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 Bioscienze90 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.

Endoderm

Mesoderm

Ectoderm

Progenitor cells

Totipotent cell

Neuron

Hepatocyte

Myoblast

Pancreatic cell

B cell

Epithelial cell

Pluristratified

ES cell

NF-Y-DNA structure

A1

A2

1(YC)2(YB)

C(YC)

TAA

C

C

K241

Q242

R245

I246

R249

R250

R253

K261

P263

R266

N239

V238

S121

T122L123

F125

F94

S97

E98

E101

E90 S93

F50

Y56

E86Q85

E52

E82

F113

D112

D109

Q110

D116

I117

A1 helix

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

The genomic strategy of NF-Y:

The ENCODEProject.

ChIp-Seq/Mass-Spec in 9 cell types of 10 histone PTMs and 72 -and counting- DNA-binding Proteins (Mostly TFs).

Clustering NF-Y with 80 nuclear proteins.

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CCNT2 20,895 8,305 8,016 1,450 2,528 65 <1.0E-300 cFOS 14,404 2,943 2,914 213 2,075 55 <1.0E-300 cFOS 14,404 6,001 5,969 76 1,246 39 <1.0E-300cFOS 14,404 2,966 2,881 521 2,279 58 <1.0E-300 CCNT2 20,895 9,303 9,217 673 2,015 53 <1.0E-300 USF1 21,313 6,413 6,384 82 869 27 <1.0E-300CHD2 6,932 3,109 3,076 556 1,605 41 <1.0E-300 E2F6 20,609 11,024 10,944 799 2,462 65 <1.0E-300 E2F6 20,609 6,674 6,617 85 619 19 <1.0E-300cMYC 13,693 6,506 6,300 1,139 2,248 57 <1.0E-300 POL2 23,586 11,589 11,497 839 2,714 72 <1.0E-300 POL2 23,586 5,775 5,706 73 587 18 <1.0E-300E2F4 9,862 7,163 7,025 1,271 2,615 67 <1.0E-300 ORC2 15,401 4,337 4,258 311 1,123 30 <1.0E-300 TBP 14,496 3,516 3,494 45 471 15 <1.0E-300E2F6 20,609 9,516 9,187 1,662 3,037 78 <1.0E-300 ELF1 17,951 4,718 4,692 342 1,198 32 <1.0E-300 E2F4 9,862 1,589 1,587 20 384 12 <1.0E-300

HMGN3 18,815 8,880 8,612 1,558 2,695 69 <1.0E-300 HMGN3 18,815 9,921 9,854 719 2,167 57 <1.0E-300 USF2 1,623 517 517 7 242 8 <1.0E-300POL2 23,586 10,316 9,954 1,800 3,347 86 <1.0E-300 cMYC 13,693 7,222 7,138 521 1,919 51 <1.0E-300 HMGN3 18,815 4,691 4,655 59 503 16 2.5E-300

ps2-POL2 29,410 9,741 9,466 1,712 3,126 80 <1.0E-300 TBP 14,496 9,305 9,206 672 2,499 66 <1.0E-300 CCNT2 20,895 8,724 8,639 110 649 20 1.9E-297TBP 14,496 8,261 8,053 1,456 2,912 74 <1.0E-300 ps2-POL2 29,410 10,436 10,386 758 2,546 67 <1.0E-300 CHD2 6,932 1,206 1,205 15 302 9 1.9E-290

HEY1 9,229 4,549 4,475 809 1,695 43 2.4E-285 E2F4 9,862 7,287 7,230 528 2,153 57 <1.0E-300 cMYC 13,693 5,047 4,985 64 478 15 2.5E-261ORC2 15,401 3,522 3,404 616 1,286 33 5.3E-199 MAX 6,402 2,667 2,641 193 823 22 <1.0E-300 MAX 6,402 2,011 2,002 26 321 10 4.7E-243

BHLHE40 16,358 4,341 4,268 772 1,455 37 4.4E-179 CHD2 6,932 3,296 3,283 240 1,371 36 <1.0E-300 ELF1 17,951 7,935 7,866 100 539 17 5.4E-225ELF1 17,951 3,936 3,852 697 1,346 34 3.3E-173 HEY1 9,229 5,400 5,352 391 1,547 41 <1.0E-300 ps2-POL2 29,410 4,844 4,819 62 431 13 1.4E-222MAX 6,402 2,534 2,500 452 1,006 26 1.8E-171 GABP 5,025 2,915 2,912 212 835 22 4.2E-289 ORC2 15,401 9,013 8,890 114 562 18 4.0E-218

cJUN 18,480 3,394 3,277 593 1,138 29 1.4E-138 BHLHE40 16,358 5,170 5,149 376 1,132 30 5.3E-286 HEY1 9,229 2,372 2,340 30 296 9 1.9E-193TFIIF 10,662 5,241 5,127 927 1,540 39 5.2E-131 GTF2B 2,475 1,594 1,576 115 588 16 4.6E-266 BHLHE40 16,358 7,309 7,291 93 468 15 2.2E-182

