifically, the expression overlapped a region that develops into the coxa, an adult appendage connecting the leg to the thorax . nub-41 drove expression in both the haltere and wing imaginal disc. However, compared to nub-31 and nub-36, there was no leg disc expression. In the haltere (also referred to as the rudimentary wing) disc, the expression pattern was composed of cells that develop into the pedicel and capitellum segments of the adult rudimentary wing based on their location  (Fig. 7h). In the wing disc, the enhancer regulated expression in cells that will become part of the proximal wing  (Fig. 7h).
A subset of enhancers drove expression in putative larval NBs. For example, the two embryonic NB enhancers for nub and pdm-2, nub-46 and pdm2-34, are also active in larval NBs (Fig. 8a, c, respectively). In addition, nub-49b and pdm2-37a also regulated expression during larval NB lineage development (Fig. 8b, d).
As a first step toward identifying the NBs that activate the pdm enhancers, we carried out co-localization studies with type I and type II NB markers. Previous work by others has identified two types of larval NBs that differ in their cellular division and renewal . Similar to embryonic NBs, type I NBs divide asymmetrically to produce several ganglion mother cells (GMCs), each of which undergo a single round of division to form two progeny. In contrast, type II NBs first produce a NB-like cell called an intermediate neural progenitor (INP) which then divides asymmetrically to create GMCs. Differences between type I and type II NBs suggests that distinct expression programs may regulate their cellular identities. Indeed, type I NBs express the TFs Deadpan (Dpn) and Asense (Ase), whereas only Dpn is detected in type II NBs . Our coexpression studies using the Dpn and Ase markers revealed that nub-46 (Fig. 8a’, a”), nub-49b (Fig. 8b’, b”), and pdm2-37a (Fig. 8d’, d”) drove expression in type I and type II NBs. In contrast, pdm2-34 enhancer activity was detected only in type I NBs (Fig. 8c’, c”).
Enhancer-reporter transgene analysis in the adult brain
Our survey revealed 46 enhancers that drove expression within the adult brain and each activated expression in overlapping patterns (see Additional file 4: Table S1 and shown at cisPatterns). For example, twenty-five enhancers directed expression in putative median neurosecretory cells (mNSCs) based on their previously described distinct morphology and location (see Additional file 4: Table S1) [38–40]. mNSCs are located in the superior medial protocerebrum and send their projections to a Drosophila gustatory system known as the tritocerebrum – reflecting the cellular morphology that overlaps enhancer activity. nub-15 is a 1.2 kb enhancer that activates expression in putative mNSCs (Fig. 9a). We also detected expression in putative central complex neurons, which play a role in locomotion, vision, learning and memory . The nub-15 enhancer regulated expression in the ellipsoid body, lateral triangle and cell body – three structures readily identifiable according to their position and morphology . Twenty-three enhancers were identified that drove neuronal expression in the subesophageal ganglion (SOG), another gustatory center located in the most ventral region of the central brain (see Additional file 4: Table S1) . Unlike a majority of the SOG enhancers that directed broad expression, pdm2-24 enhancer activity was limited to a single symmetric pair of putative SOG neurons (Fig. 9d).
Interestingly, we identified 22 enhancers that regulated neuronal expression in both mNSCs and SOG neurons, albeit in non-identical subsets of SOG neurons (see Additional file 4: Table S1 and cisPatterns). For example, pdm2-36 directed expression in mNSCs and a symmetric medial pair of SOG cells (Fig. 9f). These SOG neurons ascend to the tritrocerebrum, decussate, and form dense axonal arborizations in the dorsolateral protocerebrum. In addition, we detected pdm2-36 enhancer activity in optic lobe structures, including the lobula plate, optic glomerulus and medulla. Further, similar to the nub-15 enhancer, pdm2-36 drove expression in cells of the central complex; namely, the ellipsoid body, lateral triangle and cell body.
The screen also identified other cis-acting elements that directed expression in the central complex. pdm2-31a is located 6 kb upstream of pdm2-36 and was also sufficient for expression in the ellipsoid body and cell body (Fig. 9e). We observed pdm2-31a enhancer activity in putative ventromedial protocerebrum and medulla neurons. nub-54 was largely restricted to a pair of putative central complex neuropils termed noduli (Fig. 9c) . Previous work has indicated that noduli are connected to neural circuitry for visual processing in insects . This is consistent with our findings showing that axonal projections of these neuropils decussate immediately at the dorsal side of the esophagus and continue laterally to innervate the lobula plate in the optic lobe (Fig. 9c). We have also identified enhancers that drive non-neural expression in the adult. For example, nub-29 regulated expression in both the optic lobe and central brain tracheal branches (Fig. 9b).
