functional genomics - department of molecular & cell...
TRANSCRIPT
1
1M
CB
140
Func
tiona
l gen
omic
s
2M
CB
140
Jacq
ues
Mon
od (1
970)
:
“The
sec
ret o
f life
?
But i
n pr
inci
ple
we
alre
ady
know
the
secr
et o
f life
.”
Hor
ace
Juds
on T
he E
ight
h D
ay o
f Cre
atio
n
3M
CB
140
Dr.
Syd
ney
Bre
nner
:In
late
196
2, F
ranc
is C
rick
and
I beg
an a
long
se
ries
of c
onve
rsat
ions
abo
ut th
e ne
xt s
teps
to
be
take
n in
our
rese
arch
. Bot
h of
us
felt
very
stro
ngly
that
mos
t of t
he c
lass
ical
pr
oble
ms
of m
olec
ular
bio
logy
had
bee
n so
lved
and
that
the
futu
re la
y in
tack
ling
mor
e co
mpl
ex b
iolo
gica
l pro
blem
s. I
rem
embe
r tha
t w
e de
cide
d ag
ains
t wor
king
on
anim
al
viru
ses,
on
the
stru
ctur
e of
ribo
som
es, o
n m
embr
anes
, and
oth
er s
imila
r triv
ial
prob
lem
s in
mol
ecul
ar b
iolo
gy. I
had
com
e to
be
lieve
that
mos
t of m
olec
ular
bio
logy
had
be
com
e in
evita
ble
and
that
, as
I put
it in
a
draf
t pap
er, "
we
mus
t mov
e on
to o
ther
pr
oble
ms
of b
iolo
gy w
hich
are
new
, m
yste
rious
and
exc
iting
. Bro
adly
spe
akin
g,
the
field
s w
hich
we
shou
ld n
ow e
nter
are
de
velo
pmen
t and
the
nerv
ous
syst
em."
4M
CB
140
The
spec
ies
with
the
smal
lest
gen
ome
size
in th
is c
lass
is
Myc
opla
sma
geni
taliu
m (5
80 k
b), w
hich
was
orig
inal
ly is
olat
ed
from
ure
thra
l spe
cim
ens
of p
atie
nts
with
non
-gon
occo
cal
uret
hriti
s an
d ha
s si
nce
been
sho
wn
to e
xist
in p
aras
itic
asso
ciat
ion
with
cili
ated
epi
thel
ial c
ells
of p
rimat
e ge
nita
l and
re
spira
tory
trac
ts. M
ycop
lasm
as a
re o
f int
eres
t bec
ause
they
ar
e be
lieve
d to
repr
esen
t a m
inim
al li
fe fo
rm, h
avin
g yi
elde
d to
se
lect
ive
pres
sure
to re
duce
gen
ome
size
.
http
://w
ww
.tigr
.org
/CM
R2/
Bac
kGro
und/
gmg.
htm
l
2
5M
CB
140
The
min
imal
gen
e co
mpl
emen
t of M
ycop
lasm
a ge
nita
lium
.
Fras
er C
M, G
ocay
ne J
D, W
hite
O, A
dam
s M
D, C
layt
on R
A,
Flei
schm
ann
RD
, Bul
t CJ,
Ker
lava
ge A
R, S
utto
n G
, Kel
ley
JM, e
t al.
Inst
itute
for G
enom
ic R
esea
rch,
Roc
kville
, MD
208
50, U
SA
.
The
com
plet
e nu
cleo
tide
sequ
ence
(580
,070
bas
e pa
irs) o
f the
M
ycop
lasm
a ge
nita
lium
geno
me,
the
smal
lest
kno
wn
geno
me
of a
ny fr
ee-
livin
g or
gani
sm, h
as b
een
dete
rmin
ed b
y w
hole
-gen
ome
rand
om
sequ
enci
ng a
nd a
ssem
bly.
A to
tal o
f onl
y 47
0 pr
edic
ted
codi
ng re
gion
s w
ere
iden
tifie
d th
at in
clud
e ge
nes
requ
ired
for D
NA
repl
icat
ion,
trans
crip
tion
and
trans
latio
n, D
NA
repa
ir, c
ellu
lar t
rans
port,
and
ene
rgy
met
abol
ism
.
Sci
ence
, 199
5.
6M
CB
140
How
doe
s lif
e w
ork?
How
doe
s th
e ge
nom
e w
ork?
Seq
uenc
e of
gen
ome →
answ
erP
robl
em: v
ery
man
y ge
nes
of u
nkno
wn
func
tion:
In h
uman
, at l
east
12,
000
(30%
).In
mou
se, <
5,0
00 h
ave
expe
rimen
tally
de
fined
func
tion.
7M
CB
140
Mys
terio
us y
east
8M
CB
140
Bra
ve n
ew w
orld
Cla
ssic
al g
enet
ics
–ge
ne-b
y-ge
ne, c
ircui
t-by
-circ
uit.
