1

1M

CB

140

11/

27/0

6

E. c

oli=

E. l

epha

nt ?

F. J

acob

J. M

onod

A. P

arde

e

D. H

awth

orne

H. D

ougl

asY.

Osh

ima

1965

1966

2M

CB

140

11/

27/0

6

Ana

logy

and

hom

olog

y as

tool

s in

ge

netic

inve

stig

atio

n

Sta

pes

Incu

sM

alle

usM

amm

alS

tape

sQ

uadr

ate

(bon

e)A

rticu

lar (

bone

)A

mph

ibia

n

Hyo

man

dibu

lar

carti

liage

Pal

atoq

uadr

ate

carti

lage

Mec

kel's

car

tilag

eS

hark

Hyo

id A

rch

(dor

sal)

Man

dibu

lar A

rch

(dor

sal)

Man

dibu

lar A

rch

(ven

tral)

Ani

mal

3M

CB

140

11/

27/0

64

MC

B 1

40 1

1/27

/06

a ce

lls p

rodu

ce a

pher

omon

e an

d α

rece

ptor

αce

lls p

rodu

ce α

pher

omon

e an

d a

rece

ptor

dipl

oid

(a/α

) cel

ls p

rodu

ce n

one

of th

e ab

ove

2

5M

CB

140

11/

27/0

6

Shm

ooA

l Cap

p (1

948)

–Li

’l A

bner

6M

CB

140

11/

27/0

6

Mar

sh a

nd R

ose

diag

ram

7M

CB

140

11/

27/0

6

The

phen

otyp

e of

a h

aplo

id y

east

cel

l with

re

spec

t to

mat

ing

is d

eter

min

ed b

y tra

nscr

iptio

n fa

ctor

s

An α

cell

prod

uces

two

trans

crip

tion

fact

ors,

M

atα

1p a

nd M

atα

2p, t

hat e

nsur

e ex

pres

sion

of

αsp

ecifi

c ge

nes,

incl

udin

g th

e ph

erom

one

and

rece

ptor

, and

repr

ess

expr

essi

on o

f asp

ecifi

c ge

nes.

In a

n a

cell,

Matα

1p a

nd M

atα

2p a

re n

ot

expr

esse

d, a

nd a

diff

eren

t tra

nscr

iptio

n fa

ctor

is

expr

esse

d, M

ata1

p. T

he α

gene

s ar

e of

f, an

d th

e a

gene

s (p

hero

mon

e an

d re

cept

or) a

re o

n.

8M

CB

140

11/

27/0

6

A.9

3

9M

CB

140

11/

27/0

6

Am

azin

g bu

t tru

e

A w

ild-ty

pe h

aplo

id y

east

cel

l con

tain

s TH

RE

E

copi

es o

f mat

ing

type

-det

erm

inin

g ge

nes:

•C

opy

#1: t

he α

1 an

d α

2 ge

nes

(sile

nt).

•C

opy

#2: t

he a

1an

d a2

gene

s (a

lso

sile

nt).

•C

opy

#3: A

n ad

ditio

nal c

opy

of g

enes

in it

em 1

, or

of th

e ge

nes

in it

em 2

, but

act

ive.

Whi

chev

er g

enes

are

con

tain

ed in

cop

y #3

de

term

ines

the

mat

ing

type

.

10M

CB

140

11/

27/0

6

A.1

1

A.1

2

11M

CB

140

11/

27/0

6

“An

easi

ly u

nder

stoo

d, w

orka

ble

fals

ehoo

d is

mor

e us

eful

than

an

inco

mpr

ehen

sibl

e tru

th.”

12M

CB

140

11/

27/0

6

cen

MA

TH

MLα

HM

Ra

α1

α2

a1a2

αce

ll

α1

α2 ac

tive

sile

ntsi

lent

4

13M

CB

140

11/

27/0

6

Loss

of s

ilenc

ing

at th

e si

lent

mat

ing

type

ca

sset

tes

crea

tes

a “n

onm

ater

” –a

hapl

oid

that

is a

/αan

d th

at th

inks

it’s

a d

iplo

id.

cen

MA

TH

MLα

HM

Ra

α1

α2

a1a2

αce

ll

α1

α2 ac

tive

activ

eac

tive

14M

CB

140

11/

27/0

6

Scr

een

for s

ilenc

ing

mut

ants

A s

ampl

e “s

cree

n”:

1.Ta

ke h

aplo

id c

ells

.2.

Mut

ate

them

.3.

Scr

een

for t

hose

that

don

’t m

ate.

Pro

blem

: mat

ing

is s

o m

uch

mor

e th

an

prop

er s

ilenc

ing

of m

atin

g ty

pe lo

ci!!

15M

CB

140

11/

27/0

6

The

mat

ing

pher

omon

e re

spon

se

Jere

my

Thor

ner

Thor

ner d

iagr

amA

lso

see

Fig.