Comparative sequence analysis reveals unique combinations of shared conserved elements among functionally related enhancers
To investigate whether the functionally related enhancers discovered in this study can be classified based on their shared conserved sequence elements, we compared the 23 enhancers that drove neuronal expression in the SOG of adult Drosophila. To determine if they share conserved sequences, we developed a computational method to handle all pairwise combinations of these enhancers. We also assessed whether conserved elements shared among the SOG enhancers were also found in pdm locus CSCs that did not activate reporter expression in SOGs. To accomplish this, we generated a library of shared conserved sequence elements within SOG enhancers, measured the frequency of these elements within SOG and non-SOG CSCs, and preprocessed this information for elements occurring predominantly in SOG enhancers. This approach returned 254 unique conserved DNA elements, the length of each n-mer ranging from 6 to 12 bp (Additional file 5: Table S2). Hierarchical cluster analysis revealed that these shared elements are sufficient to distinguish the SOG enhancers from other pdm locus CSCs (Fig. 10). Interestingly, we also observed that each CSC contained a different combination of these conserved sequence elements. For example, nub-31 and nub-32a contain 68 and 71 of the 254 conserved DNA elements, respectively, but only share 41 of these conserved elements. We also identified quantitative differences among the shared their elements. While the two enhancers both contain the conserved DNA sequence TGCTGCTGTTG, the 11-mer is present twice in nub-31 and once in nub-32a. It is worth noting that we identified 4 of the 93 non-SOG CSCs (nub-27, nub-34, nub-49a, and pdm2-23b) clustered within the SOG enhancer group (Fig. 10b, asterisks). We next determined whether this approach could group other functionally related pdm enhancers. As previously mentioned, we identified 25 enhancers that drove expression in adult median neurosecretory cells. Similar to the SOG enhancers, these cis-regulatory modules clustered together in the hierarchical clustering analysis based on their uniquely shared conserved sequence elements that are largely absent in non-mNSC CSCs within the pdm locus (data not shown). Further comparative analysis is required to enhance resolution of this comparative method. Nevertheless, these common elements suggest a possible shared combinatorial nature within functionally related enhancers.
Structurally similar sets of neural enhancers were also found tandemly arrayed in multiple locations within the pdm locus (Fig. 3). For example, the consecutively arrayed enhancers pdm2-17, pdm2-18, and pdm2-19 drove overlapping neural expression patterns in larvae and adults. As described above, pdm2-17 and pdm2-19 regulated expression in larval brain and VNC neurons (Fig. 7a, b). Similarly, the enhancer activity of pdm2-18 was detected in brain and VNC neurons and is similar to pdm2-19 enhancer function, albeit, in fewer medial VNC neurons and in a greater number of lateral VNC neurons (see Additional file 4: Table S1 and cisPatterns). Another example of adjacent enhancers spans ~6 kb of noncoding DNA and is located ~22.5 kb upstream to the nub long isoform. This array contains 6 CSCs: nub-8 thru nub-13 (Fig. 2). Regulatory activity differed among these enhancers in the three tested developmental phases (Fig. 3). For example, we detected embryonic enhancer activity for nub-9, nub-11, and nub-12, whereas nub-8, nub-10, and nub-13 did not activate reporter expression during embryogenesis. In the adult brain, all enhancers drove CNS expression except for nub-10. Further, these enhancers are active and have overlapping function during larval CNS development. In particular, each enhancer regulated expression in lateral VNC neurons (Additional file 6: Figure S4); however, each enhancer directed expression in a different number of lateral VNC neurons. For example, nub-9 drove reporter expression in most but not all lateral neurons in every thoracic and abdominal VNC segment (Additional file 6: Figure S4B), whereas nub-8 enhancer activity was restricted to markedly fewer cells in comparison (Additional file 6: Figure S4A).