“Fun
ctio
nal g
enom
ics”
–m
assi
vely
par
alle
l (=
man
y at
onc
e) a
naly
sis
of g
ene
func
tion
by a
com
bina
tion
of re
vers
e ge
netic
s an
d ot
her t
hing
s.
3
9M
CB
140
Nor
ther
n –
gene
-by-
gene
m
easu
rem
ent o
f mR
NA
leve
ls
Sud
arsa
nam
et a
l. (2
000)
PN
AS
97:
336
4.
10M
CB
140
Mas
sive
ly p
aral
lel N
orth
ern:
geno
me-
wid
e ex
pres
sion
pro
filin
g1.
Silic
on c
hip
(or g
lass
slid
e) c
onta
inin
g si
ngle
-stra
nded
pro
bes
com
plem
enta
ry
to e
ach
gene
in th
e ge
nom
e.2.
A m
etho
d fo
r ext
ract
ing
RN
A fr
om c
ells
an
d m
akin
g it
fluor
esce
nt.
3.A
hyb
ridiz
atio
n ch
ambe
r in
whi
ch 2
will
be
hyb
ridiz
ed to
1.
4.A
lase
r tha
t will
sca
n th
e ch
ip a
fter t
he
hybr
idiz
atio
n.
11M
CB
140
12M
CB
140
4
13M
CB
140
14M
CB
140
15M
CB
140
“Com
preh
ensi
ve id
entif
icat
ion
of c
ell c
ycle
-re
gula
ted
gene
s of
the
yeas
t Sac
char
omyc
es
cere
visi
aeby
mic
roar
ray
hybr
idiz
atio
n”H
ow d
oes
trans
crip
tion
in y
east
cha
nge
as th
e ce
ll cy
cle
prog
ress
es?
1.Ta
ke a
sync
hron
ous
yeas
t2.
Syn
chro
nize
them
in G
1by
DIF
FER
EN
T M
ETH
OD
S3.
Rel
ease
from
arre
st4.
Ext
ract
RN
A a
t set
tim
epoi
nts
post
-arr
est
5.C
ompa
re le
vels
to th
at in
asy
nchr
onou
s cu
lture
Spe
llman
et a
l. (1
998)
Mol
. Bio
l. C
ell 9
: 327
3.16
MC
B 14
0
5
17M
CB
140
800
gene
s.
18M
CB
140
19M
CB
140
“The
maj
or fu
nctio
ns o
f the
cel
l cyc
le re
gula
ted
gene
s w
e id
entif
ied
are:
1.ce
ll cy
cle
cont
rol
2.D
NA
repl
icat
ion
3.D
NA
repa
ir4.
budd
ing
5.gl
ycos
ylat
ion
6.nu
clea
r div
isio
n7.
mito
sis
8.st
ruct
ure
of th
ecy
tosk
elet
on9.
mat
ing”
20M
CB
140
phen
omen
on ↔
wha
t cau
sed
it
6
21M
CB
140
“The
tran
scrip
tiona
l pro
gram
in th
e re
spon
se
of h
uman
fibr
obla
sts
to s
erum
”
•Ta
ke h
uman
fibr
obla
sts
arre
sted
in G
0.•
Add
ser
um (t
hey
star
t div
idin
g)•
Ext
ract
RN
A a
t def
ined
tim
epoi
nts
and
do
Affy
.
Iyer
et a
l. (2
000)
Sci
ence
285
: 83.
22M
CB
140
“Prim
ary
cultu
red
fibro
blas
ts fr
om h
uman
neon
atal
fore
skin
w
ere
indu
ced
to e
nter
a q
uies
cent
sta
teby
ser
umde
priv
atio
n fo
r 48
hour
s an
d th
en s
timul
ated
by a
dditi
on o
f med
ium
cont
aini
ng 1
0% F
BS
.D
NA
mic
roar
ray
hybr
idiz
atio
nw
as u
sed
to m
easu
re t
he
tem
pora
l cha
nges
in m
RN
A le
vels
of 8
613
hum
an g
enes
at
12 ti
mes
, ran
ging
from
15
min
to24
hou
rs a
fter s
erum
st
imul
atio
n.”
Iyer
et a
l. (2
000)
Sci
ence
285
: 83.
23M
CB
140
103,
356
indi
vidu
alm
easu
rem
ents
24M
CB
140
7
25M
CB
140
Wou
nd
heal
ing
26M
CB
140
The
cent
ral c
halle
nge
in
expe
rimen
tal b
iolo
gy
“How
to c
onve
rt da
ta in
to k
now
ledg
e”
27M
CB
140
Pro
blem
On
the
one
hand
, it i
s in
cred
ibly
gra
tifyi
ng th
at th
e ce
ll’s
resp
onse
to th
e st
imul
us m
akes
bio
logi
cal s
ense
(a
hum
an s
kin
fibro
blas
t nor
mal
ly e
noun
ters
ser
um –
i.e.,
bloo
d –
in th
e co
ntex
t of a
wou
nd).
