Università degli Studi di Milano.
Member of LERU (League of European Research Universities).
1° University in Italy for scientific productivity (Leiden ranking
2012).
1° University in Italy in Biomedical Sciences.
Dipartimento di Bioscienze
90 Faculty members, 6 EMBO Members.
Genetics, Molecular Biology, Structural Biology,
Biochemistry, Bioinformatics, Developmental Biology,
Physiology, Plant Biology, Ecology.
PhD program in Biomolecular Sciences.
50 students.
Joint PhD program with EMBL, Heidelberg.
Progenitor
cells
Pancreatic
cell
Endoderm
Hepatocyte
ES cell
Myoblast
Mesoderm
B cell
Totipotent cell
Ectoderm
Neuron
Epithelial cell
Pluristratified
NF-Y-DNA structure
NF-YA/NF-YB/NF-YC interface
• A1 helix contacts extensively NF-YB/NF-YC (1760 Å2)
• heterotrimerization through side-chain and backbone polar interactions
• A1A2-linker: extended conformation that directs A2 helix towards the DNA
A
T
A1 helix
A
C
K261
A2
P263
C
E52
R266 Y56
F50
E82
Q85
E86
I117
R253
D116
a2(YB)
aC(YC)
a1(YC)
R249
E90
S93
S97
F113
R250
R245
F94
Q110
I246
F125
D112 V238
A1
Q242
E98
E101
L123 T122
D109
N239
K241
S121
The genomic
strategy of NF-Y:
The ENCODE
Project.
ChIp-Seq/Mass-Spec in 9 cell types of
10 histone PTMs and 72 -and countingDNA-binding Proteins (Mostly TFs).
Clustering NF-Y with 80 nuclear proteins.
Actual Overlap
% of NFYB bound
Promoters
Fisher Exact Test
51,916
3788
Expected Overlap
n=
n-
# Enhancers (all)
with Factor
21,641
3914
# Peaks in
Enhancers (all)
n=
n=
14,404 2,943
20,895 9,303
20,609 11,024
23,586 11,589
15,401 4,337
17,951 4,718
18,815 9,921
13,693 7,222
14,496 9,305
29,410 10,436
9,862
7,287
6,402
2,667
6,932
3,296
9,229
5,400
5,025
2,915
16,358 5,170
2,475
1,594
18,480 3,733
21,313 2,746
10,662 6,203
9,860
2,412
5,250
3,107
3,328
2,181
10,746 3,779
3,020
1,592
2,701
1,180
44,168 3,215
1,623
602
10,004 2,765
19,094 3,194
885
415
939
486
5,576
494
8,031
2,459
46,476 6,027
1,136
338
1,606
501
945
323
8,379
1,032
3,397
416
1,839
277
11,209 1,770
24,841 2,681
2,514
578
3,477
439
8,061
1,369
8,128
1,444
612
237
2,607
460
5,514
502
25,479 1,454
3,924
265
4,126
551
2,174
477
4,530
368
1,057
203
9,025
1,039
2,005
222
1,245
262
17,914
890
2,075
480
6,616
618
8,572
971
17,401 1,424
3,182
328
4,536
335
317
173
1,794
246
5,715
286
520
251
23,337 2,689
563
219
67
12
8,831
498
11,393
571
2,969
126
10,209
643
12,314
48
794
3
201
5
# Genomic Peaks
cFOS
CCNT2
E2F6
POL2
ORC2
ELF1
HMGN3
cMYC
TBP
ps2-POL2
E2F4
MAX
CHD2
HEY1
GABP
BHLHE40
GTF2B
cJUN
USF1
TFIIF
HDAC8
YY1
NRF1
BRD4
MXI1
SIN3A
CEBPB
USF2
TFIIIC
EGR1
GTF2F1