To determine whether these functionally related enhancers share sequence motifs, we then performed a pairwise comparative analysis to identify shared conserved sequences. We employed a specialized feature of cis-Decoder called Advanced Search that computes a pairwise alignment between a reference CSC and a user-generated library of CSCs. For this, we chose nub-9 (Fig. 11a) as the reference CSC and added the remaining five CSCs to a library. Our comparative analysis revealed that the CSCs share many conserved sequences. For example, all of the CSCs except nub-11 contain several copies of the 6-mer CATAAA that corresponds to the DNA-binding site for Hb [13, 14] and Cas . In particular, the putative Hb/Cas docking site was detected multiple times within conserved sequences in nub-8 (2 sites), nub-9 (6 sites), nub-10 (2 sites), and nub-12 (5 sites) (Fig. 11b, c). Only nub-13 has a single but extended Hunchback/Castor DNA-binding motif (CATAAAAAA/TTTTTATG, Fig. 10b), which has a greater similarity to the consensus sequence [3, 13, 14] than does the 6-mer.
Our analysis of the pdm cis-regulation indicates that the spatiotemporal dynamics of their expression is controlled by a functionally diverse array of modular enhancers. Analysis of the 125 kb pdm locus identified 77 cis-regulatory enhancers that activate gene expression in the embryo, larvae and/or adult. Our studies also revealed that many of the functionally related neural enhancers that direct overlapping expression patterns are tandemly arrayed. We found 41 enhancers directed embryonic expression, an overlapping set of 46 activated larval expression, and another overlapping set of 46 activated expression in the adult CNS. While many of these enhancers were activated only in the nervous system, a subset activated reporter gene expression outside of the nervous system, including in larval appendages and in the trachea. Roughly a third of the tested CSCs did not exhibit any detectable cis-regulatory activity in the nervous system. Since our focused on identifying neural enhancers, the possibility exists that some or all of these CSCs that lack neural system activity may regulated gene expression in the larval and adult tissues that were not examined.
There are other online resources of documented enhancers in the Drosophila genome, namely, FlyLight [43–46] and Vienna Tiles . While these cis-regulatory libraries provide useful information, the coverage of the pdm locus in these databases is not complete. For example, FlyLight analysis did not detect 14 enhancers that flank the nub transcribed sequence. These include those located upstream to the nub long transcript (nub-12 and nub-13), its first intron (nub-28), second exon (nub-32a), second intron (nub-32b, nub-32c, nub-33, nub-36, nub-40b, nub-41, nub-42, nub-44, and nub-45a), and third intron (nub-49b) (Fig. 3). The FlyLight library also does not include seven pdm-2 enhancers: located in the upstream region (pdm2-21); within the second intron (pdm2-27 and pdm2-28) and lacks information regarding its downstream region (pdm2-45, pdm2-46, pdm2-47 and pdm2-48) (Fig. 3). Vienna Tiles also provides only partial coverage of the pdm locus, omitting the following 11 pdm locus enhancers: nub-58a, nub-58b, pdm2-13, pdm2-17, pdm2-21, pdm2-22, pdm2-23a, pdm2-31b, pdm2-32, pdm-33, and pdm2-48 (Fig. 3). While the Vienna Tiles database provides information on embryonic and adult enhancers, it does not supply information on cis-regulatory activity during larval development. In addition, based on our analysis, most of the reporter transgenes in these two libraries contain multiple enhancers. For example, we observed that the Vienna Tiles enhancer denoted as VT6436 enhancer is made up of two embryonic enhancers (nub-28 and nub-29).
Analysis of the pdm locus enhancers identified four functionally related enhancers (nub-46, nub-49b, pdm2-34, and pdm2-37a) that activated expression during NB lineage development. The nub-46 and pdm2-34 enhancers are both located in the third intron of the nub and pdm-2 long transcript, respectively, whereas nub-49b and pdm2-37a are positioned immediately 5’ to the transcriptional start site of their respective short isoform (Additional file 7: Figure S5). While the nub-46 and pdm2-34 enhancers drove overlapping but nonidentical expression during embryonic and larval NB lineage development (Fig. 5d, h, Fig. 8a, c), nub-49b and pdm2-37a regulated similar expression patterns during postembryonic NB lineage development (Fig. 8b, d). Analysis of nub-46 and pdm2-34 revealed that these enhancers share multiple conserved DNA elements, albeit in largely unique configurations (data not shown). Although these observations suggest these enhancers are related, additional studies are needed to further resolve subtle differences between their regulatory activities.
