Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identical n-mers (n âĽ 7) identified in the zebrafish, mouse, and human sequences of the five syntenic CNS were examined for the presence of transcription factor binding motifs; only motifs with E-value E â¤ 0.1 are shown. (XLSX 15 kb

Alexander Poliakov

Dario Boffelli

Inna Dubchak

Nadav Ahituv

Nir Oksenberg

Sachiko Takayama

Seok-Jin Heo

Song Yang

PubMed

List of primers used in the cloning of the reporter vectors. (XLSX 11 kb

Song Yang (162335)

Nir Oksenberg (102535)

Sachiko Takayama (3555278)

Seok-Jin Heo (46279)

Alexander Poliakov (35431)

Nadav Ahituv (34361)

Inna Dubchak (3021)

Dario Boffelli (219692)

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Additional file 5: Table S4. of Functionally conserved enhancers with divergent sequences in distant vertebrates

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Functionally conserved enhancers with divergent sequences in distant vertebrates

Additional file 4: Table S3. of Functionally conserved enhancers with divergent sequences in distant vertebrates

BackgroundTo examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. Our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.ResultsWe searched for sequences that were conserved within groups of closely related species but not between groups of more distant species, and were associated with an epigenetic mark of enhancer activity. To facilitate inferring orthology between non-conserved sequences, we limited our search to introns whose orthology could be unambiguously established by mapping the bracketing exons. We show that a subset of these non-conserved but syntenic sequences from the mouse and zebrafish genomes have homologous functions in a zebrafish transgenic enhancer assay. The conserved expression patterns driven by these enhancers are probably associated with short transcription factor-binding motifs present in the divergent sequences.ConclusionsWe have identified numerous potential enhancers with divergent sequences but a conserved function. These results indicate that selection on function, rather than sequence, may be a common mode of enhancer evolution; evidence for selection at the sequence level is not a necessary criterion to define a gene regulatory element

Yang, Song

Oksenberg, Nir

Takayama, Sachiko

Heo, Seok-Jin

Poliakov, Alexander

Ahituv, Nadav

Dubchak, Inna

Boffelli, Dario

eScholarship - University of California

https://figshare.com/articles/Additional_file_5_Table_S4_of_Functionally_conserved_enhancers_with_divergent_sequences_in_distant_vertebrates/4443665

Functionally conserved enhancers with divergent sequences in distant vertebrates

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Springer - Publisher Connector

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eScholarship - University of California

Springer - Publisher Connector