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

1. BiP-­‐Day
2013
Bari,
5
dicembre

2. Epigene'cs
• ‘Epi’gene'cs
-­‐
‘On’
or
‘over’
the
gene'c
informa'on
encoded
in
the
DNA

3. 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

4. Molecular
Mechanisms
that
Mediate
Epigene'c
Phenomena
• DNA
methyla'on
(CpG
dinucleo'des)
• Histone
modifica'ons
• ncRNAs
/
RNA
edi'ng
Nucleosome

5. 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.

6. 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

7. 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.

8. 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

9. 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

10. 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.

11. 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

12. EPIGEN
workflows

13. 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

14. 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

15. Dissemina'on
&
Health
Care
Policy
(Coordinator:
Giuseppe
Testa)

16. 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

17. 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