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Graziano Pesole - il progetto EPIGEN
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Graziano Pesole - il progetto EPIGEN



La ricerca epigenetica per l’economia globale, la salute umana e l’ambiente

La ricerca epigenetica per l’economia globale, la salute umana e l’ambiente



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    Graziano Pesole - il progetto EPIGEN Graziano Pesole - il progetto EPIGEN Presentation Transcript

    • BiP-­‐Day  2013   Bari,  5  dicembre  
    • Epigene'cs   •  ‘Epi’gene'cs  -­‐  ‘On’  or  ‘over’  the  gene'c   informa'on  encoded  in  the  DNA  
    • Epigene'cs   •  The  study  of  reversible  heritable  changes  in  gene   func'on  that  occur  without  a  change  in  the   sequence  of  nuclear  DNA     •  Gene-­‐regulatory  informa'on  that  is  not  expressed   in  DNA  sequences  is  transmiBed  from  one   genera'on  (of  cells  or  organisms)  to  the  next    
    • Molecular  Mechanisms  that  Mediate   Epigene'c  Phenomena   •  DNA  methyla'on  (CpG  dinucleo'des)   •  Histone  modifica'ons   •  ncRNAs  /  RNA  edi'ng   Nucleosome  
    • EPIGEN:  Vision  and  goals   EPIGEN  project  was  conceived  to  nucleate  the  exper'se,  available  all   over  the  country,  with  the  goal  of  promo'ng  excellence  and  boos'ng   development  in  research  areas  considered  of  strategic  relevance  to   the  country’s  society  and  economy.                   The  main  scien'fic  goal  of  the  EPIGEN  project  is  to  understand  how   epigene'c  mechanisms  regulate  normal  biological  processes,  generate   diversity  and  contribute  to  pathological  altera'ons  in  organisms   ranging  from  plants  to  humans.    
    • EPIGEN  structure   >70  labs,  8  subprojects.  20  million  €  for  3  yrs.     Coordinator   Prof.  Giuseppe  Macino   ExecuHve  CommiSee   Vice-­‐directors  +  subproject  coordinators   Subproject  1:  NGS  plaEorm   SP4:  ChromaHn  structure  &  dynamics   SP5:  EpigeneHc  control  by  ncRNA   Subproject  2:  BioinformaHcs  plaE.   SP6:  EpigeneHc  control  of  cell  idenHty   SP7:  EpigeneHc  drugs   Subproject  3:  Cell  imaging  plaEorm     SP8:  Epigenomics  plants  of  agricultural  interest  
    • EPIGEN  has  successfully  created  centralised   plaSorms  for  epigenomic  research    Many  Italian  ins'tu'ons  lag  behind  those  in  other   European  countries  when  it  comes  to  availability  of  the   latest  technologies  required  for  epigenomic  studies.      Our  first  cri'cal  milestone  was  the  crea'on  of  centralized   plaSorms  to  provide  all  the  par'cipants  with  rapid  access  to   next  genera'on  sequencing,  data  storage,  bioinforma'c   pipelines,  supercompu'ng  capacity  as  well  as  cell  imaging   technologies.    
    • SP1:    NGS  PlaSorm   Coordinator:  Michele  Morgante  -­‐  IGA,  Udine   NGS  Center    exclusive  for  EPIGEN   DNA-­‐seq   RNA-­‐seq   SmallRNA-­‐ seq   ChIP-­‐seq   BS-­‐seq   Exome-­‐seq   Amplicon-­‐ seq   NEXT…   NEW   NEW   NEW   •  Development  of  new  applica'ons    in  collabora'on  with  Epigen  groups    
    • SP2:  Bioinforma'cs  PlaSorm   Coordinator:  Graziano  Pesole.  IBBE  –  CNR  &  University  of  Bari   •  Development  of  so_wares  and  pipelines  for  NGS  data  analysis    Anna  Tramontano,  Sapienza  University  of  Rome      Giulio  Pavesi,  University  of  Milan    Raffaele  Calogero,  University  of  Turin    Tiziana  Castrignanò,  CINECA,  Rome    Giorgio  Valle,  University  of  Padua    Alberto  Policri',  Ins'tute  of  Applied  Genomics,  Udine    Diego  Di  Bernardo,  Telethon  Ins'tute  of  Gene'cs  &  Medicine,  Naples    Silvio  Bicciato,  University  of  Modena  &  Reggio  Emilia    Claudia  Angelini,  IAC  –  CNR,  Naples    Paola  Paci,  IASI  –  CNR,  Rome    Flavio  Licciulli  ITB  –  CNR,  Bari    Manuela  Helmer-­‐CiBerich  –  Rome  “Tor  Vergata“      Centralized  data  Repository    (CASPUR-­‐CINECA)    up  to  a  700  Terabyte    
