bi-directional promoters

BI-DIRECTIONALPROMOTERS

By:Sanju SinhaDate: 21-05-2014

Promoters is a region of DNA that initiates the transcription of a particular gene.

What is Promoter?

Promoter is a Important element for gene regulation.

TSS

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.

Promoter is a Important element for gene regulation.

TSS

On Basis of Directions they can transcribe, Promoters can be classified into two sub-classes-

1.Unidirectional 2.Bi-Directional*

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

Head-To-Head Fashion Alignment

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So Lets Increase This Window

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f(x) = 1251.38499631088 ln(x) − 3205.50840193062

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So Lets Increase This Window

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Chart Title

what is the promoter length Distribution then?

Promoter Length Histogram (window =1500)

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f(x) = 1251.38499631088 ln(x) − 3205.50840193062

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On Basis of these Results:

Mean Promoter length is : 335 Median of Promoter length is: 189

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.

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.

1. All Further Data is beingtaken from a review paper.

2. All the sources and platforms are mentioned on last slide.

PART - 2

Is it possible to identify consistent pattern that distinguish Bidirectional and Unidirectional ???

What to Look for …..

GC content

INR

TATA Box

BRE

DPE

CCAAT

Location of different elements of PROMOTER(lacking TATA)

GC content

INR

TATA Box

BRE

DPE

CCAAT

Statistical Results of GC content:Average GC content percentage

Bidirectional: 66%

Unidirectional: 53%

• Bidirectional: 66%• Unidirectional: 53%GC content

INR

TATA Box

BRE

DPE

CCAAT

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%

• Bidirectional: 66%• Unidirectional: 53%GC content• Bidirectional: 25.3%• Unidirectional: 30.8%INR

TATA Box

BRE

DPE

CCAAT

TATA box:

Bidirectional: Most of them Lacks.

Unidirectional: Comparatively high.

• Located at -30 both in Unidirec and Bi-direc Promoters

• 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

BRE(B-recognition element)• Located directly in front of TATA• TFIIB recognizes it and binds.


Unidirectional: 11%

• 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

DPE(Downstream Promoter Element)• Located at +30 position• Binds to common transcription

factor(TFIID) in absence of TATA


Unidirectional: 50.6%



frequently

TATA Box • Bidirectional: 16.5%• Unidirectional: 11%BRE• Bidirectional: 46.6%• Unidirectional: 50.6%DPE

CCAAT

CCAAT box:• Located at 75-80 BP before TSS• signals the binding site for the

RNA transcription factor





frequently

TATA Box • Bidirectional: 16.5%• Unidirectional: 11.1%BRE• Bidirectional: 46.6%• Unidirectional: 50.6%DPE• Bidirectional: 12.9%• Unidirectional: 6.9%CCAAT

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.

Bi-Directional promoters enrich with following specific Binding sites of TF.

• GABPA• MYC• E2F1• E2F4• Nrf1• YY1• NFY• SP1

PART- 3Follow the tunnel

So the first thing is- GC CONTENT

Lets check the GC content-

Wait..Wait..Wait..

Where’s the length of Unidirectional Promoters??

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

Comparison of GC content between

Unidirectional (Mean Length)Bidirectional VS Unidirectional (Median Length)

Unidirectional (1000bp Length)

GC content Distribution- Unidirectional_MEAN

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AVERAGE: 54.6%

GC content Distribution- Unidirectional_MEDIAN

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AVERAGE: 56.9%

GC content Distribution- Unidirectional_1000 BP

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AVERAGE: 49.7%

Comparison of GC content between

Unidirectional (Mean Length)Bidirectional VS Unidirectional (Median Length)

Unidirectional (1000bp Length)

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%

Statistical Conclusion:


Bidirectional: 64%

Average GC content :

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.

THANKS

bi-directional promoters

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