Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila
© Costas et al; licensee BioMed Central Ltd. 2003
Received: 10 September 2003
Accepted: 16 December 2003
Published: 16 December 2003
Non-coding DNA represents a high proportion of all metazoan genomes. Although an undetermined fraction of this DNA may be considered devoid of any function, it also contains important information residing in specific cis-regulatory sequences.
We report a 27 bp motif that is overrepresented within the fly genome. This motif does not show any significant similarity with transposon sequences and is strongly associated with genes involved in development and/or signal transduction. The 27 bp motif is preferentially located within introns, and has a tendency to be present in multiple copies around genes. Furthermore, it is often found embedded in known non-coding regulatory regions. The regulatory network defined by this motif is partially shared in D. pseudoobscura.
We have identified a 27 bp cis-regulatory sequence widely distributed within the Drosophila genome in association with developmental genes. This motif may be very useful towards the annotation of functional regulatory regions within the Drosophila genome and the construction of regulatory networks of Drosophila development.
Coding regions constitute a small portion of metazoan genomes, representing ~24% of the small genome of Drosophila melanogaster and less than 2% of the larger human genome [1, 2]. Although an unknown proportion of non-coding DNA might be regarded as "junk DNA", non-coding regions also include important information related to essential processes such as transcriptional and post-transcriptional regulation, splicing, higher-order chromatin structure and DNA replication. This information generally lays in specific DNA sequences located both in intergenic regions and introns. Nevertheless, this information remains largely inaccessible to the researchers, due to the reduced knowledge about structure and function of non-coding DNA.
Different approaches have been proposed to infer putative cis-regulatory regions. One strategy is based on the identification of overrepresented motifs in sets of coexpressed genes [3–5]. This approach requires prior data on gene expression of large number of genes, generally determined by microarray technology or expressed sequence tags (ESTs).
A second method to locate novel regulatory regions within the genome is the search for statistically improbable concentration of putative binding sites for a transcription factor or a set of functionally related transcription factors. This method generates testable predictions about the function of the putative regulatory regions. For instance, identification of clusters of binding sites for dorsal, dl, and Suppresor of Hairless, Su(H), have led to the identification of new regulatory regions within the Drosophila genome controlled by these genes [6, 7]. In other cases, clustering of binding sites for different transcription factors, such as those active in early Drosophila development or those determining mesoderm activation also revealed new enhancers [8–10].
A third approach (evolutionary comparative approach) relies on the availability of full genome sequences of several eukaryotes, and is based on the fact that conservation of blocks of non-coding sequence between distantly related species is unlikely and thus implies functional constraint on the conserved blocks (called phylogenetic footprints) [11, 12].
All of these approaches represent an essential contribution to one of the major goals in genome research, the construction of regulatory networks, consisting of the linkages between different cis-regulatory systems the genes they govern .
The wingless (wg) gene is a member of the Wnt gene family that encode for secreted glycoproteins, which act as key intercellular signaling molecules during animal development . Although the mechanisms of wg signaling are beginning to be understood , much less is known about how the complex pattern of expression of wg is regulated.
While searching the D. melanogaster wg intron sequences for putative regulatory regions using an evolutionary comparative approach, we identified a 27 bp long motif that is overrepresented within the D. melanogaster genome and that is strongly associated with genes involved in development and/or signal transduction. This motif does not bear any similarity with any of the described D. melanogaster transposons. The gene network defined for D. melanogaster is partially present in D. pseudoobscura. This motif might prove useful in searching for new genes involved in Drosophila development, in genome annotation and in the construction of regulatory networks.
Identification of a 27 bp long motif overrepresented in the fly genome
Two transcripts have been found for the D. melanogaster wg gene. The longer transcript codes for five exons, while the shorter one codes for only four exons. The 3' end of the first intron of the longer transcript is part of the 5' untranslated region (UTR) of the shorter transcript since the alternative wg start codon is located within the second exon of the longer transcript (Release 3.1 of the D. melanogaster genome, February 2003). Three out of the four introns of the longer transcript are large (more than 1 Kb long) considering that more than half of D. melanogaster introns are less than 80 nucleotides in length . Regulatory sequences are often found within intron sequences (see for instance [17–19]). A detailed analysis of wg non-coding regions, including the intron regions, could therefore help understanding how wg expression is regulated.