ATF3
SP1
ZBTB7A
CTCF
NELFE
THAP1
JUND
SETDB1
SIX5
SPT5
BRG1
TAL1
STAT2_30m
NFE2
INI1
ZNF263
TR4
ETS1
NR4A1
PU1
BCL3
TAF1
STAT2_6h
ZBTB33
STAT1_30m
GATA2
SRF
STAT1_6h
MAFK
RPC155
BCLAF
CTCFL
RAD21
GATA1
TAF7
BRF1
SIRT6
NRSF
BDP1
SMC3
POL3
BRF2
HDAC2
FOSL
P300
MEF2A
KAP1
ZNF274
XRCC4
Overlapping Factor
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
2.4E-285
5.3E-199
4.4E-179
3.3E-173
1.8E-171
1.4E-138
5.2E-131
1.3E-118
3.1E-117
2.7E-115
5.2E-114
2.9E-104
1.0E-85
2.7E-85
1.1E-82
1.6E-81
6.7E-71
7.4E-63
1.1E-62
1.6E-55
1.2E-54
1.9E-53
6.7E-39
1.7E-38
3.1E-37
1.4E-29
2.0E-24
9.2E-23
1.0E-22
3.6E-21
5.3E-20
1.5E-18
1.9E-15
2.7E-14
1.8E-12
1.1E-11
5.2E-09
1.0E-07
7.6E-08
3.8E-06
1.0E-05
3.5E-05
1.3E-04
1.7E-04
1.9E-04
5.3E-04
4.7E-04
2.1E-03
3.3E-03
4.1E-02
1.4E-02
1.6E-02
2.0E-02
4.6E-02
3.9E-02
4.6E-02
2.5E-01
2.5E-01
1.0E-01
7.4E-02
4.6E-01
5.6E-01
1.8E-01
3.9E-01
7.2E-01
5.8E-01
5.5E-01
6.2E-01
1.0E+00
1.0E+00
Fisher Exact Test
65
58
41
57
67
78
69
86
80
74
43
33
37
34
26
29
39
16
23
25
24
22
23
25
19
14
19
5
7
11
28
19
4
13
4
4
13
5
7
3
3
7
5
4
4
3
2
2
2
8
2
2
2
1
1
4
2
5
6
9
1
1
2
4
2
1
4
4
1
0
1
2
0
1
1
0
0
0
0
0
% of NFYB bound
Promoters
2,528
2,279
1,605
2,248
2,615
3,037
2,695
3,347
3,126
2,912
1,695
1,286
1,455
1,346
1,006
1,138
1,540
620
912
959
939
878
910
982
742
542
732
191
268
421
1,088
748
175
494
156
176
502
181
257
108
124
287
180
142
150
122
88
87
78
299
74
82
88
50
57
145
78
195
230
357
55
43
59
141
63
49
173
139
33
13
41
62
15
22
39
18
11
2
1
0
Actual Overlap
Overlapping Factor
1,450
521
556
1,139
1,271
1,662
1,558
1,800
1,712
1,456
809
616
772
697
452
593
927
258
458
496
483
454
511
568
390
250
403
58
99
204
821
453
67
289
57
77
333
90
144
44
56
177
103
77
87
68
48
50
44
235
45
53
60
30
36
111
54
160
193
325
41
31
45
121
80
38
112
127
26
8
46
58
11
26
37
16
14
1
1
1
Expected Overlap
Fisher Exact Test
20,895 8,305
14,404 2,966
6,932
3,109
13,693 6,506
9,862
7,163
20,609 9,516
18,815 8,880
23,586 10,316
29,410 9,741
14,496 8,261
9,229
4,549
15,401 3,522
16,358 4,341
17,951 3,936
6,402
2,534
18,480 3,394
10,662 5,241
2,475
1,445
21,313 2,584
5,025
2,765
9,860
2,793
5,250
2,534
44,168 2,972
10,746 3,203
3,328
2,170
3,020
1,390
10,004 2,310
5,576
324
1,623
547
2,701
1,137
46,476 4,790
19,094 2,549
885
368
24,841 1,641
1,136
317
1,606
427
8,031
1,864
939
496
11,209
830
1,839
249
945
308
8,379
997
8,061
592
3,397
431
2,514
482
3,477
380
2,607
272
2,075
282
612
241
8,128
1,327
4,530
253
4,126
297
2,174
341
4,536
170
2,005
198
5,514
636
3,924
307
17,401
898
25,479 1,093
23,337 1,835
3,182
225