On
the
othe
r han
d, k
now
ing
that
all
thes
e ge
nes
resp
ond
to
seru
m te
lls u
s ve
ry li
ttle
abou
t why
they
do
that
.If
we
wer
e do
ing
this
in y
east
, we’
d do
a s
cree
n. O
r, al
tern
ativ
ely,
we
coul
d te
st a
stra
in w
ith a
del
etio
n fo
r the
ge
ne(s
) tha
t reg
ulat
e th
is re
spon
se.
Whi
ch g
ene
is th
at?
Wel
l, le
t’s d
elet
e ea
ch g
ene,
one
by
one,
and
see
whi
ch
defe
ct th
e st
rain
s ge
t!!“S
cree
n of
eac
h ge
ne fo
r eac
h de
fect
” →S
ATU
RA
TIO
N
28M
CB
140
8
29M
CB
140
An
addi
tiona
l, ex
trem
ely
cool
, tric
k
The
dele
tion
cass
ette
con
tain
s a
“mol
ecul
ar
bar c
ode”
–a
tag
regi
on.
The
tag
is a
san
dwic
h (2
act
ually
) –on
ei
ther
sid
e of
the
tag
are
sequ
ence
s th
at a
re
the
sam
e in
all
dele
tion
cass
ette
s, b
ut th
e “fi
lling”
is u
niqu
e to
eac
h ge
ne:
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.30
MC
B 14
0
Wha
t thi
s m
eans
With
in e
ach
dele
ted
gene
lies
a u
niqu
e,
iden
tifia
ble
sequ
ence
.
This
repr
esen
ts a
“tag
” tha
t can
be
used
as
a un
ique
iden
tifie
r for
that
stra
in a
nd th
at
stra
in o
nly.
Mor
e on
this
ver
y so
on.
31M
CB
140
“Fun
ctio
nal C
hara
cter
izat
ion
of th
e S
.cer
evis
iae
Gen
ome
by G
ene
Del
etio
n an
d P
aral
lel A
naly
sis”
Wha
t abo
ut e
ssen
tial g
enes
? →
use
hete
rozy
gous
dip
loid
s!
1.“W
hen
spor
es fr
om th
e 20
26he
tero
zygo
us s
train
s w
ere
germ
inat
ed o
n Y
PD
med
ia a
t 30°
C h
aplo
id d
elet
ants
cou
ld
not b
e re
cove
red
for 3
56 O
RFs
(17%
)”2.
“In to
tal,
we
dele
ted
5,91
6 ge
nes
(96.
5% o
f tot
al
atte
mpt
ed).
Som
e 18
.7%
(1,1
05) o
f the
gen
es p
rove
d es
sent
ial f
or g
row
th o
n ric
h gl
ucos
e m
ediu
m.”
1. W
inze
ler e
t al.
(199
9) 2
85: 9
01.
2. G
iaev
er e
t al.
(200
2) N
atur
e 41
8, 3
87.
32M
CB
140
The
seve
n ph
enot
ypic
cat
egor
ies
of d
elet
ion
mut
ant m
orph
olog
ies
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
9
33M
CB
140
Now
wha
t?
Eig
hty
two
perc
ent o
f yea
st g
enes
are
non
-es
sent
ial i
n ric
h m
ediu
m.
Wha
t do
all t
hese
yea
st g
enes
do?
→fit
ness
pro
filin
g:m
easu
re h
ow th
e de
letio
n of
gen
e X
affe
cts
the
cell’s
abi
lity
to re
act t
o, o
r liv
e in
, co
nditi
on Y
.A
h, th
e go
od o
ld d
ays…
34M
CB
140
Scr
een
for g
al c
ells
H. D
ougl
as, D
. Haw
thor
ne (1
964)
:
1. T
ake
wt h
aplo
id y
east
.2.
Zap
them
with
UV
ligh
t.3.
Rep
lica-
plat
e to
find
thos
e th
at a
re g
al.
4. 1
:100
0 ar
e m
utan
t.
Dou
glas
HC
, Haw
thor
ne D
(196
4) E
nzym
atic
exp
ress
ion
and
gene
tic li
nkag
e of
gen
es c
ontro
lling
lact
ose
utili
zatio
n in
Sac
char
omyc
es. G
enet
ics
49:
837
.
35M
CB
140
This
is w
hat o
ne c
ould
do
Take
5,1
00 v
ials
, int
o ea
ch in
ocul
ate
a di
ffere
nt s
train
. Lab
el th
e vi
al w
ith th
e na
me
of th
e ge
ne d
elet
ed in
the
stra
in.
Do
this
in d
uplic
ate.
To o
ne v
ial,
add
som
ethi
ng (I
don
’t kn
ow, a
to
xin
or D
iet C
oke
or s
omet
hing
).S
ee, w
hich
stra
ins
have
a d
efec
t in
grow
ing
in th
e pr
esen
ce o
f asp
arta
me.
36M
CB
140
The
way
this
was
act
ually
don
e
(are
you
read
y fo
r thi
s?!)