Comparative analysis of the nub and pdm-2 coding sequences revealed that their sequence relationship was mostly limited to the exons that encode their POU domains and homeodomains. In contrast, we did not detect any evidence of collinearity within their noncoding regions, suggesting that they have diverged at a faster rate than the coding sequences. We also identified only one pdm ortholog in the mosquito, whereas the medfly and housefly carry both genes. Given this observation and accounting for the divergence of Drosophila from these distant Diptera [16, 17], the pdm duplication event may have occurred in the Dipteran line between 100 and 260 million years ago.
Despite the lack of sequence relationship within the noncoding sequences, the pdm locus is enriched with clusters of conserved sequences and some of them have been maintained in other Diptera. Our studies revealed that two-thirds of the CSCs function as cis-regulatory enhancers that regulate gene expression in a diverse array of spatiotemporal aspects, which taken together reflect pdm expression domains. These observations suggest that the pdm genes are dynamically regulated by multiple cis-regulatory modules, and that these enhancers are more amenable to evolutionary restructuring than their protein encoding exons. This is in agreement with recent reviews on the evolution of Dipteran enhancers highlighting the flexibility of enhancers to maintain their function after loss and/or gain of TF DNA binding sites [48, 49]. Also consistent with these observations, we discovered functionally related enhancers within the pdm locus that share conserved sequences, albeit in different arrangements and orientations.
From a mechanistic perspective, our observations suggest that enhancer behavior can be predicted based on the combination of the conserved elements shared among functionally related enhancers. Similar observations have been made by Aerts and Schweisguth laboratories [50, 51]. Hierarchical clustering analysis of shared conserved sequences revealed that pdm SOG enhancers may be grouped based on shared elements that are for the most part not present within other pdm locus CSCs. A similar analysis of adult median neurosecretory cell (mNSC) enhancers revealed that they grouped together, as evidenced by sharing of conserved sequence elements, which were largely absent in non-mNSC CSCs with the pdm locus. While further work is required to determine whether these shared elements are important for enhancer activity, these findings suggest a level of structural complexity in the presence and clustering of enhancers that requires further analysis. To construct a better representation of enhancer structure and thus cis-regulatory prediction, one would ideally prefer to use a larger training set of enhancers to improve the accuracy of prediction . These approaches will be addressed in future studies.
One of the principal findings of this study is the discovery of 77 enhancers that exhibit a remarkably diverse range of cis-regulatory activities during embryonic and postembryonic development. The biological significance of this enhancer diversity most likely reflects the diversity of the developmental programs in which these transcription factors participate. We also identified functionally related enhancers that share multiple conserved DNA sequences and determined that these enhancers could be classified using hierarchical clustering techniques. In addition, our analysis has revealed that the collinearity between the pdm genes is predominantly confined to their POU domain and homeodomain exons, suggesting that their noncoding sequences are diverging at a faster rate than their coding sequences. These results should provide further insight into the regulatory logic that controls cis-regulatory function and thus gene regulation.
The UCSC Genome Browser was used to retrieve DNA sequences within the pdm locus (http://genome.ucsc.edu/). The pdm locus is approximately 125 kb (chr2L:12,565,558-12,690,307). The phylogenetic comparative analysis of these sequences was performed using the EvoPrinter programs (http://evoprinter.ninds.nih.gov/) and included the 12 available drosophilids. CSCs identified from overlapping EvoPrints were annotated to include gene name hyphenated with consecutive numbers and were named based on their proximity to the nub and pdm genes. Pairwise alignments of these CSCs were performed using the cis-Decoder program (http://cisdecoder.ninds.nih.gov). Instructions for both EvoPrinter and cis-Decoder are provided on their respective websites.
Hierarchal clustering and heat map analysis
We sampled inter-clustal spacing variability between 24 CSCs upstream of the nub long transcript in 8 drosophilids, including D. melanogaster, D. yakuba, D. erecta, D. ananassae, D. persimilis, D. pseudoobscura, D. virilis, and D. mojavensis. The inter-clustal spacing values for each species were stored in a data matrix file. Hierarchal clustering and heat map analysis were performed using R, a statistical programming language environment (http://www.r-project.org/). We employed the gplots package that includes heatmap.2, the hierarchal clustering and heat map algorithm. We employed a similar protocol to determine shared conserved DNA elements in functionally related pdm enhancers. Using parsing algorithms, we extracted conserved DNA elements (6- to 12-mers) from SOG enhancers identified within the pdm locus and measured their occurrence within 23 SOG and 93 non-SOG pdm enhancers. We further screened for conserved elements with relatively high frequency within SOG enhancers and performed hierarchical clustering using this data set after normalization. The same approach was used to analyze the mNSC enhancers. All algorithms are available upon request.