1,057
170
6,616
259
17,914
676
5,715
442
1,245
211
9,025
633
8,572
709
1,794
141
317
46
10,209
261
11,393
328
563
65
12,314
147
8,831
213
520
89
2,969
75
67
7
201
7
794
9
Enhancer (all)
# Promoters (all)
with Factor
% of NFYB bound
Promoters
# Genomic Peaks
CCNT2
cFOS
CHD2
cMYC
E2F4
E2F6
HMGN3
POL2
ps2-POL2
TBP
HEY1
ORC2
BHLHE40
ELF1
MAX
cJUN
TFIIF
GTF2B
USF1
GABP
HDAC8
YY1
CEBPB
BRD4
NRF1
MXI1
TFIIIC
SP1
USF2
SIN3A
CTCF
EGR1
GTF2F1
TAL1
NELFE
THAP1
ZBTB7A
ATF3
BRG1
SPT5
JUND
SETDB1
INI1
SIX5
STAT2_30m
NFE2
ETS1
RPC155
TR4
ZNF263
ZBTB33
TAF1
STAT2_6h
TAF7
SRF
NR4A1
BCL3
RAD21
PU1
SMC3
GATA1
STAT1_30m
BCLAF
MAFK
NRSF
STAT1_6h
GATA2
CTCFL
SIRT6
BRF1
MEF2A
FOSL
POL3
KAP1
HDAC2
BDP1
P300
BRF2
XRCC4
ZNF274
# Peaks in
Promoters (all)
Actual Overlap
8,016
2,881
3,076
6,300
7,025
9,187
8,612
9,954
9,466
8,053
4,475
3,404
4,268
3,852
2,500
3,277
5,127
1,424
2,535
2,741
2,672
2,510
2,824
3,139
2,154
1,383
2,229
319
547
1,129
4,537
2,503
368
1,596
316
425
1,840
495
797
245
307
979
568
427
480
375
268
278
241
1,298
251
295
332
167
198
615
297
883
1,068
1,796
224
169
247
669
440
208
621
704
141
44
255
322
61
146
206
88
75
7
7
4
40/50 TFs show correlations,
P value E-40
# Genomic Peaks
Expected Overlap
Promoters (all)
# RefSeq Promoters
with Factor
# Peaks in RefSeq
Promoters
Overlapping Factor
RefSeq Promoters (-2500bp, +500bp TSS)
2,914
9,217
10,944
11,497
4,258
4,692
9,854
7,138
9,206
10,386
7,230
2,641
3,283
5,352
2,912
5,149
1,576
3,703
2,738
6,134
2,387
3,092
2,174
3,718
1,588
1,171
3,161
602
2,714
3,177
415
486
491
2,443
5,919
337
500
323
1,031
415
276
1,713
2,660
576
437
1,325
1,438
237
458
500
1,439
263
544
474
368
202
1,036
221
261
888
467
592
970
1,424
328
333
163
246
286
244
2,677
196
12
493
570
126
639
48
3
5
213
673
799
839
311
342
719
521
672
758
528
193
240
391
212
376
115
270
200
448
174
226
159
271
116
85
231
44
198
232
30
35
36
178
432
25
36
24
75
30
20
125
194
42
32
97
105
17
33
36
105
19
40
35
27
15
76
16
19
65
34
43
71
104
24
24
12
18
21
18
195
14
1
36
42
9
47
4
0
0
2,075
2,015
2,462
2,714
1,123
1,198
2,167
1,919
2,499
2,546
2,153
823
1,371
1,547
835
1,132
588
914
754
1,184
663
749
595
791
466
380
655
255
532
564
156
163
159
413
763
125
146
114
209
119
94
270
363
130
104
209
212
65
90
89
188
54
86
78
65
43
126
41
45
109
65
75
108
66
42
41
22
30
32
28
166
23
3
29
37
10
45
3
0
0
55
53
65
72
30
32
57
51
66
67
57
22
36
41
22
30
16
24
20
31
18
20
16
21
12
10
17
7
14
15
4
4
4
11
20
3
4
3
6
3
2
7
10
3
3
6
6
2
2
2
5
1
2
2
2
1
3
1
1
3
2
2
3
2
1
1
1
1
1
1
4
1
0
1
1
0
1
0
0
0
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