Who
le-g
enom
e pa
ralle
l ana
lysi
sTh
e un
ique
seq
uenc
e ta
gs li
nked
to e
ach
gene
de
letio
n al
low
the
stra
ins
to b
e an
alys
ed in
par
alle
l. In
eac
h ex
perim
ent,
a m
ixed
cul
ture
con
tain
ing
ever
y de
letio
n m
utan
tis
grow
n, s
ampl
es a
re
colle
cted
at s
ever
al ti
mes
dur
ing
grow
th, a
nd th
e m
olec
ular
bar
-cod
e ta
gs a
re a
mpl
ified
from
ge
nom
ic D
NA
. The
abu
ndan
ce o
f eac
h de
letio
n st
rain
is th
en d
eter
min
ed b
y qu
antif
ying
the
asso
ciat
ed m
olec
ular
bar
cod
es b
y hy
brid
izat
ion
to
an o
ligon
ucle
otid
e ar
ray
of th
e co
mpl
emen
tary
bar
-co
de s
eque
nces
.G
iaev
er e
t al.
(200
2) N
atur
e 41
8, 3
87.
10
37M
CB
140
Am
azin
g bu
t tru
e1.
They
did
not
wan
t to
have
5,0
00 v
ials
of
anyt
hing
. Ins
tead
, the
y pu
t all
the
dele
tions
in
the
sam
e vi
al –
two
vial
s, a
ctua
lly, o
ne c
ontro
l (+
glu
cose
) and
one
exp
erim
enta
l (+
aspa
rtam
e), a
nd s
tarte
d gr
owin
g th
is s
trang
e “fa
mily
.”2.
Thos
e st
rain
s th
at h
ave
a gr
owth
def
icie
ncy
on
aspa
rtam
e w
ill g
row
mor
e sl
owly
than
thos
e th
at d
o no
t. 3.
At d
efin
ed ti
mep
oint
s, th
ey to
ok a
liquo
ts,
isol
ated
gen
omic
DN
A, a
nd …
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.38
MC
B 14
0
Ooo
h, m
ama!
… d
id P
CR
with
the
prim
ers
flank
ing
the
tag.
Thi
s w
ill am
plify
eve
ry ta
g in
the
mix
–th
at is
, fro
m
ever
y st
rain
in th
e vi
al. B
UT!
–th
e ta
g its
elf i
s un
ique
–th
at is
, the
ir P
CR
pro
duct
is a
PO
OL
–th
e nu
mbe
r of t
imes
a g
iven
tag
is re
pres
ente
d in
that
poo
l is
dire
ctly
pro
porti
onal
to h
ow
abun
dant
that
stra
in w
as a
t tha
t mom
ent i
n tim
e!
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
39M
CB
140
Yes
, and
wha
t?
This
mea
ns th
ey c
an d
irect
ly m
easu
re, h
ow m
any
cells
of w
hich
stra
in w
ere
pres
ent i
n th
e m
ix a
t any
tim
e by
hyb
ridiz
ing
this
poo
l to
a cu
stom
m
icro
arra
y –
plea
se u
nder
stan
d, n
ot th
e ye
ast
geno
me
arra
y –
this
was
an
arra
y th
ey m
ade
espe
cial
ly fo
r thi
s ex
perim
ent –
it co
ntai
ned
5,10
0 ta
g se
quen
ces,
eac
h on
e an
nota
ted:
GTC
AA
GA
TGC
TAC
CG
TTC
AG
= G
AL1
GG
TAG
TATG
TTTG
GG
AC
AG
= G
AL8
0
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.40
MC
B 14
0
One
que
stio
n
How
coo
l is
that
, I a
sk y
ou?
Ans
wer
: coo
ler t
han
Kea
nu R
eeve
s,
Law
renc
e Fi
shbu
rne,
and
Car
rie-A
nne
Mos
s C
OM
BIN
ED
.
