1. BI-DIRECTIONAL
PROMOTERS
By:Sanju Sinha
Date: 21-05-2014

2. Promoters is a region of DNA
that initiates the transcription
of a particular gene.
What is Promoter?

3. Promoter is a Important element for gene regulation.
TSS

4. Assumptions
• Promoters are
Usually
conceptualized as
upstream of the
sequences they
promote.
Facts
• Scientist do not really
know in which
direction promoters
usually transcribe or
if they only
transcribe in one
direction or not.
Present-Research
• Their Directions
possibilities and
parts of
promoter which
plays role in
deciding direction.

5. Promoter is a Important element for gene regulation.
TSS

6. On Basis of Directions they can
transcribe, Promoters can be
classified into two sub-classes-
1.Unidirectional
2.Bi-Directional*

7. Definition-
Bidirectional promoters
are short (<1 kbp), intergenic
regions of DNA between the
5‘ ends of the genes in a
bidirectional gene pair.

8. Head-To-Head Fashion Alignment

9. 1000 BP
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So Lets Increase This Window
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15000 BPVS

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11. 1000 BP
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13. what is the promoter length Distribution then?

14. Promoter Length Histogram (window =1500)
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On Basis of these Results:
Mean Promoter length is : 335 Median of Promoter length is: 189

16. Conclusion we can draw:
• Clusters near the gene starting position in
range of 189.
• The probability of occurrence of another
gene at a distance from one gene first
increases exponentially till 335 and then
decreases and then saturates tending to
constant*.
*Not sure as second differentiation is still positive and can even change its concavity.

17. Visions and Logics to verify data:
• Making a artificial gene distribution
like system.
• A Cyber-Refgene.txt file.
• Using the same tunnel and get the
distribution.
• Comparing the Distribution.

18. 1. All Further Data is being
taken from a review paper.
2. All the sources and platforms
are mentioned on last slide.
PART - 2

19. Is it possible to identify consistent
pattern that distinguish
Bidirectional and Unidirectional ???
What to Look for …..

20. GC content
INR
TATA Box
BRE
DPE
CCAAT

21. Location of different elements of PROMOTER(lacking TATA)

22. GC content
INR
TATA Box
BRE
DPE
CCAAT

23. Statistical Results of GC content:
Average GC content percentage
Bidirectional: 66%
Unidirectional: 53%

24. • Bidirectional: 66%
• Unidirectional: 53%GC content
INR
TATA Box
BRE
DPE
CCAAT

25. INR-Initiator element
• Functionally similar to TATA box.
• Accurate transcription initiation ,
INR btw -3 to +5 is necessary.
• Increases the strength of TATA
containing promoters.
Bidirectional: 25.3%
Unidirectional: 30.8%

26. • Bidirectional: 66%
• Unidirectional: 53%GC content
• Bidirectional: 25.3%
• Unidirectional: 30.8%INR
TATA Box
BRE
DPE
CCAAT

27. TATA box:
Bidirectional: Most of them Lacks.
Unidirectional: Comparatively high.
• Located at -30 both in Unidirec and
Bi-direc Promoters

28. • Bidirectional: 66%
• Unidirectional: 53%GC content
• Bidirectional: 25.3%
• Unidirectional: 30.8%INR
• Bidirectional: Lacks Mostly(No data)
• Unidirectional: Have more frequentlyTATA Box
BRE
DPE
CCAAT

29. BRE(B-recognition element)
• Located directly in front of TATA
• TFIIB recognizes it and binds.
Bidirectional: 16.5%
Unidirectional: 11%

30. • Bidirectional: 66%
• Unidirectional: 53%GC content
• Bidirectional: 25.3%
• Unidirectional: 30.8%INR
• Bidirectional: Lacks mostly(No Data)
• Unidirectional: Have more frequentlyTATA Box
• Bidirectional: 16.5%
• Unidirectional: 11.1%BRE
DPE
CCAAT

31. DPE(Downstream Promoter Element)
• Located at +30 position
• Binds to common transcription
factor(TFIID) in absence of TATA
Bidirectional: 46.6%
Unidirectional: 50.6%

32. • Bidirectional: 66%
• Unidirectional: 53%GC content
• Bidirectional: 25.3%
• Unidirectional: 30.8%INR
• Bidirectional: Lacks mostly(No Data)
• Unidirectional: Have more frequentlyTATA Box
• Bidirectional: 16.5%
• Unidirectional: 11%BRE
• Bidirectional: 46.6%
• Unidirectional: 50.6%DPE
CCAAT

33. CCAAT box:
• Located at 75-80 BP before TSS
• signals the binding site for the
RNA transcription factor
Bidirectional: 12.9%
Unidirectional: 6.9%

34. • Bidirectional: 66%
• Unidirectional: 53%GC content
• Bidirectional: 25.3%
• Unidirectional: 30.8%INR
• Bidirectional: Lacks mostly(No Data)
• Unidirectional: Have more frequentlyTATA Box
• Bidirectional: 16.5%
• Unidirectional: 11.1%BRE
• Bidirectional: 46.6%
• Unidirectional: 50.6%DPE
• Bidirectional: 12.9%
• Unidirectional: 6.9%CCAAT

35. CpG islands:
The CpG sites or CG sites are regions of DNA where
a cytosine nucleotide occurs next to a guanine
Source:Trinklein, N. D., Aldred, S. H., Hartman, S. J., Schroeder, D. I., Otillar, R. P., and Myers, R. M. (2004) Genome Res.,14, 6266.
• 77% B-DP located in CpG islands
compared with 38% of U-DP.
• 90% B-DP located in CpG islands
compared with 45% of U-DP.
Source: Yang, M. Q., and Elnitski, L. L. (2008) BMC Genom., 9 (Suppl. 2), S3.

36. Bi-Directional promoters enrich with
following specific Binding sites of TF.
• GABPA
• MYC
• E2F1
• E2F4
• Nrf1
• YY1
• NFY
• SP1

37. PART- 3
Follow the tunnel
So the first thing is
- GC CONTENT

38. Lets check the GC content-
Wait..Wait..Wait..
Where’s the length of
Unidirectional Promoters??

39. No, We Don’t . But we
have some Important
values which can help us.
1. Mean length of Bidirectional Promoter.
2. Median Length of Bidirectional Promoters.
3. We Know in Paper they take 1000BP

40. Comparison of GC content between
Unidirectional (Mean Length)
Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)

41. GC content Distribution- Unidirectional_MEAN
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AVERAGE: 54.6%

42. GC content Distribution- Unidirectional_MEDIAN
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AVERAGE: 56.9%

43. GC content Distribution- Unidirectional_1000 BP
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AVERAGE: 49.7%

44. Comparison of GC content between
Unidirectional (Mean Length)
Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)

45. GC content Distribution- BIDIRECTIONAL
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AVERAGE: 64%

46. Statistical Conclusion:
Unidirectional: 53.7%
Bidirectional: 64%
Average GC content :

47. NOTE**DATA SOURCE and Platforms
1. All the Data mentioned in Slides 17-36 are taken from Review:
Bidirectional Promoters in the Transcription of Mammalian Genomes.
A. S. Orekhova and P. M. Rubtsov*
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, 119991
Moscow, Russia; fax: (499) 1351405; Email: rubtsov@eimb.ru
2. All other data in these presentation belong to Sanju Sinha and he have all rights on those.
Any copying without mentioning the relevance source shall be considered as plagiarism.
3.twoBitToFa on linux platform is being used to done the calculations.
4. All coding is being done via Python language.

48. THANKS