molecular lecture 8.07

7/29/2019 Molecular Lecture 8.07

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Exam 1 will be held on Monday,

February 19 from 6:00-8:30 pm

in room 106 Biology or.

You may also take it on Tuesday,

February 20 from 6:00-8:30 pm inroom 21 Biology

Material covered - Chaps. 6 and 7+ problems and other lecture

information

There will not be a meeting of the

discussion group next week


2/16

It now appears that for at least some systems that transcription

factors (TF) find sites close to sites where remodeling can

expose a promoter.

In yeast, Pho4 protein (a TF) binding can lead to the eviction of

up to 4 nucleosomes and thus lead to activation of the PHO5gene. It binds at a site in the linker, and then recruits members

of the SWI/SNF family to initiate remodeling and lead to a

nucleosome-free region

There may also be remodeling complexes that in a more non-

targeted way, increase the abil ity of NRCs to bind to these

regions

The SWI/SNF subfamily of proteins in remodeling,

examples of ATP-dependent proteins that serve as one of

the major NRCs


3/16

Remember how we mentioned

that the posit ioning of thehistone N-terminal tails was

critical for several aspects of

regulation; now we will deal with

that topic


4/16

Modification of N-terminal ends of histones:

Proteins with Bromodomains and Chromodomains-1

Histone N-terminal tail lysine residues are typically modified with

either acetyl groups or with methyl groups; serines are often

phosphorylated (Fig. 7.38)

Bromodomain-containing proteins interact with acetylated histone N-

terminal tails (these regions are typically associated with active

transcription; the higher the level of acetylation, the lower the amountof 30 nm fiber); presumably they reduce overall positive charge of

histones. Bromodomains contain a ~70 aa conserved region that

mediates interactions with proteins necessary for transcriptional

activation. Typically bromodomains recognize acetylated lysineresidues. They adopt an all helix protein fold, often as a bundle of4 helices


5/16

Modification of N-terminal ends of histones:

Proteins with Bromodomains and Chromodomains-2

Chromodomain-containing proteins interact with methylated histone

tails (that are associated with either transcriptionally active or inactive

chromatin depending on which amino acid is modified);chromodomains are highly conserved sequences that appear to not

only help regulate transcriptional activity, but also may be important

in chromatin organization

Phosphorylation of H3 is observed in highly condensed chromatin

Some proteins that contain either bromodomains or chromodomains

are not involved in histone modification, but in regulatingtranscription directly (e.g., TFIID - bromodomain directs transcription

machinery to sites of acetylation)


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Closed versus open chromatin based on recogniton by chromodomain

or bromodomain containing proteins (from L. A. Allison, 2007)

Recognizesthis lysine

in the tail

Demethylation (and acetylation)

recognizing the same lysine +

4 helices


7/16

Sites of histone

modification

K = lysine

S = serine

R = arginine

Fig. 7.38


8/16

How some acetylases and deacetylases act on other proteins

From Clark, 2005; Molecular Biology


9/16

Some enzymes responsible for histone modification

Most are bromodomains


10/16

Effects of histone modification on N-terminal tails

Fig. 7.39

The importance of N-terminaltails are for histone

Reduces accessibility (closed)Increases accessibility (open)


11/16

Remodeling complexes

andhistone-modifyingenzymes can and do

interact to alter

chromatin structure

These can occur in

either order (modification

first, then remodeling or

remodeling then modification)

Fig. 7.40

By adding a histone

methyl transferase, a

more compact and

inaccessible chromatinis formed


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How Histones are inherited

Old H3-H4 tetramers remain

randomly bound to one of

two daughters; H2A-H2B

dimers are released andenter pool for re-assembly

Fig. 7.41

Nucleosomes are either all old or all new histones

Old histones released into the

soluable pool appear to be

reincorporated into daughter

chromosomes, close to their

original position, this localized

inheritance helps insure

similar modifications (fig. 7.42)


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H3 - H4 tetramer distribution

results in daughter

chromosomes receiving

same kinds of modificationsas parental chromosomes in

about the same locations

following replication

Fig. 7.42

I it d 1 M lt


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Assembly of nucleosomes in vivo using chromosomeassembly factors: Histone chaperones; this is called the

DNA replication-coupled chromatin assembly pathway

Replication is essential

for CAF-1 directed assembly

PCNA clamp is

the indicator for

assembly after replication;released from DNA Pol

but then used to

direct CAF-1

Fig. 7.43

In vitro need >1 M salt

(sliding clamp)

NAP-1 brings in H2A-H2B dimers

CAF-1 is a heterotrimer


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Nucleoplasmin - acidic protein that was identified as one of the first

histone chaperones; it has been shown to

decondense chromatin inXenopus

In yeast, CAF-1 does not seem to be essential for cell prol iferation.

In humans however, cells lacking CAF-1 accumulate in early and mid S

phase and replicate slowly, furthermore CAF-1-depleted cell extracts

lack DNA-coupled chromatin assembly


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End of Material for Exam 1

molecular lecture 8.07

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