4.2E-289
5.3E-286
4.6E-266
6.9E-264
4.1E-246
2.0E-245
1.6E-216
2.1E-206
2.2E-189
4.4E-181
1.2E-159
2.1E-145
2.8E-141
3.7E-128
4.0E-103
1.2E-91
1.3E-69
2.2E-64
2.0E-60
5.8E-60
4.2E-59
3.3E-55
2.8E-49
6.6E-48
3.9E-42
1.6E-39
2.9E-38
1.2E-33
1.0E-31
2.3E-31
2.5E-27
4.0E-26
7.9E-23
4.3E-21
5.9E-18
6.0E-15
6.7E-15
3.8E-12
1.3E-11
1.6E-11
3.1E-11
1.7E-10
2.2E-08
3.0E-08
6.7E-08
1.1E-07
6.1E-07
3.3E-06
1.5E-05
4.3E-05
3.9E-04
9.8E-04
5.8E-03
6.3E-03
1.6E-02
1.8E-02
2.4E-02
2.6E-02
5.2E-02
2.6E-01
5.2E-01
7.3E-01
8.8E-01
1.0E+00
1.0E+00
1.0E+00
cFOS
USF1
E2F6
POL2
TBP
E2F4
USF2
HMGN3
CCNT2
CHD2
cMYC
MAX
ELF1
ps2-POL2
ORC2
HEY1
BHLHE40
Cjun
HDAC8
SP1
EGR1
GATA2
TAL1
ZBTB7A
SIX5
GTF2B
GABP
TFIIF
BRD4
CEBPB
STAT2_30m
HDAC2
PU1
NRF1
GATA1
FOSL
ATF3
CTCF
BRG1
NFE2
MEF2A
ETS1
BCLAF
MAFK
MXI1
YY1
STAT2_6h
TFIIIC
NR4A1
P300
TAF7
SIN3A
JUND
SIRT6
GTF2F1
SRF
TAF1
BCL3
INI1
STAT1_30m
ZNF263
SMC3
THAP1
CTCFL
STAT1_6h
NELFE
SETDB1
SPT5
RPC155
ZBTB33
RAD21
NRSF
TR4
BDP1
POL3
ZNF274
BRF1
KAP1
BRF2
XRCC4
14,404
21,313
20,609
23,586
14,496
9,862
1,623
18,815
20,895
6,932
13,693
6,402
17,951
29,410
15,401
9,229
16,358
18,480
9,860
5,576
19,094
9,025
24,841
8,031
3,397
2,475
5,025
10,662
10,746
44,168
2,514
8,831
25,479
3,328
3,182
11,393
939
46,476
11,209
3,477
10,209
2,607
6,616
17,914
3,020
5,250
2,174
10,004
5,514
2,969
4,536
2,701
945
1,794
885
2,005
4,126
3,924
8,061
1,057
8,128
23,337
1,606
8,572
1,245
1,136
8,379
1,839
2,075
4,530
17,401
5,715
612
520
563
794
317
12,314
67
201
6,001
6,413
6,674
5,775
3,516
1,589
517
4,691
8,724
1,206
5,047
2,011
7,935
4,844
9,013
2,372
7,309
10,485
5,618
2,247
8,480
5,927
15,970
3,793
332
455
1,213
3,330
5,081
11,542
1,593
4,751
8,488
478
1,672
6,788
78
6,067
5,408
2,223
4,389
1,157
2,758
6,545
517
791
1,153
3,175
1,709
1,040
1,254
320
256
1,230
90
666
580
493
3,796
605
1,324
2,531
206
1,224
519
46
669
197
623
678
1,855
691
44
84
46
12
26
437
4
3
5,969
6,384
6,617
5,706
3,494
1,587
517
4,655
8,639
1,205
4,985
2,002
7,866
4,819
8,890
2,340
7,291
10,399
5,473
2,228
8,427
5,876
15,864
3,773
330
452
1,212
3,308
5,039
11,470
1,580
4,700
8,424
478
1,665
6,742
78
6,031
5,363
2,213
4,337
1,153
2,712
6,532
517
791
1,149
3,164
1,685
1,038
1,237
318
256
1,227
90
666
573
492
3,762
602
1,322
2,531
204
1,216
517
46
669
197
622
674
1,854
691
44
84
46
12
26
437
4
3
76
82
85
73
45
20
7
59
110
15
64
26
100
62
114
30
93
133
70
28
108
75
203
48
4
6
15
42
64
146
20
60
108
6
21
86
1
77
68
28
55
15
35
83
7
10
15
40
22
13
16
4
3
16
1
9
7
6
48
8
17
32
3
16
7
1
9
3
8
9
24
9
1
1
1
0
0
6
0
0
1,246
869