    • NGS  Data  Repository   NGS  Data  Repository   The   Next   Genera'on   Sequencing   (NGS)   plaSorms   are   revolu'onizing   genomics   and   trascritomics   science,   but   biological   sequencing   data   are   now   produced   in   unprecedented   amounts.   Find  NGS   Experiment   Find  Gene,   CHR,  Range   Query   NGS   Input   (iRODS)   Results   NGS  Metadata   (EBI-­‐SRA)   Query   NGS  Analysis   NGS   Output   (mySQL)   Results   Web  Results   Peaks,  variants,   introns,  exons,   promoters   NGSDR   In  order  to  adapt  to  the  much  greater  input  and  output  from  NGS  data  analyses,  the  NGS   Data   Repository   (NGSDR)   incorporates   several   improvements,   including   separa'on   of   metadata   from   the   content   and   the   crea'on   of   a   sequencing   ‘experiment’   object   to   describe  the  sequencing  library  that  the  runs  belong  to.   Cineca  users  and  IT  experts  can  query  the  metadata  to  find  and  track  data.    
    • EPIGEN:  NGS  data  produc'on   Data  type   RNAseq   NCseq   WES   RIP-­‐seq   RC-­‐seq   smallRNA   ChIp-­‐seq   number  of   billions  of  reads   billions  of  bases   lanes   10.7   2.4   0.8   0.7   2.3   0.7   3.6   21.2   877   138.3   88.5   32.8   227   33.9   180.8   1578.3   392   47   58   14   80   61   79   731  
    • EPIGEN  workflows  
    • EPIGEN  bioinforma'cs  resources   Tool   AspicDB   Pscan   Description     Alternative  splicing  resource   Identify  common  regulators  of  a  set  of  genes  using  ChIP-­‐ Seq  datasets.   highly  performing  and  sensitive  aligner  for  short  (NGS-­‐ like)  reads   Functional  interpretation  of  differential  expression   analyses   Mode  of  Action  (MoA)  of  novel  drugs  and  the   identification  of  known  and  approved  candidates  for   “drug  repositioning”   Collection  of  softwares  for  the  search  of  motifs  on  DNA   and  RNA   human  and  mouse  gene  regulatory  networks   Search  for  transcription  factor  binding  sites  in  promoters   of  co-­‐regulated  or  co-­‐expressed  genes   SpliceAidF   Database  of  human  splicing  factors  and  their  binding  sites  http://srv00.ibbe.cnr.it/SpliceAidF/   Cscan   ERNE   Fidea   MANTRA   ModTools   NetView   Web  link   http://srv00.ibbe.cnr.it/ASPicDB/   www.beaconlab.it/cscan   http://erne.sourceforge.net   http://www.biocomputing.it/fidea   http://mantra.tigem.it   www.beaconlab.it/modtools   http://netview.tigem.it   www.beaconlab.it/pscan  
    • Training  of  young  researchers   •  Workshops   -­‐NGS  &  Data  Analysis.  Udine,  June  19-­‐22,  2012   -­‐Data    sequencing  archiving.  Rome,  July  10-­‐11,  2012   -­‐ChIP-­‐Seq  Analysis.  Rome,  October  31,  2012   -­‐ChIP-­‐Seq  Analysis.  Milan,  December  11,  2012   -­‐Workshop  Epigenomics.  Bari,  December  5-­‐7,  2012   -­‐Systems  Biology  Training.  Naples,  April  22-­‐23,  2013   -­‐DNA  methyla'on  Analysis.  Padua,  June  10-­‐11,  2013   -­‐FEBS  Workshop.  Capri,  October  13-­‐16,  2013   -­‐Advanced  ChIP-­‐Seq  workshop.  Milan,  November  24-­‐25,  2013   -­‐RNA-­‐Seq  Analisis.  Bari    December  2013     •  EPIGEN  exchange  &  training  abroad  fellowships     -­‐exchange  of  young  researchers  among  EPIGEN  labs   -­‐visits  to  foreign  labs  to  learn  new  methods  &  for  collabora'ons  
    • Dissemina'on  &  Health  Care  Policy   (Coordinator:  Giuseppe  Testa)  
    • ImpaBo   •  Strategico  -­‐  scienHfico    Network  tra  gli  epigene's'  italiani    -­‐aumenta  compe''vitá  e  visibilitá  della  ricerca  italiana    -­‐sviluppo  di  tecnologie  avanzate    -­‐collaborazioni  ed  infrastruBure  che  perdureranno   •  Biomedico  -­‐  economico    I  nostri  risulta'  permeBono  di    -­‐comprendere  meccanismi  del  cancro,  distrofia  muscolare    -­‐produzione  di  farmaci  per  nuove  terapie  epigene'che    -­‐opmizzare  processi  nell´ambito  agricolo   •  Socio-­‐economico    -­‐Formazione  di  giovani  =>  nuove  competenze  =>  lavoro    
    • Contap   DireSore:  Giuseppe  Macino     Project  Manager:  Cecilia  Poli     www.epigen.it    /  epigen@cnr.it     Consiglio  Nazionale  delle  Ricerche   P.le  Aldo  Moro  7   00185  Roma   Tel.  064  9932371  /  2995