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BI-DIRECTIONALPROMOTERS
By:Sanju SinhaDate: 21-05-2014
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Promoters is a region of DNA that initiates the transcription of a particular gene.
What is Promoter?
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Promoter is a Important element for gene regulation.
TSS
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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.
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Promoter is a Important element for gene regulation.
TSS
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On Basis of Directions they can transcribe, Promoters can be classified into two sub-classes-
1.Unidirectional 2.Bi-Directional*
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Definition-Bidirectional promoters are short (<1 kbp), intergenic regions of DNA between the 5‘ ends of the genes in a bidirectional gene pair.
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Head-To-Head Fashion Alignment
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1000 BP1200 BP1500 BP
So Lets Increase This Window
10000 BP12000 BP15000 BPVS
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f(x) = 1251.38499631088 ln(x) − 3205.50840193062
Series1 Logarithmic (Series1)
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1000 BP1200 BP1500 BP
So Lets Increase This Window
10000 BP12000 BP15000 BPVS
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Chart Title
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what is the promoter length Distribution then?
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Promoter Length Histogram (window =1500)
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0 5000 10000 15000 20000 250000
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f(x) = 1251.38499631088 ln(x) − 3205.50840193062
Series1Logarithmic (Series1)
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On Basis of these Results:
Mean Promoter length is : 335 Median of Promoter length is: 189
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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.
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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.
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1. All Further Data is beingtaken from a review paper.
2. All the sources and platforms are mentioned on last slide.
PART - 2
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Is it possible to identify consistent pattern that distinguish Bidirectional and Unidirectional ???
What to Look for …..
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GC content
INR
TATA Box
BRE
DPE
CCAAT
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Location of different elements of PROMOTER(lacking TATA)
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GC content
INR
TATA Box
BRE
DPE
CCAAT
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Statistical Results of GC content:Average GC content percentage
Bidirectional: 66%
Unidirectional: 53%
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• Bidirectional: 66%• Unidirectional: 53%GC content
INR
TATA Box
BRE
DPE
CCAAT
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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%
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• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR
TATA Box
BRE
DPE
CCAAT
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TATA box:
Bidirectional: Most of them Lacks.
Unidirectional: Comparatively high.
• Located at -30 both in Unidirec and Bi-direc Promoters
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• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR• Bidirectional: Lacks Mostly(No
data)• Unidirectional: Have more
frequently
TATA Box
BRE
DPE
CCAAT
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BRE(B-recognition element)• Located directly in front of TATA• TFIIB recognizes it and binds.
Bidirectional: 16.5%
Unidirectional: 11%
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• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR• Bidirectional: Lacks mostly(No
Data)• Unidirectional: Have more
frequently
TATA Box • Bidirectional: 16.5%• Unidirectional: 11.1%BRE
DPE
CCAAT
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DPE(Downstream Promoter Element)• Located at +30 position• Binds to common transcription
factor(TFIID) in absence of TATA
Bidirectional: 46.6%
Unidirectional: 50.6%
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• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR• Bidirectional: Lacks mostly(No
Data)• Unidirectional: Have more
frequently
TATA Box • Bidirectional: 16.5%• Unidirectional: 11%BRE• Bidirectional: 46.6%• Unidirectional: 50.6%DPE
CCAAT
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CCAAT box:• Located at 75-80 BP before TSS• signals the binding site for the
RNA transcription factor
Bidirectional: 12.9%
Unidirectional: 6.9%
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• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR• Bidirectional: Lacks mostly(No
Data)• Unidirectional: Have more
frequently
TATA Box • Bidirectional: 16.5%• Unidirectional: 11.1%BRE• Bidirectional: 46.6%• Unidirectional: 50.6%DPE• Bidirectional: 12.9%• Unidirectional: 6.9%CCAAT
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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.
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Bi-Directional promoters enrich with following specific Binding sites of TF.
• GABPA• MYC• E2F1• E2F4• Nrf1• YY1• NFY• SP1
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PART- 3Follow the tunnel
So the first thing is- GC CONTENT
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Lets check the GC content-
Wait..Wait..Wait..
Where’s the length of Unidirectional Promoters??
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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
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Comparison of GC content between
Unidirectional (Mean Length)Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)
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GC content Distribution- Unidirectional_MEAN
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 More0
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AVERAGE: 54.6%
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GC content Distribution- Unidirectional_MEDIAN
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 More0
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AVERAGE: 56.9%
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GC content Distribution- Unidirectional_1000 BP
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 More0
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AVERAGE: 49.7%
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Comparison of GC content between
Unidirectional (Mean Length)Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)
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GC content Distribution- BIDIRECTIONAL
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 More0
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AVERAGE: 64%
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Statistical Conclusion:
Unidirectional: 53.7%
Bidirectional: 64%
Average GC content :
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NOTE**DATA SOURCE and Platforms1. 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: [email protected]
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.
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THANKS