Transcript Transcriptional Networks

Transcriptional
Networks
BINDING SITES: TRANSCRIPTION
FACTORS BIND TO THESE.
MAY INDUCE AND MAY REPRESS.
Compare Expression
Time 1
GGCGAC
CAGGTA
Time 2
CCCAAC
ACGGGC
CACAAA
Time 3
CAGGTA
CACAAA
CACAAA
Time 4
CGTTAA
CAGGTA
CACAAA
Time 3
Time 4
A
AA
A
B
B
BB
D
D
Time 1
C
Time 2
C
D
F
Correlation
Time 1
Time 2
Time 3
Time 4
TF
A
AA
A
B
B
BB
D
D
C
C
D
F
F
Correlation:Find the highest correlations
between expression level of TF of interest
(red) and number of cis-element occurrence
(normalized). AA means high numbers of A.
ARTIFICIAL
PROMOTERS
T1
T2
B1, B2
CANDIDATES
FOR BINDING
B3, B4, B2
ARTIFICIAL PROMOTER:
B1 B3 B4
If find expression, then B2 is out and T1
binds to B1 for sure.
Preliminary Testing
Preliminary Algorithm Results:
Ndt80 binds to...
Ndt80 binds to...
7 time points
Cis-element
14 time points
Cis-element
1. TCGCGA
2. TAAACT
3. CTAGAT
4. CACAAA**
TCGCGA
1. --AACT(TA)
CTAGAT
2. CACAAA**
Out of 4,096 possible candidate cis-elements
**Documented binding site (see below)
Documented Binding Site:
AAAA
Ndt80 (TF)
CACAAA
MSE (cis-element)
Documentation: promoter analysis, reporter constructs, and
binding assays (Chu and Herskowitz, Cell 1998)
Additional Results
meiosis specific sites
CACAAA - MSE SITE(Ndt80 binds)
GGCGGC - URS SITE
CCCCTT - LATE SPORULATION
mitotic sites
GCGCGC
ACGCGT
ACGCGG
TGTGG
CGCGAA - G1 PHASE
CCACA - G1 PHASE
GCAG - G2 PHASE
diauxic shift
ACTAA-
Additional Results
TRANSFAC-List of
putative regulatory
elements for specific
genes.
Algorithm results
list of putative ciselements
SEARCH
ALL YEAST CIS-ELEMENTS IN TRANSFAC
HIT RATE<10%
YEAST CIS-ELEMENTS IN TRANSFAC ON
GENES UP OR DOWN REGULATED IN
SPORULATION
HIT RATE<70%
Rosetta Dataset Results:
•microarray expession of 300 yeast
deletion lines plus several drug treatments
TF
Algorithm
Prediction
Documented
Binding Site
GCN4
BAS1
1. TGAGTC
1. GAGTCA
TGANTN*
GAGTCA*
*close to reverse complements
8 other TFs share the binding site
Most involved in amino acid biosynthesis
Create Data Sets
1.Compile data: sets of expressed transcription factors
Time 2
Time 1
Time 3
Time 4
2. Retrieve regulatory sequences
2,000 bp
CAGGCACAAATCTTACGTTATA...
(CAGGCA) (A)
(AGGCAC) (B)
(GGCACA) (C)
AAAA
3. Scan regulatory regions of
expressed genes. Compile a set
of potential cis-elements
(C)
(A)(B)
Time 1
Time 2
Time 3
Time 4
Minimal Set
Time 3
Time 4
A
AA
A
B
B
BB
D
D
Time 1
Time 2
TF
C
D
F
F
B. Minimal Set. Find time point where 1) TF
of interest (red) is present. 2)contains the
fewest # of cis-elements. Eliminate ciselement candidates absent from this time point
Transcriptional
Networks Induction
•Specificity
•Modularity
AAAA
AAAA
AAAA
e.g. cis-element
AAAA
AAAA
AAAA
Repression
AAAA
AAAA
Time 1
Time 2
AAAA
Time 3