GTF2B 2,475 1,445 1,424 258 620 16 1.3E-118 cJUN 18,480 3,733 3,703 270 914 24 6.9E-264 Cjun 18,480 10,485 10,399 133 526 16 6.6E-161USF1 21,313 2,584 2,535 458 912 23 3.1E-117 USF1 21,313 2,746 2,738 200 754 20 4.1E-246 HDAC8 9,860 5,618 5,473 70 335 10 4.4E-123GABP 5,025 2,765 2,741 496 959 25 2.7E-115 TFIIF 10,662 6,203 6,134 448 1,184 31 2.0E-245 SP1 5,576 2,247 2,228 28 204 6 9.0E-106

HDAC8 9,860 2,793 2,672 483 939 24 5.2E-114 HDAC8 9,860 2,412 2,387 174 663 18 1.6E-216 EGR1 19,094 8,480 8,427 108 386 12 3.4E-103YY1 5,250 2,534 2,510 454 878 22 2.9E-104 YY1 5,250 3,107 3,092 226 749 20 2.1E-206 GATA2 9,025 5,927 5,876 75 314 10 6.2E-100

CEBPB 44,168 2,972 2,824 511 910 23 1.0E-85 NRF1 3,328 2,181 2,174 159 595 16 2.2E-189 TAL1 24,841 15,970 15,864 203 545 17 2.2E-98BRD4 10,746 3,203 3,139 568 982 25 2.7E-85 BRD4 10,746 3,779 3,718 271 791 21 4.4E-181 ZBTB7A 8,031 3,793 3,773 48 235 7 2.5E-87NRF1 3,328 2,170 2,154 390 742 19 1.1E-82 MXI1 3,020 1,592 1,588 116 466 12 1.2E-159 SIX5 3,397 332 330 4 81 3 2.5E-77MXI1 3,020 1,390 1,383 250 542 14 1.6E-81 SIN3A 2,701 1,180 1,171 85 380 10 2.1E-145 GTF2B 2,475 455 452 6 88 3 2.1E-74

TFIIIC 10,004 2,310 2,229 403 732 19 6.7E-71 CEBPB 44,168 3,215 3,161 231 655 17 2.8E-141 GABP 5,025 1,213 1,212 15 128 4 6.3E-74SP1 5,576 324 319 58 191 5 7.4E-63 USF2 1,623 602 602 44 255 7 3.7E-128 TFIIF 10,662 3,330 3,308 42 197 6 5.6E-70

USF2 1,623 547 547 99 268 7 1.1E-62 TFIIIC 10,004 2,765 2,714 198 532 14 4.0E-103 BRD4 10,746 5,081 5,039 64 240 8 1.2E-66SIN3A 2,701 1,137 1,129 204 421 11 1.6E-55 EGR1 19,094 3,194 3,177 232 564 15 1.2E-91 CEBPB 44,168 11,542 11,470 146 387 12 2.0E-66CTCF 46,476 4,790 4,537 821 1,088 28 1.2E-54 GTF2F1 885 415 415 30 156 4 1.3E-69 STAT2_30m 2,514 1,593 1,580 20 128 4 2.0E-60EGR1 19,094 2,549 2,503 453 748 19 1.9E-53 ATF3 939 486 486 35 163 4 2.2E-64 HDAC2 8,831 4,751 4,700 60 219 7 3.4E-59

GTF2F1 885 368 368 67 175 4 6.7E-39 SP1 5,576 494 491 36 159 4 2.0E-60 PU1 25,479 8,488 8,424 108 302 9 7.6E-57TAL1 24,841 1,641 1,596 289 494 13 1.7E-38 ZBTB7A 8,031 2,459 2,443 178 413 11 5.8E-60 NRF1 3,328 478 478 6 74 2 3.1E-55