11
41M
CB
140
Firs
t
“Abo
ut 1
5% o
f all
viab
le h
omoz
ygou
s de
letio
n st
rain
s ex
hibi
t a s
low
gro
wth
ph
enot
ype
in ri
ch m
ediu
m a
t 30
°C”
~ 62
0 ge
nes
are
not e
ssen
tial,
but i
n th
eir
abse
nce
yeas
t “w
ish
they
wer
e de
ad”
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.42
MC
B 14
0R
ibos
omal
pro
tein
L27
A, p
rote
in b
iosy
nthe
sis,
stru
ctur
al p
rote
inof
ribo
som
e, c
ytos
olic
la
rge
ribos
omal
(60S
)-su
buni
t17
.1R
PL27
A
biol
ogic
al_p
roce
ss u
nkno
wn,
mol
ecul
ar_f
unct
ion
unkn
own,
cel
lula
r_co
mpo
nent
un
know
n17
.6BU
D32
vacu
olar
ATP
ase
V0 d
omai
n su
buni
t c (1
7 kD
a), e
ndoc
ytos
is*,
hyd
roge
n-tra
nspo
rting
tw
o-se
ctor
ATP
ase,
hyd
roge
n-tra
nspo
rting
ATP
ase
V0 d
omai
n17
.9C
UP5
Treh
alos
e-6-
phos
phat
e ph
osph
atas
e, s
tress
resp
onse
*, tr
ehal
ose
phos
phat
ase,
al
pha,
alph
a-tre
halo
se-p
hosp
hate
syn
thas
e (U
DP-
form
ing)
18.0
TPS
2
trans
crip
tion
fact
or, c
hrom
atin
mod
elin
g, n
on-s
peci
fic R
NA
poly
mer
ase
II tra
nscr
iptio
n fa
ctor
, nuc
leos
ome
rem
odel
ing
com
plex
18.8
SWI3
phos
phat
idyl
inos
itol 3
-kin
ase,
pro
tein
pho
spho
ryla
tion*
, pro
tein
kin
ase*
, mem
bran
e fra
ctio
n18
.9VP
S34
bud
site
sel
ectio
n, b
iolo
gica
l_pr
oces
s un
know
n, m
olec
ular
_fun
ctio
n un
know
n,
cellu
lar_
com
pone
nt u
nkno
wn
19.0
BUD
25
yeas
t dna
J ho
mol
og (n
ucle
ar e
nvel
ope
prot
ein)
; hea
t sho
ck p
rote
in
19.6
YDJ1
sim
ilar t
o N
up12
0p a
nd C
.ele
gans
R05
H5.
5 pr
otei
n an
d N
up12
0p, b
iolo
gica
l_pr
oces
s un
know
n, m
olec
ular
_fun
ctio
n un
know
n,
20.1
AR
V1
cont
ains
two
SH3
dom
ains
20
.3B
EM
1
biol
ogic
al_p
roce
ss u
nkno
wn,
mol
ecul
ar_f
unct
ion
unkn
own,
cel
lula
r_co
mpo
nent
un
know
n20
.9FY
V11
Inte
gral
vac
uola
r mem
bran
e pr
otei
n,m
olec
ular
_fun
ctio
n un
know
n,
21.0
VAC
7
ribon
ucle
otid
e re
duct
ase,
DN
A re
plic
atio
n, ri
bonu
cleo
side
-dip
hosp
hate
redu
ctas
e,
cyto
sol
22.3
RN
R1
70-k
Da
aden
ylyl
cyc
lase
-ass
ocia
ted
prot
ein,
cyt
oske
leto
n or
gani
zatio
n an
d bi
ogen
esis
*, c
ytos
kele
tal p
rote
in b
indi
ng p
rote
in*,
act
in c
ortic
al p
atch
(sen
su
Sacc
haro
myc
es)
30.6
SR
V2
Gen
e D
escr
iptio
nA
vera
ge
Rat
ioG
ene
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
43M
CB
140
Stre
ss re
spon
se
Yea
st (a
nd u
s) h
as e
volv
ed to
resp
ond
to
stre
ss (c
hang
e in
env
ironm
ent)
–te
mpe
ratu
re, s
alin
ity, n
utrie
nt c
ompo
sitio
n,
pH, U
V d
amag
e, e
tc e
tc.
Take
thos
e st
rain
s th
at a
re a
live
and
do n
ot
have
a d
eath
wis
h (~
4,70
0 ge
nes)
and
pr
ofile
them
with
resp
ect t
o th
eir a
bilit
y to
re
spon
d to
suc
h st
ress
.=
iden
tify
gene
s re
quire
d fo
r stre
ss re
spon
se
44M
CB
140
Whi
ch s
tress
stim
uli t
o pi
ck fi
rst?
They
pic
ked:
1.
Cha
nge
of c
arbo
n so
urce
(gal
acto
se o
r 1.
5M s
orbi
tol)
2.C
hang
e in
osm
olar
ity (1
M N
aCl)
3.pH
84.
DN
A d
amag
e
12
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.46
MC
B 14
0
47M
CB
140
Sur
pris
e #1
132.