Enhancer-reporter transgene constructs
A modified pCa4B vector was employed in these studies . The pCa4B vector was modified to include the following features from the pHStinger vector : the pHStinger polylinker (replacing the pCa4B polylinker), a minimal Heat shock protein 70 (Hsp70) promoter driving a GAL4 or GFP reporter gene, and gypsy chromatin insulators to block influence of flanking enhancers that would otherwise modify reporter expression via enhancer trap effects. The vector also contains bacterial attachment (attB) sites for its targeted chromosomal insertion . The site-specific integration vector was selected to ensure that all of the enhancer-reporter constructs were inserted in the same chromosomal environment. In addition to the gypsy chromatin insulators, the nonrandom integration afforded by the f31 integration further reduces integration variability on enhancer function. Integration of the pCa4B vector is facilitated by a serine integrase, phage f31, which mediates recombination between vector attB sites and genomic phage attachment (attP) sites .
Generation of transgenic fly lines
CSC-containing DNA fragments were cloned from wild-type genomic DNA using standard PCR methods. PCR products were analyzed using gel electrophoresis and were purified by a Qiagen QIAquick Gel Extraction Kit. Purified PCR products were inserted into the Invitrogen pCRII-TOPO TA vectors. Plasmids with CSC-containing DNA fragments were sequenced by the NIH DNA Sequencing Core Facility to confirm their sequences. Verified sequences were inserted into the modified pCa4B vector described above in the Enhancer-Reporter Transgene Constructs section. Construct DNA were injected into attP2 (insertion site on chromosome 3L, 68A4)  fly embryos by Rainbow Transgenic Flies, Inc. and independent transformant lines for each construct were generated. Standard genetic crosses were performed to generate homozygous transgenic fly lines. Fly lines are maintained at 18 °C using standard husbandry procedures .
Embryo collections and fixations of transgenic fly lines were performed according to procedures previously described . For in situ hybridizations, mRNA probes were generated from a PCR amplified GAL4 or GFP ORF. All pdm locus enhancers directed GAL4 reporter expression, except for nub-19, nub-53, and pdm2-8a, which was detected by enhancer-GFP expression. Roche DIG RNA Labeling Mix protocol was used and staining was visualized using anti-FITC Fab fragments coupled to alkaline phosphatase (1:2000, Roche). After whole-mount in situ hybridization, embryos were photographed using a Nikon Optiphot microscope (10X objective lens). Embryo developmental stages were determined based on morphological features previously described . In addition, larval and adult brains were dissected and fixed according to protocols previously outlined . For single immunolabeling, purified rabbit anti-GFP (1:1000, Invitrogen) and anti-rabbit Alexa 488 (1:000, Invitrogen) were used.
For triple immunolabeling of larval NBs, primary antibodies mouse anti-GFP (1:1000, Chemicon), rabbit anti-Asense (1:1000, gift from Tzumin Lee), guinea pig anti-Deadpan (1:500, gift from James Skeath) were used, together with anti-mouse Alexa 488 (1:1000, Invitrogen), anti-rabbit Alexa 568 (1:1000, Invitrogen), and anti-guinea pig Alexa 633 (1:1000, Invitrogen). For Castor co-staining, primary chicken anti-GFP (1:500, Chemicon) and rabbit anti-Castor (1:500) antibodies were used together with anti-chicken Alexa 488 (1:1000, Invitrogen), and anti-rabbit Alexa 633 (1:1000, Invitrogen) secondary antibodies. Fluorescence whole-mount immunolabeling techniques were carried out according to procedures previously described . After immunolabeling, third instar larval and adult CNS tissue were examined for GFP expression. Serial optical sections of dissected brains were photographed at 1 mm intervals using a Zeiss LSM 510 confocal microscope (10× objective lens, 40× objective lens for single larval brain lobes).
cisPatterns algorithms and database
Availability of supporting data
The results of our analysis are catalogued in cisPatterns (cispatterns.ninds.nih.gov).