NELFE 1,136 317 316 57 156 4 3.1E-37 CTCF 46,476 6,027 5,919 432 763 20 4.2E-59 GATA1 3,182 1,672 1,665 21 120 4 2.3E-51THAP1 1,606 427 425 77 176 4 1.4E-29 NELFE 1,136 338 337 25 125 3 3.3E-55 FOSL 11,393 6,788 6,742 86 246 8 1.7E-47

ZBTB7A 8,031 1,864 1,840 333 502 13 2.0E-24 THAP1 1,606 501 500 36 146 4 2.8E-49 ATF3 939 78 78 1 35 1 4.6E-45ATF3 939 496 495 90 181 5 9.2E-23 JUND 945 323 323 24 114 3 6.6E-48 CTCF 46,476 6,067 6,031 77 224 7 1.8E-44

BRG1 11,209 830 797 144 257 7 1.0E-22 SETDB1 8,379 1,032 1,031 75 209 6 3.9E-42 BRG1 11,209 5,408 5,363 68 196 6 5.0E-38SPT5 1,839 249 245 44 108 3 3.6E-21 SIX5 3,397 416 415 30 119 3 1.6E-39 NFE2 3,477 2,223 2,213 28 118 4 1.1E-37JUND 945 308 307 56 124 3 5.3E-20 SPT5 1,839 277 276 20 94 2 2.9E-38 MEF2A 10,209 4,389 4,337 55 170 5 1.1E-36

SETDB1 8,379 997 979 177 287 7 1.5E-18 BRG1 11,209 1,770 1,713 125 270 7 1.2E-33 ETS1 2,607 1,157 1,153 15 82 3 4.1E-35INI1 8,061 592 568 103 180 5 1.9E-15 TAL1 24,841 2,681 2,660 194 363 10 1.0E-31 BCLAF 6,616 2,758 2,712 35 127 4 7.1E-35

SIX5 3,397 431 427 77 142 4 2.7E-14 STAT2_30m 2,514 578 576 42 130 3 2.3E-31 MAFK 17,914 6,545 6,532 83 212 7 1.2E-33STAT2_30m 2,514 482 480 87 150 4 1.8E-12 NFE2 3,477 439 437 32 104 3 2.5E-27 MXI1 3,020 517 517 7 55 2 1.0E-32

NFE2 3,477 380 375 68 122 3 1.1E-11 INI1 8,061 1,369 1,325 97 209 6 4.0E-26 YY1 5,250 791 791 10 66 2 1.4E-32ETS1 2,607 272 268 48 88 2 5.2E-09 ZNF263 8,128 1,444 1,438 105 212 6 7.9E-23 STAT2_6h 2,174 1,153 1,149 15 78 2 4.1E-32

RPC155 2,075 282 278 50 87 2 1.0E-07 TR4 612 237 237 17 65 2 4.3E-21 TFIIIC 10,004 3,175 3,164 40 127 4 1.3E-28TR4 612 241 241 44 78 2 7.6E-08 ETS1 2,607 460 458 33 90 2 5.9E-18 NR4A1 5,514 1,709 1,685 22 85 3 6.6E-26

ZNF263 8,128 1,327 1,298 235 299 8 3.8E-06 NR4A1 5,514 502 500 36 89 2 6.0E-15 P300 2,969 1,040 1,038 13 63 2 1.2E-23ZBTB33 4,530 253 251 45 74 2 1.0E-05 PU1 25,479 1,454 1,439 105 188 5 6.7E-15 TAF7 4,536 1,254 1,237 16 65 2 4.5E-21

TAF1 4,126 297 295 53 82 2 3.5E-05 BCL3 3,924 265 263 19 54 1 3.8E-12 SIN3A 2,701 320 318 4 34 1 6.8E-21STAT2_6h 2,174 341 332 60 88 2 1.3E-04 TAF1 4,126 551 544 40 86 2 1.3E-11 JUND 945 256 256 3 31 1 8.8E-21

TAF7 4,536 170 167 30 50 1 1.7E-04 STAT2_6h 2,174 477 474 35 78 2 1.6E-11 SIRT6 1,794 1,230 1,227 16 64 2 1.3E-20SRF 2,005 198 198 36 57 1 1.9E-04 ZBTB33 4,530 368 368 27 65 2 3.1E-11 GTF2F1 885 90 90 1 20 1 2.7E-19

NR4A1 5,514 636 615 111 145 4 5.3E-04 STAT1_30m 1,057 203 202 15 43 1 1.7E-10 SRF 2,005 666 666 9 39 1 9.9E-15BCL3 3,924 307 297 54 78 2 4.7E-04 GATA2 9,025 1,039 1,036 76 126 3 2.2E-08 TAF1 4,126 580 573 7 36 1 1.3E-14