2303
PG
M2
Pho
spho
gluc
omut
ase,
gly
coge
n m
etab
olis
m*,
pho
spho
gluc
omut
ase,
cyt
opla
sm*
87.1
1409
GA
L7ga
lact
ose-
1-ph
osph
ate
urid
yl tr
ansf
eras
e, g
alac
tose
met
abol
ism
, UTP
--hex
ose-
1-ph
osph
ate
urid
ylyl
tran
80.5
2361
GA
L10
UD
P-g
luco
se 4
-epi
mer
ase,
gal
acto
se m
etab
olis
m, U
DP
-glu
cose
4-e
pim
eras
e, c
ytop
lasm
77.6
037
SN
F4as
soci
ates
with
Snf
1p
72.4
0753
IRA
2en
code
s a
GTP
ase
activ
atin
g pr
otei
n, h
ighl
y ho
mol
ogou
s to
Ira1
p, h
omol
ogue
of n
euro
fibro
min
48.9
2994
GA
L3in
volv
ed in
gal
acto
se in
duct
ion
of G
AL
gene
s, g
alac
tose
met
abol
ism
*, m
olec
ular
_fun
ctio
n un
know
n, n
u38
.042
18G
AL4
zinc
-fing
er tr
ansc
riptio
n fa
ctor
of t
he Z
n(2)
-Cys
(6) b
inuc
lear
clu
ster
dom
ain
type
, gal
acto
se m
etab
olis
m*
37.1
9342
NB
P2
inte
ract
s w
ith N
ap1,
whi
ch is
invo
lved
in h
isto
ne a
ssem
bly,
bio
logi
cal_
proc
ess
unkn
own,
33.0
685
SR
B8
RN
A p
olym
eras
e II
med
iato
r sub
unit,
repr
essi
on o
f tra
nscr
iptio
n fro
m P
ol II
pro
mot
er, R
NA
pol
ymer
ase
32.5
436
CYS
3cy
stat
hion
ine
gam
ma-
lyas
e,cy
stat
hion
ine-
gam
ma-
lyas
e,28
.116
98bi
olog
ical
_pro
cess
unk
now
n, m
olec
ular
_fun
ctio
n un
know
n,
26.4
2784
GE
F1pu
tativ
e tra
nspo
rt pr
otei
n in
volv
ed in
intra
cellu
lar i
ron
met
abol
ism
, tra
nspo
rt,24
.642
94S
MI1
57 k
Da
nucl
ear p
rote
in
24.4
1729
biol
ogic
al_p
roce
ss u
nkno
wn,
mol
ecul
ar_f
unct
ion
unkn
own,
20
.401
32G
AL2
gala
ctos
e pe
rmea
se, g
alac
tose
met
abol
ism
*, g
alac
tose
tran
spor
ter,
plas
ma
mem
bran
e18
.549
63R
ML2
mito
chon
dria
l rib
osom
al p
rote
in L
2 of
the
larg
e su
buni
t, pr
otei
n bi
osyn
thes
is*,
stru
ctur
al p
rote
in o
f rib
os13
.940
38S
EC
22S
ynap
tobr
evin
(v-S
NA
RE
) hom
olog
, non
-sel
ectiv
e ve
sicl
e fu
sion
*, v
-SN
AR
E, i
nter
-Gol
gi tr
ansp
ort v
esic
13.7
0306
MD
M12
Mdm
12p
is a
mito
chon
dria
l out
er m
embr
ane
prot
ein.
An
Mdm
12p
hom
olog
exi
sts
in S
. Pom
be w
hich
c12
.561
3B
MH
1H
omol
og o
f mam
mal
ian
14-3
-3 p
rote
ins,
pse
udoh
ypha
l gro
wth
*, m
olec
ular
_fun
ctio
n un
know
n,12
.238
4FT
R1
Iron
perm
ease
, tra
nspo
rt,12
.132
23R
AV
1R
egul
ator
of (
H+)
-ATP
ase
in v
acuo
lar m
embr
ane,
mol
ecul
ar_f
unct
ion
unkn
own,
10
.771
66D
IA4
Ser
yl-tR
NA
syn
thet
ase,
pse
udoh
ypha
l gro
wth
*, s
erin
e--tR
NA
liga
se, c
ellu
lar_
com
pone
nt u
nkno
wn
10.5
0621
FET3
mul
ticop
per o
xida
se, h
igh
affin
ity ir
on tr
ansp
ort,
mul
ticop
per f
erro
xida
se ir
on tr
ansp
ort m
edia
tor,
plas
ma
9.32
1492
GA
L1ga
lact
okin
ase,
gal
acto
se m
etab
olis
m, g
alac
toki
nase
, pla
sma
mem
bran
e*8.
8831
9bi
olog
ical
_pro
cess
unk
now
n, m
olec
ular
_fun
ctio
n un
know
n,
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.48
MC
B 14
0
Sur
pris
e #1
“The
use
of g
alac
tose
is o
ne o
f the
bes
t-st
udie
d pa
thw
ays
in y
east
, yet
we
iden
tifie
d te
nge
nes
not p
revi
ousl
y kn
own
to b
e re
quire
d fo
r opt
imal
gro
wth
on
this
car
bon
sour
ce: M
SN
2, F
TR1,
FE
T3, Y
DR
290W
, A
TX1,
YN
L077
W, Y
DR
269C
, GE
F1,
YM
L090
w, Y
KL0
37W
. Thu
s, fi
tnes
s pr
ofilin
g ca
n di
scov
er g
enes
invo
lved
eve
n in
pr
evio
usly
wel
l-stu
died
pat
hway
s. “
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
13
49M
CB
140
Mes
sage
This
was
the
first
real
sat
urat
ion
scre
en e
ver
done
for a
nyth
ing.