Distribution of the motif on the different chromosomal arms
About 200 sequences, 100 bp long and centered around the motif were collected and aligned using the program diAlign . The software diAlign is especially suitable to perform local multiple alignments to identify homologous stretches of DNA interspersed between sequences of no homology. For a contiguous stretch of 27 bp the most abundant nucleotide is always at a frequency higher than 50%, while elsewhere the frequency of the most frequent nucleotide is always lower than 50%. For 10 out of the 27 positions of the contiguous DNA stretch, the same nucleotide is present in more than 99% of the sequences and is therefore presumed to be critical for the function of the motif. The frequency of the most abundant nucleotide reaches more than 70% in all other positions except nucleotide 23, where C is present in ~55% of the sequences and T in the other 45%. For these positions, the frequency of the 2nd most abundant nucleotide is always lower than 25%. The length of the motif was thus established as 27 bp.
In order to locate all motifs in the D. melanogaster genome and to avoid the inclusion of false positives we decided to use an approach similar to the use of PWM to identify binding sites for transcription factors. BLAST E-values are not suitable when analyzing short sequences since they depend on the size of the retrieved sequence. Motifs with mismatches at the end of the sequence relative to the query's sequence will usually be retrieved as shorter sequences than motifs having the same total number of mismatches, but with the mismatches located internally. Therefore different E-values are going to be reported even though the two sequences have the same total number of mismatches relative to the query sequence.
Using the same criterion, no matches were found in a set of 20 random sequences of 250000 bp with the same nucleotide composition as the D. melanogaster intergenic regions, while ~15 motifs were expected based on the proportion within the Drosophila genome (368 repeats / 120 Mb). Thus, the repeat is significantly highly overrepresented within the Drosophila genome.
Distribution of the sequence motif
As shown in Table 1, the 27 bp motif is present in all chromosome arms but the small chromosome 4. Nevertheless, this distribution departs from the random expectation based on the total length of each chromosome arm (χ2 = 13.433, 5df, P < 0.0196), due mainly to an underrepresentation of the motif in the X chromosome, coupled to an overrepresentation on both arms of chromosome 3.
Gene Ontology classification of genes associated with the motifs
One repeat per cluster
There are 102 well-known genes putatively associated with the repeat, considering both genes around intergenic motifs. Fifty-four of these genes are included in at least one of the overrepresented categories of the Gene Ontology tree. See additional file 1 for the complete list of genes putatively associated with the repeat.
Conservation of the sequence motif in other species
In order to infer general facts about the evolution of the motif, we searched for its presence in the genome of D. pseudoobscura, a species with an ongoing genome project . We located the orthologous region of 322 out of the 368 motifs detected in D. melanogaster, amounting to 87.5% of the sequences. Using the same criterion as in D. melanogaster, we identified 178 conserved motifs within the orthologous region of D. pseudoobscura, accounting for 55.3% of the 322 sequences.
If the information associated with each one of the motifs from the same cluster is at least partially redundant, those motifs not belonging to clusters are expected to be more constrained than the clustered ones. Nevertheless, we identified only 62 motifs in D. pseudoobscura within the 120 orthologous regions with motif not associated in clusters in D. melanogaster. These values do not differ significantly from the null hypothesis of equal degree of conservation in both subsets (χ2 = 1.010, 1 df, P < 0.3150).