RAD21 17,401 898 883 160 195 5 2.1E-03 SRF 2,005 222 221 16 41 1 3.0E-08 BCL3 3,924 493 492 6 32 1 1.4E-13PU1 25,479 1,093 1,068 193 230 6 3.3E-03 STAT1_6h 1,245 262 261 19 45 1 6.7E-08 INI1 8,061 3,796 3,762 48 106 3 1.6E-13

SMC3 23,337 1,835 1,796 325 357 9 4.1E-02 MAFK 17,914 890 888 65 109 3 1.1E-07 STAT1_30m 1,057 605 602 8 33 1 6.2E-12GATA1 3,182 225 224 41 55 1 1.4E-02 RPC155 2,075 480 467 34 65 2 6.1E-07 ZNF263 8,128 1,324 1,322 17 48 2 2.8E-10

STAT1_30m 1,057 170 169 31 43 1 1.6E-02 BCLAF 6,616 618 592 43 75 2 3.3E-06 SMC3 23,337 2,531 2,531 32 73 2 3.6E-10BCLAF 6,616 259 247 45 59 2 2.0E-02 CTCFL 8,572 971 970 71 108 3 1.5E-05 THAP1 1,606 206 204 3 17 1 1.7E-09

MAFK 17,914 676 669 121 141 4 4.6E-02 RAD21 17,401 1,424 1,424 104 66 2 4.3E-05 CTCFL 8,572 1,224 1,216 16 43 1 5.0E-09NRSF 5,715 442 440 80 63 2 3.9E-02 GATA1 3,182 328 328 24 42 1 3.9E-04 STAT1_6h 1,245 519 517 7 26 1 6.0E-09

STAT1_6h 1,245 211 208 38 49 1 4.6E-02 TAF7 4,536 335 333 24 41 1 9.8E-04 NELFE 1,136 46 46 1 9 0 6.4E-09GATA2 9,025 633 621 112 173 4 2.5E-01 BRF1 317 173 163 12 22 1 5.8E-03 SETDB1 8,379 669 669 9 29 1 2.2E-08CTCFL 8,572 709 704 127 139 4 2.5E-01 SIRT6 1,794 246 246 18 30 1 6.3E-03 SPT5 1,839 197 197 3 15 0 5.0E-08SIRT6 1,794 141 141 26 33 1 1.0E-01 NRSF 5,715 286 286 21 32 1 1.6E-02 RPC155 2,075 623 622 8 25 1 7.9E-07BRF1 317 46 44 8 13 0 7.4E-02 BDP1 520 251 244 18 28 1 1.8E-02 ZBTB33 4,530 678 674 9 25 1 3.3E-06

MEF2A 10,209 261 255 46 41 1 4.6E-01 SMC3 23,337 2,689 2,677 195 166 4 2.4E-02 RAD21 17,401 1,855 1,854 24 49 2 3.4E-06FOSL 11,393 328 322 58 62 2 5.6E-01 POL3 563 219 196 14 23 1 2.6E-02 NRSF 5,715 691 691 9 25 1 5.0E-06POL3 563 65 61 11 15 0 1.8E-01 BRF2 67 12 12 1 3 0 5.2E-02 TR4 612 44 44 1 3 0 1.9E-02KAP1 12,314 147 146 26 22 1 3.9E-01 HDAC2 8,831 498 493 36 29 1 2.6E-01 BDP1 520 84 84 1 4 0 2.3E-02

HDAC2 8,831 213 206 37 39 1 7.2E-01 FOSL 11,393 571 570 42 37 1 5.2E-01 POL3 563 46 46 1 2 0 1.2E-01BDP1 520 89 88 16 18 0 5.8E-01 P300 2,969 126 126 9 10 0 7.3E-01 ZNF274 794 12 12 0 1 0 1.4E-01P300 2,969 75 75 14 11 0 5.5E-01 MEF2A 10,209 643 639 47 45 1 8.8E-01 BRF1 317 26 26 0 1 0 2.8E-01

BRF2 67 7 7 1 2 0 6.2E-01 KAP1 12,314 48 48 4 3 0 1.0E+00 KAP1 12,314 437 437 6 7 0 5.2E-01XRCC4 201 7 7 1 1 0 1.0E+00 ZNF274 794 3 3 0 0 0 1.0E+00 BRF2 67 4 4 0 0 0 1.0E+00ZNF274 794 9 4 1 0 0 1.0E+00 XRCC4 201 5 5 0 0 0 1.0E+00 XRCC4 201 3 3 0 0 0 1.0E+00

n = 21,641 n= 51,916 n= 249,997n = 3914 n- 3788 n= 3193

Promoters (all) Enhancer (all)

40/50 TFs show correlations,P value E-40

  # Peaks# Peaks in promoters

# Promoters with Factor

Expected Overlap w YB

Actual Overlap w YB (a)

Hypergeo. Prob.

