Tregwiki:Recent bibliography

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Application of motif search but simple ERE-steroird inverted repeat model]

  • PSSM and extensions:
  • Transcription factor binding domains:
  • Ultraconserved and Co:
    • The strange story of Evf-2 which is at the same time enhancer AND ncRNA binding to a homf-function studies in flies and mice indicate that these three genes may have a conserved role in regional specification, there is no obvious conservation of the particular cell fates deriving from corresponding domains. The three-column expression pattern may thus represent a developmental mechanism that is more resistant to evolutionary changes than genetic events upstream or downstream of it.
    • nature paper describing how regulation of yeast has changed yet phenotype is almost identical between S cerevisia and C albins
  • ultraconserved elements:
    • ultras avoid segmental duplications
  • RNA and regulation:

quote from abstract: "Finally, we conducted DNAse I-footprinting assays in nuclear extracts for the 184bp region and detected two protected sequences. Data bank search indicates that these sites contain consensus binding sites for transcription factors." Wonder if they ever pasted a random sequence into transfac match...

  • Bio papers about chosen transcription factors:
    • Regulation of the transcription factor FOXM1c by Cyclin E/CDK2 PMID 16504183
  • combinatorial detection
    • CodeFinder tries to find overrepresented combinations

Applikation of motif discovery in plants]

  • Motif Scanning
    • Yeast Dyad scanning distances conserved, direction as well. Tf active in Multiple conditions -> variable distances
  • Chip-Chip or similar, large sequence biology data:
    • E2F1 Chip2Chip suggests that 20% of all promoters are bound by E2F1, usual proximal, sites do not correspond to matrix (!)
    • Yeast one hybrid assay to determine matrices for given transcription factor, WITHOUT selex and without Chip-Chip
  • Redundancy in Regulation:
    • Demonstration that you can delete functional binding sites without changing expression (note: at a certain tissue/development stage/pathway status!!)
    • Another example that binding sites cluster together
    • Drosophila colocalization hotspots bind many different factors: "we predict that many more factors will show strong colocalization and that hotspots may recruit up to a few hundred different proteins. This observation contrasts with results in yeast where overlap between transcription factors was relatively rare and hotspots were not apparent (7, 8)."