619
587
471
384
242
503
649
302
478
321
539
431
562
296
468
526
335
204
386
314
545
235
81
88
128
197
240
387
128
219
302
74
120
246
35
224
196
118
170
82
127
212
55
66
78
127
85
63
65
34
31
64
20
39
36
32
106
33
48
73
17
43
26
9
29
15
25
25
49
25
3
4
2
1
1
7
0
0
39
27
19
18
15
12
8
16
20
9
15
10
17
13
18
9
15
16
10
6
12
10
17
7
3
3
4
6
8
12
4
7
9
2
4
8
1
7
6
4
5
3
4
7
2
2
2
4
3
2
2
1
1
2
1
1
1
1
3
1
2
2
1
1
1
0
1
0
1
1
2
1
0
0
0
0
0
0
0
0
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
<1.0E-300
2.5E-300
1.9E-297
1.9E-290
2.5E-261
4.7E-243
5.4E-225
1.4E-222
4.0E-218
1.9E-193
2.2E-182
6.6E-161
4.4E-123
9.0E-106
3.4E-103
6.2E-100
2.2E-98
2.5E-87
2.5E-77
2.1E-74
6.3E-74
5.6E-70
1.2E-66
2.0E-66
2.0E-60
3.4E-59
7.6E-57
3.1E-55
2.3E-51
1.7E-47
4.6E-45
1.8E-44
5.0E-38
1.1E-37
1.1E-36
4.1E-35
7.1E-35
1.2E-33
1.0E-32
1.4E-32
4.1E-32
1.3E-28
6.6E-26
1.2E-23
4.5E-21
6.8E-21
8.8E-21
1.3E-20
2.7E-19
9.9E-15
1.3E-14
1.4E-13
1.6E-13
6.2E-12
2.8E-10
3.6E-10
1.7E-09
5.0E-09
6.0E-09
6.4E-09
2.2E-08
5.0E-08
7.9E-07
3.3E-06
3.4E-06
5.0E-06
1.9E-02
2.3E-02
1.2E-01
1.4E-01
2.8E-01
5.2E-01
1.0E+00
1.0E+00
n=
n=
249,997
3193
NF-Y friends
Actual Overlap w Hypergeo.
# Peaks in # Promoters
Expected
YB (a)
Prob.
# Peaks promoters with Factor Overlap w YB
RPC155
2075
282
278
53
87
3.11E-08
RAD21
17401
898
883
169
195
0.0002953
XRCC4
201
7
7
1
1
0.3825
TR4
612
241
241
45
78
3.22E-08
ORC2
15401
3522
3404
664
1286
3.18E-199
TFIIIC
10004
2310
2229
436
732
2.52E-71
Pol3
563
65
61
12
15
0.05282
TFIIF
10662
5241
5127
989
1540
1.80E-131
TBP
9933
6068
5945
1145
2295
0.00E+00
SPT5
1839
249
245
47
108
2.32E-21
pS2Pol2
29410
9741
9466
1838
3126
0.00E+00
Pol2
10316
9954
1946
3347
0.00E+00
TFIIB
2475
1445
1424
273
620
9.13E-119
NFE2
3477
380
375
72
122
4.55E-12
ZNF274
794
9
4
2
0
0.4502
ZNF263
8128
1327
1298
250
299
5.84E-07
Ifna6hStat2
2173
341
332
64
88
3.40E-05
Ifna6hStat1
1245
211
208
40
49
0.009042
GATA2
9025
633
621
119
173
3.66E-10
GATA1
3182
225
224
42
55
0.003265
YY1
5250
2534
2510
478
878
1.61E-104
E2F6
20609
9516
9187
1795
3037
0.00E+00
E2F4
9862
7163
7025
1351
2615
0.00E+00
cMYC
13693
6506
6300
1227
2248
0.00E+00
MAX
6402
2534
2500
478
1006
8.17E-172
cJUN
18480
3394
3277
640
1138
8.36E-139
cFOS
14404
2966
2881
560
2279
0.00E+00
JUND
945
308
307
58
124
2.20E-20
ATF3
939
496
495
94
181
3.34E-23
SIRT6
1794
141
141
27
33
0.02241
SETDB1
8379
997
979
188
287
5.13E-19
BRF2
67
7
7
1
2
0.2534
BRF1
317
46
44
9
13
0.02365
BRD4
10746
3203
3139
604
982
1.16E-85
BDP1
520
89
88
17
18
0.08943
GTFs
TFs
Cofactors
NF-Y and friends
stay together...