RPC155 2075 282 278 53 87 3.11E-08RAD21 17401 898 883 169 195 0.0002953XRCC4 201 7 7 1 1 0.3825

TR4 612 241 241 45 78 3.22E-08ORC2 15401 3522 3404 664 1286 3.18E-199TFIIIC 10004 2310 2229 436 732 2.52E-71Pol3 563 65 61 12 15 0.05282TFIIF 10662 5241 5127 989 1540 1.80E-131TBP 9933 6068 5945 1145 2295 0.00E+00SPT5 1839 249 245 47 108 2.32E-21

pS2Pol2 29410 9741 9466 1838 3126 0.00E+00Pol2 10316 9954 1946 3347 0.00E+00TFIIB 2475 1445 1424 273 620 9.13E-119NFE2 3477 380 375 72 122 4.55E-12

ZNF274 794 9 4 2 0 0.4502ZNF263 8128 1327 1298 250 299 5.84E-07

Ifna6hStat2 2173 341 332 64 88 3.40E-05Ifna6hStat1 1245 211 208 40 49 0.009042

GATA2 9025 633 621 119 173 3.66E-10GATA1 3182 225 224 42 55 0.003265

YY1 5250 2534 2510 478 878 1.61E-104E2F6 20609 9516 9187 1795 3037 0.00E+00E2F4 9862 7163 7025 1351 2615 0.00E+00cMYC 13693 6506 6300 1227 2248 0.00E+00MAX 6402 2534 2500 478 1006 8.17E-172cJUN 18480 3394 3277 640 1138 8.36E-139cFOS 14404 2966 2881 560 2279 0.00E+00JUND 945 308 307 58 124 2.20E-20ATF3 939 496 495 94 181 3.34E-23SIRT6 1794 141 141 27 33 0.02241

SETDB1 8379 997 979 188 287 5.13E-19BRF2 67 7 7 1 2 0.2534BRF1 317 46 44 9 13 0.02365BRD4 10746 3203 3139 604 982 1.16E-85BDP1 520 89 88 17 18 0.08943

GTFs

TFs

Cofactors

NF-Y friends

NF-Y and friends stay together...

cFos NF-YB cJun Function (p-value <1e-05)Yes No No 2884 Cellular Assembly and OrganizationNo Yes No 6345 None

No No Yes 10719Cell Death, Protein Synthesis, Gene Expression, Cellular Growth and Proliferation, Molecular Transport, Protein Trafficking, Cell Cycle

Yes Yes No 4472 Cell Cycle, Gene Expression, DNA Replication, Recombination, Repair, Cellular Assembly and OrganizationYes No Yes 5980 NoneNo Yes Yes 683 None

Yes Yes Yes 1155 Cell Cycle, Cellular Function and Maintenance, Cell Death

cFos

cJun

NFYB

RefSeq

...to make life and death decisions

TA 1-1

TA 2-2

TA 4-4

C G 5-5

CG 3-3

T A 6-6

C G 7-7

12-12

10-10

11-11

CG 13-13

T A 14-14

CG 15-15

CG 16-16

C G 17-17

T A 18-18

C G 19-19

CG 20-20

TA 21-21

CG 22-22

C G 23-23

T A 24-24

TA 25-25

5’

5’

8-8

9-9

Lys 78

Ala 77

Ile 76

Lys 81

Ser 273

His 271

Gln 53

Ala 46

Lys 109

Ala 63

Ser 62

Lys 49

Ile 61

Lys 53

Lys 50

Leu 45

L1 (B)

L2 (B)

2 (B)

1 (C)

L1 (C)

2 Asn 611 (B)

Met 279

Gln 97

Arg 94

Thr 95

Arg 93

Lys 75

Arg 288

Ser 291

Pro 44

Arg 281

His 277

Arg 47

Met 60

Arg 64

Ile 59

Ala 60

Pro 58

His 271

Leu 270

His 275 Arg 283

Gly 287

Gly 286

Lys 75

CG

CG

T A

T A

TA

Phe 289

Arg 274

2-linker

L2 (C)

L1 (B)

2 (B)

2

2-linker

1 (C)

The amazing precision of ChIP-Seq

E box

CCAAT

TBP

AP1

E2F

?