Correlation between values for differences from consensus between D. melanogaster and D. pseudoobscura
D. pseu\D. mel a
We also searched for the presence of the motif in other species using BLAST search. We identified one sequence within the first intron of the gene Om(1D) (Accession No. X56682) from D. ananassae, species that belongs also to the subgenus Sophophora (as D. melanogaster and D. pseudoobscura). This gene is the orthologous to the D. melanogaster Bar-H1 (B-H1) that also presents the motif in orthologous location. We also identified the motif in two genes of D. virilis, from the Drosophila subgenus. One copy is located 5' from the actin E2 gene (Accession No. AF358263). The orthologous sequence in D. melanogaster also contains a sequence equivalent to those of the motif, but presenting 5 differences from the consensus. The other copy located in D. virilis is present within the enhancer region of the achaete-scute (ac-sc) complex (Accession No. AF132809). The orthologous sequences in D. melanogaster and D. pseudoobscura lacked the motif. The 27 bp motif seems not to be present in the Anopheles gambiae genome. BLAST searches against the A. gambiae genome using as a query the first intron of the A. gambiae wg gene does not retrieve any sequence with similar characteristics to the Drosophila 27 bp motif (data not shown).
Most essential processes, such as transcriptional and post-transcriptional regulation, DNA replication, or higher-order chromatin structure, are under the control of cis-acting elements located within non-coding DNA (see for instance, [32–34]). Here, we describe a 27 bp long repetitive DNA sequence within the Drosophila genome that, based on its characteristics, may be considered one of these cis-acting elements.
Mainly, there is a significant association of the 27 bp long motif to genes involved in development, whose molecular function is related to signal transduction and/or transcriptional regulation (Table 2). This association may be indeed stronger than shown in Table 2, taking into account that any given gene is usually classified under several different categories of the Gene Ontology classification. For instance, although only 41.3% of the biological process classifications of the 22 genes with the motif present within an intron are annotated as involved in development (Table 2), 19 of them (~86%) are indeed known to be involved in development.
Several components of main signaling pathways are associated with the motif, such as: Delta (Dl) and Serrate (Ser) (ligands), Notch (N) (receptor) and Su(H) (nuclear transducer) of the N signaling pathway; wg (ligand) and frizzled3 (fz3) (receptor) of the Wnt signaling pathway; Epidermal growth factor receptor (Egfr) (receptor) and vein (vn) (ligand) of the Egfr signaling pathway; hedgehog (hh) (ligand) of the hh signaling pathway; or decapentaplegic (dpp) (ligand) of the TGF-β receptor signaling pathway. There are also several selector or selector-like genes , conserved transcription factors that act controlling the development of morphogenetic fields giving rise to specific adult structures, such as twist (twi) in mesoderm tissues, Distal-less (Dll) in the ventral appendages, pannier (pnr) in dorso-medial domains of trunk and head, brachyenteron (byn) in posterior terminal structures, engrailed (en) in posterior compartments, and B-H1 and Bar-H2 (B-H2) in neural tissues (see FlyBase  for a description of these genes' function, plus references therein). Thus, this motif may define an important regulatory network, linking together several fundamental genes active during Drosophila development (Table 2 and Additional file 1).
Second, our strategy to search for the conservation of the motif in D. pseudoobscura (see Methods) revealed that 70% of the regions around the motif in D. melanogaster present at least 70 identical nucleotides out of 100 bp of sequence in D. pseudoobscura. A recent comparison of non-coding regions between D. melanogaster and D. pseudoobscura  revealed that only 28% of the non-coding sequences are conserved between these two species. The conserved non-coding sequences (defined as windows of at least 10 bp with at least 90% of nucleotide identity) tend to be spatially clustered. Therefore, these data strongly indicate that the motif described in this paper is generally located within regulatory regions of genes.
In agreement with this prediction, several copies of the motif are located within known regulatory regions. Thus, the six motifs associated to dpp (Additional file 1) are located within the 3' "disk region" of the gene, an enhancer controlling the expression of dpp in imaginal discs . Two motifs located between 10 and 15 Kb upstream of Ser are included within the "dorsal wing regulator" enhancer (DWR), which directs the expression of Ser in the wing disc . The motif associated to Su(H) is located within the autoregulatory socket enhancer (ASE), a discrete cell specific transcriptional enhancer active only in the socket cells of external sensory organs . This enhancer is regulated by the Su(H)'s own protein product, containing eight predicted high-affinity binding sites for the Su(H) protein. The motif is embedded within these binding sites. In contrast to the previous examples, the regulatory sequences of Dl are dispersed over a large stretch of DNA rather than being concentrated in discrete zones. The first intron of Dl, which presents one motif, contains a quantitative enhancer of transcription acting on several different organs .
