ATG

Coding DNA

Non-coding DNA

…

cis

trans

What is a transcription factor?

A transcription factor is a protein that regulates transcription

- after nuclear translocation

- by specific interaction with DNA

- or by stoichiometric interaction with a protein that can be assembled into a sequence-specific DNA-protein complex.

Transcription factors

Sequence-specific DNA binding

Non-DNA binding

TF1

TF2

TF3

TF4

adapter

Co-activator

HAT

DNA

Layer I

Layer III

Layer II

DNA binding domain

Activation domain

oligomerization domain

Ligand- binding domain

Protein-protein interaction domain

Structure of transcription factors

AP-1 (human)

…

Search for new TF binding sites with PWMs

AP-1

• HOCOMOCO,
• JASPAR,
• FactorBook,
• UniPROBE,
• TRANSFAC (10290 PWMs)

• MATCH™

• HOMER

Motif databases:

Motif anaslysis tools:

Alignment of binding site sequences with conserved, ungapped region

Making a TRANSFAC® matrix from a TFBS alignment

TFBS matrices

Alignment of binding site sequences with conserved, ungapped region

0

0

0

8

A

C

G

T

T

8

0

0

0

A

0

0

0

8

T

8

0

0

0

A

8

0

0

0

A

6

0

1

1

A

3

1

2

2

A

2

2

3

1

G

Position-specific count matrix

Making a TRANSFAC® matrix from a TFBS alignment

0/8

0/8

0/8

8/8

A

C

G

T

8/8

0/8

0/8

0/8

3/8

1/8

2/8

2/8

2/8

2/8

3/8

1/8

Position-specific frequency matrix

TFBS matrices

TFBS prediction with a PWM

(using residue counts to score potential binding sites)

0

0

0

8

A

C

G

T

8

0

0

0

0

0

0

8

8

0

0

0

8

0

0

0

6

0

1

1

3

1

2

2

2

2

3

1

A

C

T

T

G

G

T

A

C

G

T

A

Score: 8 + 8 + 8 + 0 + 8 + 1 + 1 + 3

TFBS matrices

Describing DNA-sequence patterns using PWM

(or more precisly -Position-specific frequency matrix (PFM) )

Motif logo of TRANSFAC matrix: V$AP1_02

L = 7

N = 5

n_ik , k=1..L

i=A,C,G,T

p_ik , k=1..L

i=A,C,G,T

Binding site scores:

HOMER

V$E2F_Q6 PWM cut-offs

%

FP

FN

Calculation of optimized cut-offs for PWMs

minFN

minFP

minSUM

q -score

tgccacacaggtagactcttTTGAAAATAtgTGTAATAtgtaaaa catcgtgaca cccccatatt… …

. . . . . . .

-96

-79

ST

NF-ATp

AP-1

Mouse Interleukin-2

gene promoter

TGAGTCA

AP-1 consensus

Score of the real site can be very low. Binding is compensated by TF interaction.

Score=0.74

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Motif enrichment analysis

• Use cases:
• Find transcription factors for co-regulated gene set
• Identify motifs “co-enriched” in the mutated regions

​

​

• Which binding sites are significantly enriched in the Yes sequences?
• Site optimization tool
• Automatic threshold optimization
• One-sided binomial test for significant enrichment of sites

​

Fuzzy puzzle!

DNA

Gene

Silent

Repressor

Problem of the choice of background sequences.

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