...to make life and death decisions
cFos
Yes
No
NF-YB
No
Yes
cJun
No
No
No
Yes
Yes
No
Yes
No
Yes
No
Yes
Yes
Yes
No
Yes
Yes
Yes
Function (p-value <1e-05)
Cellular Assembly and Organization
None
Cell Death, Protein Synthesis, Gene Expression, Cellular Growth and Proliferation, Molecular Transport, Protein Trafficking,
10719 Cell Cycle
4472 Cell Cycle, Gene Expression, DNA Replication, Recombination, Repair, Cellular Assembly and Organization
5980 None
683 None
1155 Cell Cycle, Cellular Function and Maintenance, Cell Death
2884
6345
ChIP-Seq Tag Distribution
14
cFos
cJun
NFYB
RefSeq
Normalized Tag Count
12
10
8
cFos
cJun
NFYA
NFYB
Input_Struhl
6
4
2
0
-500
-250
0
250
Distance from cFos peak summit (bps)
500
5’
The amazing
precision of ChIP-Seq
-1
A
T
1
-2
A
T
2
-3
G
C
3
-4
A
T
4
Gln 97
Arg 93
L2 (C)
Arg 94
Thr 95
Lys 75
L1 (B)
-5
G
C
5
a2 (B)
Lys 78
Ala 77
-6
6
A
T
L1 (B)
Ile 76
Lys 75
-7
G
C
7
a2 (B)
Lys 81
Gly 287
-8
Met 279
A2
C
8
G
C
9
Arg 288
-9
His 275
Phe 289
Arg 283
His 271
A1A2-linker
G
Gly 286
-10
T
A
-11
T
A
Ser 291
10
Leu 270
Arg 281
Pro 58
Ile 59
Ala 60
a1 (B)
11
His 277
-12
A
T
12
-13
G
C
13
Asn 61
Arg 64
A2
Arg 274
-14
A
T
14
-15
G
C
15
-16
G
C
16
Ser 273
His 271
A1A2-linker
Gln 53
Lys 50
Arg 47
a1 (C)
Ala 46
Leu 45
Met 60
Lys 53
Lys 49
L1 (C)
a1 (C)
-17
C
G
17
-18
T
A
18
-19
C
G
19
-20
G
C
20
-21
A
T
21
-22
G
C
22
Pro 44
Ile 61
Ser 62
Ala 63
-23
C
G
23
-24
T
A
24
Lys 109
-25
5’
A
T
25
L2 (B)
Where do the friends
sit at the table?
?
CCAAT
?
E2F
E box
AP1
TBP
We can tell
Reconstructing
promoters
architecures
10
E box
AP1
50
CCAAT
E2F
TBP
Protein transfections
of TAT-NF-YA in vivo.
Domashenko, Blood, 2010.