Several characteristics of the motif, such as its trend to form clusters within/around genes (Fig. 5) or its biased location in regard to the transcription units (Fig. 3), might be a consequence of its association with regulatory regions of genes associated with signal transduction pathways, and transcription factors involved in several developmental processes. In general, these genes present several independent enhancers located not only upstream, but also downstream or in intronic regions. The modularity of the enhancer architecture  is in agreement with our observation of similar constraints acting on those motifs belonging to clusters and the remaining, non-clustered, motifs.
In a similar way, one could image that the underrepresentation of the motif in the X chromosome might be due to a biased distribution of developmental genes on this chromosome. Nevertheless, this does not seem to be the case, since137 of the 681 fly genes associated with the GO term "development", and whose chromosomal locations are known, lay on the X chromosome, slightly over the expected value of 128, estimated based on the sequence length of each chromosomal arm (χ2 test; P > 0.05). Alternatively the explanation for the underrepresentation of the motif in the X chromosome might be related to the lower effective population size of this chromosome when compared to autosomes (3/4 that of autosomes). Because of that, according to the nearly neutral theory of molecular evolution (see  for a recent review), natural selection is expected to be less efficient to create and/or maintain this sequence motif in the X chromosome.
It should be noted that although this 27 bp motif does not show any significant similarity with any of the transposable elements listed in the transposon database at the Berkeley Drosophila Genome Project , we cannot rule out a transposable element origin for this motif. All transposons are known to be underrepresented on the X chromosome relative to the autosomes . The underrepresentation of the 27 bp motif in the X chromosome could thus simply reflect its origin. It has been suggested that in an unknown proportion of cases transposons might be a source of "ready-to-use" regulatory motifs [43, 44].
The comparative genomic approach revealed that the regulatory network defined by this motif in D. melanogaster is partially shared with D. pseudoobscura. Furthermore, conserved motifs seem to be constrained to maintain not only location but also the exact sequence variant at each particular position (Table 3 and Fig. 6), as described previously in the case of binding sites for transcription factors envolved in early Drosophila development . Although the early stage of the D. pseudoobscura genome project precludes a full comparison, our results indicate that more than half of the motifs are conserved between the two species. Two facts suggest that this figure might underestimate the actual number of conserved sequences. First, while the consensus sequence for the motif is identical in both species, the inferred PWM might be different, as we used the PWM derived from D. melanogaster to classify a sequence from D. pseudoobscura as matching the motif. In fact, the average number of differences between the 178 motifs of D. melanogaster whose orthologous has been identified in D. pseudoobscura and the consensus sequence is 2.07, while this figure reaches 2.43 in the case of the D. pseudoobscura motifs. Second, the cut-off score (allowing for a maximum of four differences from consensus in the changing positions) might be too stringent, leading to the detection of only high affinity binding sites-containing motifs conserved in both species. In fact, we found several cases of orthologous regions in D. pseudoobscura containing a sequence that differs from the consensus in only 5 or 6 differences, but that were, nevertheless, excluded from our data set for further analysis. A similar situation occurs in the case of the actin E2 from D. virilis, whose orthologous sequence in D. melanogaster presents 5 differences from consensus.
The detection of the motif in other Drosophila species from the Drosophila subgenus shows that this motif arose within the genome before the radiation of the genus. Its absence in Anopheles is expected, taking into account that only a very small proportion of regulatory regions are conserved between these two genera of Diptera [12, 45].
Finally, it is interesting to remark that one concern of cis-regulatory prediction algorithms is the rate of false positives [9, 10]. This problem is not present in the case of the motif described here due to its unusually long length compared to other regulatory motifs, which makes its appearance by chance highly improbable. This characteristic and the others discussed previously, makes this motif very useful towards the annotation of functional regulatory regions within the Drosophila genome and the construction of regulatory networks of Drosophila development. It may also be useful for inferring the function of a number of genes that show no similarity with other known genes. Functional tests will be required to characterize the function of this motif.