?

Where do the friends sit at the table?

We can tell

E box CCAAT

10

TBP

50

AP1

E2F

Reconstructing promoters architecures

Endoderm

Mesoderm

Ectoderm

Progenitor cells

Totipotent cell

Neuron

Hepatocyte

Myoblast

Pancreatic cell

Hematopoieticcells

Epithelial cell

Pluristratified

ES cell

HSCs

Protein transfections of TAT-NF-YA in vivo.Domashenko, Blood, 2010.

VINCULIN

SOX2

NANOG

KLF5

UN

TR

EA

TE

D

-LIF

-LIF

+T

AT

-LIF

+T

AT

-NF

-YA

s

Fo

ld e

nri

chm

ent

NF-YAs

TAT-NF-YAs

NF-YAl

GENOME PROMOTERS PROMOTERS WITH CCAAT PSFM SCORE>0.8 %

ChIP-Seq dataNF-YA promoters

BACKGROUND 21747 5493 25.26 2400

TFs PROMOTERS ( -500 +100) PROMOTERS WITH CCAAT PSFM SCORE>0.8 P-value P-value

E2F1 6102 2183 35.78 5.11E-106 1472 0

NANOG 343 163 47.52 9.61E-020 144 7.25178E-50

KLF4 2966 900 30.34 6.52E-012 505 1.25421E-25

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

ChIP:NF-YB

ChIP:NANOG

Fo

ld e

nri

chm

ent

Fo

ld e

nri

chm

ent

ChIP-Seq: NANOG - + + + + + + + + +

ChIP-Seq: NF-YA + + - + + - + + + -

NF-YC

NF-YC NF-YAs

NF-YAsm29

89.382.2

TF NAME MATRIX ID P-VALUE

NFYA MA0060.1 4.86E-27

MIZF MA0131.1 1.92E-17

ELK4 MA0076.1 2.36E-16

GABPA MA0062.2 1.18E-14

ELK1 MA0028.1 1.50E-13

E2F1 MA0024.1 1.22E-11

HIF1A::ARNT MA0259.1 5.98192

TF NAME MATRIX ID P-VALUE

GABPA MA0062.2 1.83E-234

ELK4 MA0076.1 2.94E-220

ELK1 MA0028.1 5.17E-168

E2F1 MA0024.1 9.10E-156

MIZF MA0131.1 2.36E-152

TFAP2A MA0003.1 7.63E-111

NFYA MA0060.1 3.65E-108

Human Mouse

Mouse promoters Nanog peaks

TFBs analysis on Nanog core promoters Nanog peaks de novo discovery analysis

Ranking positions third

Ranking positions first

Human promoters Nanog peaks

NF-YB

NF-YA

NF-YC

NANOG

SOX2OCT4

Short

37

KLF4

SALL4

A growing network of TFs in ESC.

STAT3

MYC

C Imbriano U Modena (I)L Tora IGBMC (F)C Romier IGBMC (F)C Castagnoli B.Cute Torino (I)G Melino MRC Leicester (I)A Terrinoni IDI (I)E Candi U. Roma (I)D Aberdam INSERM-Nice (F)GP Dotto U. Lausanne (CH)E Berti U. Mi-Bicocca (I)M d’Incalci Ist Mario Negri (I)D. Hochhauser UCL (UK)J. Fleming/K. Struhl Harvard (USA)

Active Motif (USA)

DSBB U. MilanoPost-DocsKhalid ZemzoumiAlberto Di Silvio (Axxam I)Fabienne Cocchiarella (UniMo)Marià Pitarque MartìAnna TestaNicoletta Cordani (HSR, I)Silvia Pozzi (Reg Emilia)Alessandra Viganò (U. Basel, CH)

PhDsMaria Carla Motta (U. Manchester UK)Patricia LievensChiara 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 BelloriniChiara Vecchi (UniMo I)Valentina Salsi (UniMo I)Giulia Petrovich (U. Edimburgh UK)

Serena BorrelliRaffaella GattaDiletta DolfiniElena MartynovaMario MinuzzoNerina GnesuttaMariangela Lorenzo

Federico ZambelliGiulio Pavesi

Marco NardiniMartino Bolognesi

Past

Present Collaborators