General Information
Name
mE1_TFBS_HSA
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000258
Project
Data Provider
Title
Transcription factor hot spots (high occupancy sites) identified by ChIP of 41 factors in embryos.
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Other tissues studied
    Cell line
    Key genes
    (transgene_used)
    Methods
    Sample preparation
    Embryos were collected aged appropriately, then dechorionated and formaldehyde fixed. Fixed embryos were then homogenized, nuclei were pelleted, and chromatin was sheared by sonication.
    Biosamples analyzed by this result (53)
    Biosample
    Type
    Title
    D. melanogaster, embryo (stage 11), source for chromatin (z ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (bcd ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (da ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (dl ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (gt ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (hb ChIP).
    D. melanogaster, embryo (stage 4-5), source for chromatin (kni ChIP).
    D. melanogaster, embryo (stage 5), source for chromatin (ftz ChIP).
    D. melanogaster, embryo (stage 5), source for chromatin (Mad ChIP).
    D. melanogaster, embryo (stage 5), source for chromatin (Med ChIP).
    Showing 10 / 53 records. Use Export to HitList above to see all
    Data Analyzed
    Protocol
    Chromatin was immunoprecipitated using the appropriate antibody and the recovered material was amplified by PCR.
    Mode of Assay
    The recovered material was characterized by Affymetrix whole-genome tiling array.
    Raw Data Analyzed (53)
    Assay / Reagent collection
    Type
    Title
    ChIP-chip of kni in D. melanogaster, embryo (stage 4-5).
    ChIP-chip of Mad in D. melanogaster, embryo (stage 5).
    ChIP-chip of Trl in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of Ubx in D. melanogaster, iso-1 strain, embryo (3-8 hr AEL).
    ChIP-chip of ttk in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of ftz-f1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of sbb in D. melanogaster, iso-1 strain, embryo (0-4 hr AEL).
    ChIP-chip of cad in D. melanogaster, iso-1 strain, embryo (0-4 hr AEL).
    ChIP-chip of GATAe in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL).
    ChIP-chip of hkb in D. melanogaster, iso-1 strain, embryo (0-8 hr AEL).
    Showing 10 / 53 records. Use Export to HitList above to see all
    Processed Data Analyzed (41)
    Result
    Type
    Title
    ChIP-chip peak calls for da in D. melanogaster, embryo (stage 4-5).
    ChIP-chip peak calls for dorsal in D. melanogaster, embryo (stage 4-5).
    ChIP-chip peak calls for ftz in D. melanogaster, embryo (stage 5).
    ChIP-chip peak calls for gt in D. melanogaster, embryo (stage 4-5).
    ChIP-chip peak calls for hb in D. melanogaster, embryo (stage 4-5).
    ChIP-chip peak calls for kni in D. melanogaster, embryo (stage 4-5).
    ChIP-chip peak calls for Mad in D. melanogaster, embryo (stage 5).
    ChIP-chip peak calls for prd in D. melanogaster, embryo (stage 5).
    ChIP-chip peak calls for shn in D. melanogaster, embryo (stage 5).
    ChIP-chip peak calls for slp1 in D. melanogaster, embryo (stage 5).
    Showing 10 / 41 records. Use Export to HitList above to see all
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis
    To investigate the co-localization of transcription factors, modENCODE ChIP-chip data sets for 25 factors were integrated with ChIP-chip data sets for an 16 additional factors produced by the Berkeley Drosophila Transcription Network Project (BDTNP, FBrf0192397, FBrf0205197, FBrf0205197). Data sets generated for the same factor were merged and the union was used for further analysis. Highly occupied target (HOT) regions were identified using a Gaussian kernel density estimation across the genome with a bandwidth of 300 bp, using the centers of each of the TF binding peaks as points. The density was then scanned for peaks, and each peak was denoted a HOT region. To determine the complexity of the HOT region, the sum of the Gaussian kernalized distance from the peak to each transcription factor that contributed at least 0.1 to peak's strength was calculated. The reported window around each HOT peak was derived by finding the maximum distance (in bp) from the HOT peak to a contributing TF, and then adding 150 bp (one half of the bandwidth). Each window is centered on the HOT peak. A TF complexity score was assigned to each of 38,562 distinct TF binding sites, corresponding to the number of distinct TFs bound (from 1 to ~21). Of these distinct TF binding sites, a subset of 1,962 hot regions (hotspots) had a TF complexity of eight or greater.
    Comments
    Binding profiles of 41 TFs in early embryo development were used to assign a TF complexity score to each of 38,562 distinct TF binding sites, corresponding to the number of distinct TFs bound (from 1 to ~21). Of these distinct TF binding sites, a subset of 1,962 hot regions (hotspots) had a TF complexity of eight or greater, corresponding to ~10 overlapping factors bound.
    HOT spots of increasing TF complexity were strongly correlated to regions of decreased nucleosome density and increased nucleosome turnover.
    This data set is available at http://www.modencode.org/publications/integrative_fly_2010/.
    HOT regions are primarily associated with open chromatin but they do not always demarcate cis-regulatory elements.
    Associated Data
    Size
    Associated features
    38,562 TF_binding_site(s)
    Files
    Additional Information
    Synonyms and Secondary IDs (9)
    Reported As
    Symbol Synonym
    HOT regions analysis
    combined TFBS
    mE1_TFBS_HSA
    mE_Transcription_Factor_Binding_Site_Complexity
    unique binding sites
    Name Synonyms
    Transcription factor hot spots (high occupancy sites) identified by ChIP of 41 factors in embryos.
    Secondary FlyBase IDs
      References (8)