Difference between revisions of "Part:BBa K203126:Design"

 
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===Design Notes===
 
===Design Notes===
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To be updated
 
  
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More than 4000 promoter sequences from the human genome were scanned by promotersweep[1]. Transcription Factor binding sites (TFBS) thus identified were stored in HEARTBEAT DB[2], a database of transcription factor binding preferences. From HEARTBEAT DB, we calculated probability density functions (pdf) for the positioning of SREBP along promoters. Transcription factors co-occurring with SREBP were identified from HEARTBEAT DB. A number of sequences was designed (TFBS were placed under the peaks of the pdf), some of which include Sp1 sites as a transcription factor showing a high level of co-occurrence with Sp1.  Of all Sequences, HB 9 (this part) and HB 8 ([[Part:BBa_K203125]]) showed activity. These were the sequences best reflecting the predictions of HEARTBEAT, in that they contained TFBS for SREBP under both peaks of the pdf, and contain Sp1 binding sites under the peak of the Sp1 pdf (not shown).
  
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[[Image:HD09_highlight.jpg|thumb|none|480px|Fig 1: HEARTBEAT describes the spatial distribution of Transcription Factor Binding Sites along a mammalian promoter. The diagram on the top shows this distribution for SREBP. HEARTBEAT also describes Transcription Factors co-occurring with a given TF, which, for SREBP, is Sp1. We placed SREBP and Sp1 Binding sites according to the predicted distribution and found only promoters which resemble the distribution closest to be induced by SREBP (see small diagram). Other promoter sequences are not functional (not shown).]]
  
 
===Source===
 
===Source===
  
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To be updated
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Sequence ordered from GeneArt
  
 
===References===
 
===References===
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[1] del Val C. et al. Promotersweep: a tool for identi�cation of transcription factor binding sites. Theor. Chem. Acc., 2009. Available online at http://www.springerlink.com/content/92r518nq585q716j/.
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[2] HEARTBEAT, a database describing transcription factor binding preferences. iGEM 2009 Heidelberg team wiki. http://2009.igem.org/Team:Heidelberg/HEARTBEAT_database

Latest revision as of 19:43, 21 October 2009

SREBP regulated promoter, predicted, tested HB9


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

More than 4000 promoter sequences from the human genome were scanned by promotersweep[1]. Transcription Factor binding sites (TFBS) thus identified were stored in HEARTBEAT DB[2], a database of transcription factor binding preferences. From HEARTBEAT DB, we calculated probability density functions (pdf) for the positioning of SREBP along promoters. Transcription factors co-occurring with SREBP were identified from HEARTBEAT DB. A number of sequences was designed (TFBS were placed under the peaks of the pdf), some of which include Sp1 sites as a transcription factor showing a high level of co-occurrence with Sp1. Of all Sequences, HB 9 (this part) and HB 8 (Part:BBa_K203125) showed activity. These were the sequences best reflecting the predictions of HEARTBEAT, in that they contained TFBS for SREBP under both peaks of the pdf, and contain Sp1 binding sites under the peak of the Sp1 pdf (not shown).

Fig 1: HEARTBEAT describes the spatial distribution of Transcription Factor Binding Sites along a mammalian promoter. The diagram on the top shows this distribution for SREBP. HEARTBEAT also describes Transcription Factors co-occurring with a given TF, which, for SREBP, is Sp1. We placed SREBP and Sp1 Binding sites according to the predicted distribution and found only promoters which resemble the distribution closest to be induced by SREBP (see small diagram). Other promoter sequences are not functional (not shown).

Source

Sequence ordered from GeneArt

References

[1] del Val C. et al. Promotersweep: a tool for identi�cation of transcription factor binding sites. Theor. Chem. Acc., 2009. Available online at http://www.springerlink.com/content/92r518nq585q716j/.

[2] HEARTBEAT, a database describing transcription factor binding preferences. iGEM 2009 Heidelberg team wiki. http://2009.igem.org/Team:Heidelberg/HEARTBEAT_database