A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.
BACKGROUND
Transcription initiation is controlled by cis-regulatory modules. Although these modules are usually made of clusters of short transcription factor binding sites, a small minority of such clusters in the genome have cis-regulatory activity. This paradox is currently unsolved.


RESULTS
To identify what discriminates active from inactive clusters, we focused our attention on short topologically unconstrained clusters of two ETS and two GATA binding sites, similar to the early neural enhancer of Ciona intestinalis Otx. We first computationally identified 55 such clusters, conserved between the two Ciona genomes. In vivo assay of the activity of 19 hits identified three novel early neural enhancers, all located next to genes coexpressed with Otx. Optimization of ETS and GATA binding sites was not always sufficient to confer activity to inactive clusters. Rather, a dinucleotide sequence code associated to nucleosome depletion showed a robust correlation with enhancer potential. Identification of a large collection of Ciona regulatory regions revealed that predicted nucleosome depletion constitutes a general signature of Ciona enhancers, which is conserved between orthologous loci in the two Ciona genomes and which partitions conserved noncoding sequences into a major nucleosome-bound fraction and a minor nucleosome-free fraction with higher cis-regulatory potential. We also found this signature in a large fraction of short Drosophila cis-regulatory modules.


CONCLUSIONS
This study indicates that a sequence-based dinucleotide signature, previously associated with nucleosome depletion and independent of transcription factor binding sites, contributes to the definition of a local cis-regulatory potential in two metazoa, Ciona intestinalis and Drosophila melanogaster.
Khoueiry
Pierre
P
Institut du Biologie de Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy Case 907, F-13288, Marseille Cedex 9, France. pierre.khoueiry@embl.de
Rothbächer
Ute
U
Ohtsuka
Yukio
Y
Daian
Fabrice
F
Frangulian
Eric
E
Roure
Agnès
A
Dubchak
Inna
I
Lemaire
Patrick
P
D000818:Animals; D001665:Binding Sites / Q000502:physiology; D002938:Ciona intestinalis / Q000235:genetics / Q000502:physiology; D017124:Conserved Sequence / Q000235:genetics / Q000502:physiology; D004331:Drosophila melanogaster / Q000235:genetics / Q000502:physiology; D004742:Enhancer Elements, Genetic / Q000235:genetics / Q000502:physiology; D005346:Fibroblast Growth Factors / Q000235:genetics; D050980:GATA Transcription Factors / Q000235:genetics / Q000502:physiology; D050437:Genes, Developmental / Q000235:genetics / Q000502:physiology; D016678:Genome / Q000235:genetics; D006801:Humans; D009474:Neurons / Q000502:physiology; D009707:Nucleosomes / Q000235:genetics / Q000502:physiology; D050783:Proto-Oncogene Proteins c-ets / Q000235:genetics / Q000502:physiology; D050436:Regulatory Elements, Transcriptional / Q000235:genetics / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism* / Q000502:physiology
D050980:GATA Transcription Factors; D009707:Nucleosomes; D050783:Proto-Oncogene Proteins c-ets; D014157:Transcription Factors; D005346:Fibroblast Growth Factors