Sat
urat
ion
scre
ens
have
bee
n do
ne in
the
past
, but
the
clai
m o
f sat
urat
ion
(“we’
ve
mad
e a
mut
atio
n in
eve
ry g
ene”
) has
al
way
s be
en a
sta
tistic
al, n
ot a
n em
piric
al
one.
It’s
amaz
ing
how
muc
h m
ore
one
can
find
whe
n on
e do
es a
true
satu
ratio
n sc
reen
!
50M
CB
140
Exp
ress
ion
prof
iling
vs.
gen
etic
s?
The
stim
uli (
gala
ctos
e, 1
M N
aCl,
DN
A
dam
age,
etc
.) pi
cked
wer
e no
t cho
sen
rand
omly
. The
y ch
ose
the
ones
for w
hich
th
e ex
pres
sion
pro
filin
g ha
d al
read
y be
en
done
.C
ompa
re tw
o lis
ts:
1.G
enes
act
ivat
ed (r
epre
ssed
) by
stim
ulus
.2.
Gen
es th
at a
re re
quire
d fo
r gro
wth
fo
llow
ing
that
stim
ulus
.
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
51M
CB
140
Let’s
thin
k ab
out t
his
for a
sec
ond
If a
stim
ulus
act
ivat
es (o
r rep
ress
es) a
gen
e,
this
mus
t be
for a
reas
on!
For e
xam
ple,
whe
n yo
u ad
d la
ctos
e to
E.
coli,
one
gen
e th
at is
indu
ced
is, o
f cou
rse,
b-
gala
ctos
idas
e.P
redi
ctio
n:If
a ge
ne is
indu
ced
by th
e st
imul
us, i
t mus
t ha
ve s
omet
hing
to d
o w
ith re
spon
ding
to
the
stim
ulus
!
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.52
MC
B 14
0
Buc
kle
your
sea
tbel
ts a
nd re
turn
yo
ur tr
ay ta
bles
to a
n up
right
and
fu
lly lo
cked
pos
ition
14
53M
CB
140
Hol
y co
w“O
ur h
ypot
hesi
s w
as th
is: i
f a g
ene
exhi
bits
a s
igni
fican
t in
crea
se in
exp
ress
ion
in a
giv
en c
ondi
tion,
then
it s
houl
d al
so b
e re
quire
d fo
r opt
imal
gro
wth
in th
at c
ondi
tion.
We
foun
d th
at in
gal
acto
se, l
ess
than
7%
of t
he g
enes
that
ex
hibi
ted
a si
gnifi
cant
incr
ease
in m
RN
A e
xpre
ssio
n al
so
exhi
bite
d a
sign
ifica
nt d
ecre
ase
in fi
tnes
s.In
the
case
of p
H
8, 1
M N
aCl a
nd 1
.5M
sor
bito
l, 3.
0%, 0
.88%
and
0.3
4%,
resp
ectiv
ely,
of t
he g
enes
that
exh
ibite
d a
sign
ifica
nt
incr
ease
in m
RN
A e
xpre
ssio
n al
so e
xhib
ited
a si
gnifi
cant
de
crea
se in
fitn
ess.
”
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.54
MC
B 14
0
Hm
mm
mm
mm
mm
mm
mm
“We
obse
rved
littl
e ov
erla
p of
gen
es id
entif
ied
both
as
sign
ifica
nt b
y fit
ness
pro
filin
g an
d as
sig
nific
antly
upr
egul
ated
by
gene
exp
ress
ion
prof
iling
in c
ondi
tions
of 1
M N
aCl,
1.5
M s
orbi
tol,
pH 8
and
gal
acto
se.
It is
eas
y to
imag
ine
why
som
e ge
nes
requ
ired
for g
row
th u
nder
apa
rticu
lar c
ondi
tion
do n
ot e
xhib
it a
chan
ge in
exp
ress
ion
in th
at
cond
ition
, bec
ause
the
resp
onse
to th
e ch
ange
in c
ondi
tion
may
op
erat
e po
st-tr
ansc
riptio
nally
. The
con
vers
e si
tuat
ion—
a ge
ne th
at
exhi
bits
a s
igni
fican
t inc
reas
e in
exp
ress
ion
but i
s no
t req
uire
d fo
r gr
owth
—is
qui
te s
urpr
isin
g, a
nd m
ore
diffi
cult
to c
ompr
ehen
d. It
is
poss
ible
that
und
er s
tress
con
ditio
ns, m
ultip
le g
ene
prod
ucts
are
ex
pres
sed,
onl
y a
smal
l fra
ctio
n of
whi
ch a
re e
ssen
tial f
or a
dapt
atio
n to
th
e sp
ecifi
c co
nditi
on in
que
stio
n.”
Gia
ever
et a
l. (2
002)
Nat
ure
418,
387
.
