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Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers.

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF - BMC Genomics (2008)

Bottom Line: The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function.Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements.These data establish a basis for further analysis and understanding of neural enhancer function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA. brodyt@ninds.nih.gov

ABSTRACT

Background: The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers.

Results: Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs) made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS.

Conclusion: The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.

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Related in: MedlinePlus

Shared cDTs that contain Pbx/Extradenticle core DNA-binding sites. Cytoscape analysis of shared Pbx/Extradenticle DNA-binding site (TGAT) containing cDT elements present in CNS NB and/or PNS enhancers. cDTs flanking the enhancer names are shared by CSBs of a single enhancer type, and cDTs positioned between the enhancer names are shared in common by CSBs of the two different enhancer types.
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Figure 2: Shared cDTs that contain Pbx/Extradenticle core DNA-binding sites. Cytoscape analysis of shared Pbx/Extradenticle DNA-binding site (TGAT) containing cDT elements present in CNS NB and/or PNS enhancers. cDTs flanking the enhancer names are shared by CSBs of a single enhancer type, and cDTs positioned between the enhancer names are shared in common by CSBs of the two different enhancer types.

Mentions: Our analysis revealed that 8 of the Pbx motifs were shared between CNS and PNS enhancer types, and 16 were shared between similarly expressed enhancers (Figure 2), thus indicating that there appears to be some degree of specificity to Pbx site function when flanking bases are taken into account. Three of the Pbx binding-site containing elements also exhibit ATTA Hox sites: 1) the dodecamer GATGATTAATCT (Pbx site is ATGA, Hox sites in bold) shared by the PNS enhancers edl and amos (references in Table 1), contains a homeodomain ATTA site that overlaps the Pbx site by a single base, and 2) the smaller heptamer ATGATTA, shared by pfe and ato, likewise contains a homeodomain ATTA site (bold) that overlaps ATGA Pbx site by a single base. Adjacent Hox and Pbx sites have been documented to facilitate synergy between the two factors [44]. Taken together our findings suggest that, as with homeodomain-binding sites, the conserved bases flanking putative Pbx sites are functionally important. These flanking bases are likely to confer different DNA-binding affinities for Pbx factors or are required for binding of other TFs.


Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers.

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF - BMC Genomics (2008)

Shared cDTs that contain Pbx/Extradenticle core DNA-binding sites. Cytoscape analysis of shared Pbx/Extradenticle DNA-binding site (TGAT) containing cDT elements present in CNS NB and/or PNS enhancers. cDTs flanking the enhancer names are shared by CSBs of a single enhancer type, and cDTs positioned between the enhancer names are shared in common by CSBs of the two different enhancer types.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2529316&req=5

Figure 2: Shared cDTs that contain Pbx/Extradenticle core DNA-binding sites. Cytoscape analysis of shared Pbx/Extradenticle DNA-binding site (TGAT) containing cDT elements present in CNS NB and/or PNS enhancers. cDTs flanking the enhancer names are shared by CSBs of a single enhancer type, and cDTs positioned between the enhancer names are shared in common by CSBs of the two different enhancer types.
Mentions: Our analysis revealed that 8 of the Pbx motifs were shared between CNS and PNS enhancer types, and 16 were shared between similarly expressed enhancers (Figure 2), thus indicating that there appears to be some degree of specificity to Pbx site function when flanking bases are taken into account. Three of the Pbx binding-site containing elements also exhibit ATTA Hox sites: 1) the dodecamer GATGATTAATCT (Pbx site is ATGA, Hox sites in bold) shared by the PNS enhancers edl and amos (references in Table 1), contains a homeodomain ATTA site that overlaps the Pbx site by a single base, and 2) the smaller heptamer ATGATTA, shared by pfe and ato, likewise contains a homeodomain ATTA site (bold) that overlaps ATGA Pbx site by a single base. Adjacent Hox and Pbx sites have been documented to facilitate synergy between the two factors [44]. Taken together our findings suggest that, as with homeodomain-binding sites, the conserved bases flanking putative Pbx sites are functionally important. These flanking bases are likely to confer different DNA-binding affinities for Pbx factors or are required for binding of other TFs.

Bottom Line: The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function.Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements.These data establish a basis for further analysis and understanding of neural enhancer function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Neural Cell-Fate Determinants Section, NINDS, NIH, Bethesda, Maryland, USA. brodyt@ninds.nih.gov

ABSTRACT

Background: The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers.

Results: Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs) made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS.

Conclusion: The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.

Show MeSH
Related in: MedlinePlus