A.1

3.

16M

CB

140

11/

27/0

6

How

to s

cree

n fo

r sile

ncin

g m

utan

ts

cen

MA

TH

MLα

HM

Ra

α1

α2

a1a2

ace

ll

a1a2 ac

tive

sile

ntsi

lent

Jasp

er R

ine

and

Ira H

ersk

owitz

(198

7) G

enet

ics

116:

9-22

.

5

17M

CB

140

11/

27/0

6

How

to s

cree

n fo

r sile

ncin

g m

utan

ts

cen

mat

a1-1

HM

Lαα1

α2

a1a2 ac

tive

sile

ntsi

lent

Jasp

er R

ine

and

Ira H

ersk

owitz

(198

7) G

enet

ics

116:

9-22

.

HM

Lαα1

α2

Not

e: m

ata1

-1 is

a s

peci

al a

llele

of t

he a

gene

–it

is re

cess

ive

to α

18M

CB

140

11/

27/0

6Ja

sper

Rin

e an

d Ira

Her

skow

itz (1

987)

Gen

etic

s 11

6: 9-

22.

Rin

e sc

hem

atic

mat

e to

ace

lls

19M

CB

140

11/

27/0

6

The

data

•C

olon

ies

scre

ened

: 675

,000

•C

olon

ies

that

mat

ed to

a: 2

95•

Maj

or c

ompl

emen

tatio

n gr

oups

: 4

sile

nt in

form

atio

n re

gula

tors

:

SIR

1, S

IR2,

SIR

3, S

IR4

Jasp

er R

ine

and

Ira H

ersk

owitz

(198

7) G

enet

ics

116:

9-22

.20

MC

B 1

40 1

1/27

/06

Que

stio

n

Wha

t mol

ecul

ar m

echa

nism

s ar

e re

spon

sibl

e fo

r si

lenc

ing

at th

e m

atin

g ty

pe lo

ci?

→he

tero

chro

mat

in fo

rmat

ion

in m

etaz

oa→

pros

tate

can

cer

→br

east

can

cer

→ag

eing

→“n

orm

al”g

ene

regu

latio

n in

mam

mal

s

6

21M

CB

140

11/

27/0

6

Hom

ewor

k

22M

CB

140

11/

27/0

6

How

can

one

exp

lain

the

evol

utio

n of

two

dist

inct

mat

ing

type

s in

bud

ding

yea

st?

Sur

ely

a pa

thw

ay c

ould

hav

e ju

st

evol

ved

for t

he fu

sion

of t

wo

iden

tical

hap

loid

cel

ls?

23M

CB

140

11/

27/0

6

Two

mat

ing

type

s ha

ve e

volv

ed u

nder

se

lect

ive

pres

sure

to a

void

inbr

eedi

ng

M

D1

D2

D1

D2

One

evo

lutio

nary

adv

anta

ge o

f mat

ing

is th

e pr

oduc

tion

of n

ovel

gen

otyp

ic c

ombi

natio

ns v

ia th

e fu

sion

of t

wo

geno

mes

with

diff

eren

t life

his

torie

s.

x

24M

CB

140

11/

27/0

6

Gra

ndda

ught

ers

of a

ny g

iven

m

othe

r can

sw

itch

mat

ing

type

7

25M

CB

140

11/

27/0

626

MC

B 1

40 1

1/27

/06

urno

v@be

rkel

ey.e

du

27M

CB

140

11/

27/0

6

cen

MA

TH

MLα

HM

Ra

α1

α2

a1a2

αce

ll

α1

α2

cen

MA

TH

MLα

HM

Ra

α1

α2

a1a2

ace

ll

a1a2ac

tive

sile

ntsi

lent

28M

CB

140

11/

27/0

6

Epi

gene

tic in

herit

ance

•In

an α

stra

in, t

he g

enet

ic in

form

atio

n at

MA

T an

d at

HM

L αis

iden

tical

.•

The

one

at M

AT

is e

xpre

ssed

, but

the

one

at

HM

L is

not

–it

is e

pige

netic

ally

sile

nced

.

Epi

gene

tic: m

itotic

ally

sta

ble

(per

sist

s th

roug

h ce

ll di

visi

on) c

hang

e in

gen

e ex

pres

sion

sta

te th

at is

no

t ass

ocia

ted

with

a c

hang

e in

DN

A s

eque

nce.

Exa

mpl

es: X

chr

omos

ome

inac

tivat

ion;

impr

inte

d ge

nes;

tran

sgen

e si

lenc

ing

in g

ene

ther

apy.