55M
CB
140
Sev
ente
en th
ousa
nd th
ree
hund
red
and
eigh
teen
“Exp
ress
ion
prof
iling
” = 1
7,31
8 pa
pers
.Ta
ke c
ell,
do s
omet
hing
to it
, obs
erve
cha
nge
in
gene
exp
ress
ion
and
chan
ge in
cel
l.W
hat i
s th
e re
latio
nshi
p be
twee
n ch
ange
s in
gen
e ex
pres
sion
and
wha
t hap
pene
d to
the
cell?
Ass
umpt
ion:
a c
ausa
l one
.Th
at is
, gen
e ex
pres
sion
cha
nged
bec
ause
of w
hat
we
did
to th
e ce
ll, a
nd, f
urth
erm
ore,
how
the
cell
resp
onde
d to
wha
t we
did
is d
ue to
the
gene
ex
pres
sion
cha
nge.
56M
CB
140
Coi
ncid
enta
l cor
rela
tion
Pos
t hoc
, erg
o pr
opte
r hoc
.“A
fter s
omet
hing
, the
refo
re b
ecau
se o
f so
met
hing
.”
15
57M
CB
140
“Tra
nscr
iptio
nal r
espo
nse
of S
. cer
evis
iae
to D
NA
-dam
agin
g ag
ents
do
es n
ot id
entif
y th
e ge
nes
that
pro
tect
aga
inst
thes
e ag
ents
”
The
rece
nt c
ompl
etio
n of
the
dele
tion
of a
ll of
the
none
ssen
tialg
enes
in
budd
ing
yeas
t has
pro
vide
d a
pow
erfu
l new
way
of d
eter
min
ing
thos
e ge
nes
that
affe
ct th
e se
nsiti
vity
of t
his
orga
nism
to c
ytot
oxic
age
nts.
We
have
use
d th
is s
yste
m to
test
the
hypo
thes
is th
at g
enes
who
se tr
ansc
riptio
n is
in
crea
sed
afte
r DN
A da
mag
e ar
e im
porta
nt fo
r the
sur
viva
l to
that
dam
age.
W
e us
ed a
poo
l of 4
,627
dip
loid
stra
ins
each
with
hom
ozyg
ous
dele
tion
of a
no
ness
entia
l gen
e to
iden
tify
thos
e ge
nes
that
are
impo
rtant
fort
he s
urvi
val
of y
east
to fo
ur D
NA
-dam
agin
g ag
ents
: ion
izin
g ra
diat
ion,
UV
radi
atio
n, a
nd
expo
sure
to c
ispl
atin
or t
o hy
drog
en p
erox
ide.
In a
dditi
on w
e m
easu
red
the
trans
crip
tiona
l res
pons
e of
the
wild
-type
par
enta
l stra
in to
the
sam
e D
NA
-da
mag
ing
agen
ts. W
e fo
und
no re
latio
nshi
p be
twee
n th
e ge
nes
nece
ssar
y fo
r sur
viva
l to
the
DN
A-d
amag
ing
agen
ts a
nd th
ose
gene
s w
hose
tra
nscr
iptio
n is
incr
ease
d af
ter e
xpos
ure.
The
se d
ata
show
that
few
, if a
ny, o
f th
e ge
nes
invo
lved
in re
pairi
ng th
e D
NA
lesi
ons
prod
uced
in th
isst
udy,
in
clud
ing
doub
le-s
trand
bre
aks,
pyr
imid
ine
dim
ers,
sin
gle-
stra
nd b
reak
s,
base
dam
age,
and
DN
A c
ross
-link
s, a
re in
duce
d in
resp
onse
to to
xic
dose
s of
the
agen
ts th
at p
rodu
ce th
ese
lesi
ons.
This
find
ing
sugg
ests
that
the
enzy
mes
nec
essa
ry fo
r the
repa
ir of
thes
e le
sion
s ar
e at
suf
ficie
nt le
vels
w
ithin
the
cell.
The
dat
a al
so s
ugge
st th
at th
e na
ture
of t
he le
sion
s pr
oduc
ed
by D
NA-
dam
agin
g ag
ents
can
not e
asily
be
dedu
ced
from
gen
e ex
pres
sion
pr
ofili
ng.
Birr
ell e
t al.
(200
2) P
NA
S 9
9: 8
778.
58M
CB
140
Ple
ase
unde
rsta
nd
This
doe
s no
t mea
n th
at g
enes
that
resp
ond
to s
timul
i are
irre
leva
nt to
that
resp
onse
.Th
is o
nly
mea
ns th
at y
ou c
anno
t tak
e a
list
of g
enes
that
hav
e re
spon
ded
and
mak
e a
swee
ping
cla
im a
s to
the
rele
vanc
e of
all
the
gene
s th
at re
spon
ded
to th
e ac
tual
fu
nctio
nal p
athw
ay o
f the
resp
onse
.Fo
r som
e pa
thw
ays
(DN
A d
amag
e in
yea
st)
the
Ven
n di
agra
m h
as n
ear-
zero
ove
rlap!
59M
CB
140
Nex
t tim
e
Use
of f
unct
iona
l gen
omic
s to
und
erst
and
canc
er c
ell b
iolo
gy.