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Università degli Studi di Milano. Member of LERU (League of European Research Universities).

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.

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Università degli Studi di Milano. Member of LERU (League of European Research Universities).

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  1. 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.

  2. Progenitor cells Pancreatic cell Endoderm Hepatocyte Myoblast Mesoderm B cell Totipotent cell Neuron Ectoderm Epithelial cell Pluristratified ES cell

  3. A1 helix K261 P263 F50 E52 Y56 R266 E82 Q85 E86 R249 R253 I117 E90 S93 S97 D116 F113 R250 R245 F94 Q110 I246 E98 F125 V238 D112 E101 L123 T122 Q242 D109 S121 K241 N239 T A A C A2 C a2(YB) a1(YC) aC(YC) A1 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

  4. The genomic strategy of NF-Y: The ENCODE Project. ChIp-Seq/Mass-Spec in 9 cell types of 10 histone PTMs and 72 -and counting- DNA-binding Proteins (Mostly TFs).

  5. Clustering NF-Y with 80 nuclear proteins.

  6. 40/50 TFs show correlations, P value E-40

  7. NF-Y friends GTFs TFs Cofactors

  8. NF-Y and friends stay together...

  9. ...to make life and death decisions cFos cJun NFYB RefSeq

  10. 5’ T A -1 1 T C G A Gln 97 Arg 93 L2 (C) -2 2 C G G G G G C C C C Arg 94 Thr 95 C G -3 3 L1 (B) Lys 75 T A -4 T T A A 4 a2 (B) Lys 78 -5 5 Ala 77 A T L1 (B) Ile 76 -6 6 A A T T Lys 75 a2 (B) G C Lys 81 -7 7 Gly 287 -8 Phe 289 Met 279 8 Gly 286 Arg 288 A2 -9 9 His 275 Arg 283 Ser 291 His 271 -10 10 A1A2-linker Leu 270 Arg 281 Pro 58 -11 11 Ile 59 His 277 Ala 60 a1 (B) -12 12 Asn 61 A2 Arg 64 C G -13 13 Arg 274 Ser 273 A T A1A2-linker -14 14 His 271 C G Gln 53 -15 15 Lys 50 Arg 47 a1 (C) C G -16 16 Ala 46 Leu 45 Pro 44 -17 17 A T -18 18 -19 19 C G -20 20 Met 60 Lys 53 -21 21 a1 (C) Lys 49 L1 (C) Ile 61 C G Ser 62 -22 22 Ala 63 -23 23 A T -24 24 L2 (B) Lys 109 T A -25 25 5’ The amazing precision of ChIP-Seq

  11. Where do the friends sit at the table? ? CCAAT ? E2F E box TBP AP1

  12. We can tell

  13. Reconstructing promoters architecures 10 50 CCAAT E2F E box TBP AP1

  14. 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 Neuron Ectoderm Epithelial cell Pluristratified

  15. -LIF +TAT-NF-YAs UNTREATED -LIF +TAT -LIF VINCULIN TAT-NF-YAs NF-YAl NF-YAs SOX2 NANOG KLF5 Fold enrichment

  16. TFBs analysis on Nanog core promoters Nanog peaks de novo discovery analysis Mouse promoters Nanog peaks Ranking positions third Human promoters Nanog peaks Ranking positions first Mouse Human 82.2 ChIP:NF-YB 89.3 Fold enrichment NF-YAs NF-YC ChIP:NANOG NF-YAsm29 Fold enrichment NF-YC

  17. NF-YC NF-YB NF-YA A growing network of TFs in ESC. 37 Short KLF4 SALL4 MYC STAT3 OCT4 SOX2 NANOG

  18. Past DSBB U. Milano 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) Present Collaborators Serena Borrelli Raffaella Gatta Diletta Dolfini Elena Martynova Mario Minuzzo Nerina Gnesutta Mariangela Lorenzo Federico Zambelli Giulio Pavesi Marco Nardini Martino Bolognesi 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)

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