- hb :
- Kr :
- pdm :
nubbin and pdm-2
- cas :
conserved sequence cluster
- nub :
Mediterranean fruit fly
Conserved sequence blocks
Ventral nerve cord
median neurosecretory cells
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We are grateful to Chi-Hon lee, Anne Hart, and Gilad Barnea for helpful discussions and advice during the project. We also would like to acknowledge the editorial expertise and assistance of Judith Brody. This work was completed as a partial requirement for a doctoral degree from the Brown University-NIH cooperative Ph.D. program. This research was supported by the Intramural Research Program of the NIH, NINDS.
The authors declare that they have no competing interests.
JR and WFO designed and implemented the experiments in the manuscript. TB assisted in drafting the manuscript and performed the protein comparative analysis. AK provided technical assistance with immunoassays and genetics. All authors read and approved the final manuscript.
Three-way alignment of ultraconserved sequences in conserved sequence clusters identified in Drosophila, housefly, and medfly. Shown are conserved sequences shared in Drosophila conserved sequence clusters (nub-35, nub-37, pdm2-6, pdm2-12, and pdm2-21) and detected in the housefly (Musca domestica) and medfly (Ceratitis capitata). Vertical lines indicate agreement among all three Diptera. (TIFF 6544 kb)
The pdm2-26 enhancer contains ultraconserved sequences detected in multiple Diptera. A) Shown is a 12-drosophilid EvoPrint of the pdm2-26 enhancer sequence together with colored highlights that indicate conserved D. melanogaster sequences shared with both the housefly and medfly (Musca domestica and Ceratitis capitata, respectively; orange) or with the medfly only (blue). Black capital letters represent D. melanogaster bases conserved in D. simulans, D. sechellia, D. yakuba, D. erecta, D. ananassae, D. persimilis, D. pseudoobscura, D. virilis, and D. mojavensis. B) and C) Raw BLAST results of the pdm2-26 conserved elements aligned to the housefly (Musca domesticus) and medfly (Ceratitis capitata) genomes, respectively. The colored underlines correspond to the colored highlighted conserved sequences in panel A). (TIFF 7785 kb)
Resolution of conserved sequence clusters is enhanced by evolutionary flexibility in their flanking less-conserved DNA. Shown is a dendrogram tree that illustrates the similarity among Drosophila species based on the inter-clustal spacing of their conserved sequence clusters (CSCs). This also includes 24 consecutive CSCs across 8 Drosophila species (D. melanogaster, Mel; D. erecta, Erec; D. yakuba, Yak; D. ananassae, Ana; D. mojavensis, Moj; D. virilis, Vir; D. persimilis, Per; and D. pseudoobscura, Pse). The heat map represents a visualization of inter-clustal spacing flexibility, where blue and red blocks highlight lower and higher inter-clustal spacing flexibility, respectively; white blocks represent no data due to absence of a particular CSC in that species. Note: The calculated hierarchical clustering of the Drosophila species based on inter-clustal spacing is in near but not complete agreement with their predicted evolutionary distance from D. melanogaster. (TIFF 1668 kb)
cis-regulatory activity of the pdmlocus enhancers. (DOC 259 kb)
Shared SOG enhancer conserved DNA elements (5-->3’). (DOC 192 kb)
Clustering of larval neural pdm locus enhancers. Independent enhancer-reporter transgene analysis of nub-8 through nub-13 conserved sequence clusters (CSCs) reveal enhancer function in the third instar larvae during larval CNS development. Shown are ventral views of third instar larval brains and ventral nerve cord (anterior up) where enhancer activity is detected via membrane tagged mCD8-GFP expression (green). A) nub-8 regulates expression in a subset of anterior and posterior ventral nerve cord (VNC) neurons B) nub-9 drives expression mostly in a subset of lateral VNC neurons. C) nub-10 regulates expression in a subset of lateral VNC neurons. D) nub-11 directs expression in a subset of anterolateral VNC and central brain neurons. E) nub-12 drives expression in a subset of posterolateral VNC neurons. F) nub-13 regulates expression in a subset of posterolateral VNC neurons. Note: The expression patterns of additional pdm locus enhancers are shown on the cisPatterns website. (TIFF 9357 kb)
Genomic location of dm locus NB enhancers. A genomic schematic of the adjacent pdm genes on the 2nd chromosome. The orange boxes represent the nub-46, nub-49a, pdm2-34, and pdm2-37a enhancers that direct NB expression. (TIFF 158 kb)
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Ross, J., Kuzin, A., Brody, T. et al. cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers. BMC Genomics 16, 700 (2015). https://doi.org/10.1186/s12864-015-1897-2