We have identified a cis-regulatory sequence motif widely distributed within the Drosophila genome in association with genes involved in development and/or signal transduction. Due to the unusual long size of this motif (27 bp) in comparison with other regulatory motifs, its appearance by chance is highly improbable. Because of that, this motif may be very useful towards the annotation of functional regulatory regions within the Drosophila genome as well as the construction of regulatory networks of Drosophila development.
BLAST searches and sequence alignments
BLAST searches were conducted using the BLAST server from NCBI  and the BLAST server from the D. pseudoobscura Genome Project . The program diAlign  was used to perform local multiple alignments to identify homologous stretches of DNA interspersed between sequences of no homology.
Identification and location of a 27 bp motif in the D. melanogaster genome
A strategy similar to the use of position weigth matrices (PWMs) for the identification of binding sites for transcription factors was used to search for the presence of a 27 bp motif in the D. melanogaster genome previously identified by BLAST searches. It should be noted, however, that in our case we do not use binding affinity/functional information on the observed nucleotide frequencies to weight each position accordingly. We use the web server Target Explorer [27, 28]; that easily allows for the editing of the PWM using the following general rules. In positions where the most frequent nucleotide appears in => 90% of the sampling sequences, any non-matching nucleotide was weighted very negatively (-20), while a matching nucleotide is given a +1 weight. In the remaining positions, a weight of +1 was given to the nucleotide present in the preliminary consensus and a weight of -1 was given to the other nucleotides. In the case of nucleotide position 23, where C and T seem to be equally used, the presence of either nucleotide was weighted as +1. To identify those sequences differing from consensus in less than 5 differences, for instance, the cut-off score was set as +18. This approach completely excludes any sequence that differs at any one of the almost invariant positions. The identification of the motifs was performed using the release 3 of the D. melanogaster genome and the program Patser  as implemented by Target Explorer. Both the location of the repeats in regard to the nearest transcription units and the classification of associated genes according to Gene Ontology categories were also performed by Target Explorer.
Generation of random sequences was done by the random generator tool available at the Regulatory Sequence Analysis Tools web page . This program generates random sequences with the same oligonucleotide composition as observed in the intergenic regions of the selected organism (D. melanogaster) by a Markov chain probabilistic model.
Identification of D. pseudoobscura genomic regions orthologous to those of D. melanogaster containing the 27 bp motif
In order to identify the D. pseudoobscura genomic regions orthologous to those of D. melanogaster presenting the motif, we employed two different approaches: (1) BLAST searches against the D. pseudoobscura sequencing reads from the D. pseudoobscura Genome Project web page  using as a query each one of the motifs identified in D. melanogaster surrounded by 300 bp flanking sequences upstream and downstream from the motif. We considered a D. pseudoobscura sequencing read as the orthologous one if there was at least a stretch of 70/100 identical nucleotides. We used a word size of 7 nucleotides and a percent identity of 70%. If the orthologous region is identified but the sequencing read does not contain the motif, we search the D. pseudoobscura genomic region in between conserved orthologous blocks flanking the motif. To do so, we search for the contig containing this sequence and align this region with the D. melanogaster region using diAlign . (2) If no orthologous region is identified according to the previous criterion and the 27 bp motif is known to be within intron sequence in D. melanogaster, we searched for the D. pseudoobscura orthologous region using the corresponding D. melanogaster whole transcript. In the case of intergenic regions, we considered only those sequence contigs that include both genes around the motif, with one exception; if the motif is present close to the transcript (<1000 bp) we analyzed 10000 bp of the corresponding D. pseudoobscura orthologous region.
This work was supported by grant POCTI/37402 from Fundação para a Ciência e a Tecnologia (FCT), Portugal to FC; JC is a recipient of the postdoctoral fellowship SFRH/BPD/7094/2001 from FCT. CPV is a recipient of the postdoctoral fellowship SFRH/BPD/5592/2001 from FCT. FC is an EMBO Young Investigator and Leukemia and Lymphoma Society Special Fellow.
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