Progenitor
cells
Pancreatic
cell
Endoderm
Hepatocyte
ES cell
Myoblast
Mesoderm
Hematopoietic
cells
HSCs
Totipotent cell
Ectoderm
Neuron
Epithelial cell
Pluristratified
VINCULIN
TAT-NF-YAs
NF-YAl
NF-YAs
SOX2
NANOG
Fold enrichment
KLF5
5
4
3
NT
2
1
w/oLIF
w/oLIF+TAT
w/oLIF+TAT-YAs
0
PROMOTERS WITH CCAAT PSFM
SCORE>0.8
%
ChIP-Seq data
NF-YA promoters
21747
5493
25.26
2400
GENOME PROMOTERS
BACKGROUND
TFs
PROMOTERS ( -500 +100)
PROMOTERS WITH CCAAT PSFM
SCORE>0.8
E2F1
6102
2183
35.78
5.11E-106
1472
0
NANOG
343
163
47.52
9.61E-020
144
7.25178E-50
1.25421E-25
P-value
P-value
KLF4
2966
900
30.34
6.52E-012
505
SOX2
178
78
43.82
2.07E-008
41
2.11146E-06
ESRRB
1240
383
30.89
1.76E-006
169
0.000491226
STAT3
320
101
31.56
4.35E-003
64
8.86847E-07
OCT4
660
193
29.24
8.07E-003
131
6.53472E-12
CTCF
1308
301
23.01
9.72E-001
228
2.80016E-13
TFBs analysis on Nanog core promoters
TF NAME
MATRIX ID
P-VALUE
TF NAME
MATRIX ID
P-VALUE
NFYA
MA0060.1
4.86E-27
GABPA
MA0062.2
1.83E-234
MIZF
MA0131.1
1.92E-17
ELK4
MA0076.1
2.94E-220
ELK4
MA0076.1
2.36E-16
ELK1
MA0028.1
5.17E-168
GABPA
MA0062.2
1.18E-14
E2F1
MA0024.1
9.10E-156
ELK1
MA0028.1
1.50E-13
MIZF
MA0131.1
2.36E-152
E2F1
MA0024.1
1.22E-11
TFAP2A
MA0003.1
7.63E-111
HIF1A::ARNT
MA0259.1
5.98192
NFYA
MA0060.1
3.65E-108
Mouse
Mouse promoters Nanog peaks
Ranking positions third
Human promoters Nanog peaks
Ranking positions first
Human
82.2
60
Fold enrichment
ChIP:NF-YB
Nanog peaks de novo discovery analysis
89.3
50
40
30
20
10
ChIP:NANOG
Fold enrichment
0
10
NF-YB
FAM33A
SOX2
NF-YA
NF-YC
HMGB2
CDK2
STARD4
STIL
OTX2
LEFTY
NF-YAs
NF-YAsm29
8
6
4
2
0
HMGB2
CDK2
STARD4
ChIP-Seq: NANOG
NF-YB
-
FAM33A
+
SOX2
+
NF-YA
NF-YC
+
+
+
+
STIL
+
OTX2
+
LEFTY
+
ChIP-Seq: NF-YA
+
+
-
+
+
-
+
+
+
-
A growing network of TFs in ESC.
NF-YC
37
NF-YB
NF-YA
Short
KLF4
SALL4
MYC
STAT3
OCT4
SOX2
NANOG
Past
Post-Docs
Khalid Zemzoumi
Alberto Di Silvio (Axxam I)
Fabienne Cocchiarella (UniMo)
Marià Pitarque Martì
Anna Testa
Nicoletta Cordani (HSR, I)
Silvia Pozzi (Reg Emilia)
Alessandra Viganò (U. Basel, CH)
PhDs
Maria Carla Motta (U. Manchester UK)
Patricia Lievens
Chiara Liberati (Axxam, I)
Giuseppina Caretti (UniMi I)
Mattia Frontini (MRC UK)
Carol Imbriano (UniMo I)
Barbara Testoni (CNRS F)
Claudia Forni (Farmigea I)
Giacomo Donati (MRC UK)
Michele Ceribelli (NIH USA)
Daniele Merico (U. Toronto CA)
Andrea Fossati (UniMi I)
Marianna Bellorini
Chiara Vecchi (UniMo I)
Valentina Salsi (UniMo I)
Giulia Petrovich (U. Edimburgh UK)
DSBB U. Milano
Present
Serena Borrelli
Raffaella Gatta
Diletta Dolfini
Elena Martynova
Mario Minuzzo
Nerina Gnesutta
Mariangela Lorenzo
Federico Zambelli
Giulio Pavesi
Marco Nardini
Martino Bolognesi
Collaborators
C Imbriano
L Tora
C Romier
C Castagnoli
G Melino
A Terrinoni
E Candi
D Aberdam
GP Dotto
E Berti
M d’Incalci
D. Hochhauser
J. Fleming/K. Struhl
Active Motif (USA)
U Modena (I)
IGBMC (F)
IGBMC (F)
B.Cute Torino (I)
MRC Leicester (I)
IDI (I)
U. Roma (I)
INSERM-Nice (F)
U. Lausanne (CH)
U. Mi-Bicocca (I)
Ist Mario Negri (I)
UCL (UK)
Harvard (USA)