8

29M

CB

140

11/

27/0

6

> 1

met

re<

10-5 m

etre

s

15,0

00x

com

pact

ion

Com

pact

ion

into

chr

omat

in b

rings

th

e eu

kary

otic

gen

ome

to li

fe

30M

CB

140

11/

27/0

6

“Bea

ds o

n a

strin

g”

31M

CB

140

11/

27/0

6

The

Nuc

leos

ome

Cor

e P

artic

le:

8 hi

ston

es, 1

46 b

p of

DN

A

32M

CB

140

11/

27/0

6

His

tone

s:C

onse

rved

and

C

harg

ed

H.s

.= L

ycop

ersi

con

escu

lent

um

9

33M

CB

140

11/

27/0

634

MC

B 1

40 1

1/27

/06

“Ext

rem

ely

cons

erve

d hi

ston

e H

4 N

term

inus

is

disp

ensa

ble

for g

row

th b

ut e

ssen

tial f

or re

pres

sing

th

e si

lent

mat

ing

loci

in y

east

” (M

. Gru

nste

in)

Kay

ne e

t al.

(198

8) C

ell 5

5: 2

7-39

.

Fig.

3 k

ayne

35M

CB

140

11/

27/0

6K

ayne

et a

l. (1

988)

Cel

l 55:

27-

39.

Fig.

6 a

nd 7

of K

ayne

.

36M

CB

140

11/

27/0

6K

ayne

et a

l. (1

988)

Cel

l 55:

27-

39.

10

37M

CB

140

11/

27/0

6

Ace

tyla

tion

of ly

sine

in h

isto

ne ta

il ne

utra

lizes

its

char

ge (1

964)

38M

CB

140

11/

27/0

6

“Gen

etic

evi

denc

e fo

r an

inte

ract

ion

betw

een

SIR

3 an

d hi

ston

e H

4 in

the

repr

essi

on o

f the

sile

nt

mat

ing

loci

in S

acch

arom

yces

cer

evis

iae”

John

son

et a

l. (1

990)

PN

AS

87:

6286-

6290

.

Rev

erse

gen

etic

s: in

trodu

ce p

oint

mut

atio

ns in

H4

tail!

!

39M

CB

140

11/

27/0

6Jo

hnso

n et

al.

(199

0) P

NA

S 8

7:62

86-62

90.

Tabl

e 2

40M

CB

140

11/

27/0

6

11

41M

CB

140

11/

27/0

6

And

5 y

ears

late

r …

Sir3

p an

d S

ir4p

bind

H3

and

H4

tails

Hec

ht e

t al.

(199

5) C

ell 8

0: 5

83.

42M

CB

140

11/

27/0

6

Hou

ston

, we

have

a …

Eve

ry n

ucle

osom

e in

the

cell

has

an H

3 an

d H

4 ta

il (tw

o of

eac

h, a

ctua

lly).

Why

do

the

SIR

s bi

nd o

nly

whe

re th

ey b

ind?

43M

CB

140

11/

27/0

6

The

sile

ncer

s

“Haw

thor

ne d

elet

ion”

(196

3) a

nd o

nwar

ds:

two

sile

ncer

s fla

nk th

e m

atin

g ty

pe lo

ci:

44M

CB

140

11/

27/0

6

The

key

ques

tion

How

do

the

SIR

s sp

read

from

the

sile

ncer

and

ove

r the

m

atin

g ty

pe lo

ci

gene

s?

= ho

w d

o th

e S

IRs

actu

ally

sile

nce

txn?

12

45M

CB

140

11/

27/0

6

Roy

Fry

e (P

itt)

“Cha

ract

eriz

atio

n of

five

hum

an c

DN

As

with

hom

olog

y to

th

e ye

ast S

IR2

gene

: Sir2

-like

pro

tein

s (s

irtui

ns)

met

abol

ize

NA

D a

nd m

ay h

ave

prot

ein

AD

P-

ribos

yltra

nsfe

rase

act

ivity

” BB

RC

260

: 273

(199

9).

1. B

acte

ria h

ave

prot

eins

hom

olog

ous

to S

ir2.

2. S

o do

hum

ans

(>5)

.

3. T

he b

acte

rial p

rote

ins

are

enzy

mes

, and

use

NA

D to

A

DP

-rib

osyl

ate

othe

r pro

tein

s.

46M

CB

140

11/

27/0

6

J. D

enu:

Sir2

p is

a N

AD

-dep

ende

nthi

ston

e de

acet

ylas

e (H

DA

C)

Tann

er e

t al.,

PN

AS

97:

141

78 (2

000)

Sir2

p

47M

CB

140

11/

27/0

6R

usch

e L,

Kirc

hmai

er A

, Rin

e J

(200

2) M

ol. B

iol.

Cel

l 13:

220

7.48

MC

B 1

40 1

1/27

/06

acet

ylat

ion

His

tone

tail

acet

ylat

ion

prom

otes

ch

rom

atin

unf

oldi

ng (s

omeh

ow)

13

49M

CB

140

11/

27/0

6

Nex

t tim

e:

the

gene

tics

of h

eter

ochr

omat

in

in m

etaz

oa