1

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 Promoter ground states

2
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 Eukaryotic chromatin: higher order structure

Compaction ratio

3.4 angstroms/bp (length) 1:1

1:6

1:40

Histone H1 –
important role in
packing nucleosomes

1:10,000
3
mitotic metaphase
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 Chromatin structure regulates gene expression by controlling access
of RNAP to promoters

Euchromatin – 10 nm fiber, beads-on-a-string, relatively accessible,

associated with gene expression

Heterochromatin – 30 nm fiber (or higher order structure), tightly packed

nucleosomes, relatively inaccessible, associated with gene repression.

euchromatin

heterochromatin

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 Eukaryotic chromatin: nucleosome structure

Histone core octamer – ~146 bp DNA

2 each of:
• H2A
• H2B
• H3
• H4

Histone H1
Important role in packing nucleosomes

5
221.S16 Hartwell et al. (2011) Figure 12-5
 Modification of histone tails results in altered chromatin

histone histone
acetyltransferase deacetylase
(HAT) (HDAC)

Acetylation of lysine residues neutralizes the positive charge on lysine residues,

weakening their association with negatively charged phosphates in the DNA
backbone and promotes interactions with other proteins.

These marks are also reversible – allowing for changes in gene expression. 6
221.S16
 Histone tails contain many amino acids that can be modified

7
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 Eukaryotic chromatin and the histone code: acetylation

enhancers and promoters

HAT Activating acetylation marks:

• H3K9ac
• H3K27ac

HDAC

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221.S16 Krebs et al (2011) Figure 4-41
 Eukaryotic chromatin and the histone code: methylation

Transcription units

Activating methylation marks:

Histone methyltransferase • H3K4me1
• H3K4me2
Histone demethylase
• H3K4me3

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Krebs et al (2011) Figure 4-41
221.S16
2012
 Promoter-proximal elements are necessary for efficient transcription

Human b-globin promoter

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 Nucleosome position influences gene expression by
exposing cis-acting regulatory sequences

Let’s imagine the CCAAT box and TATA box

DNA sequences are wrapped around a
histone octamer. For these consensus
sequences to be recognized and bound by
the proper proteins, they must first be
positioned to make them accessible.

This is achieved by chromatin remodeling

proteins (“SWI/SNF”), that reposition the
nucleosomes to expose regulatory
sequences.

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221.S16 B. Keith
 Eukaryotic RNA polymerase II: regulatory elements

Promoter-distal
DNA elements Enhancer = Upstream Activator Sequence (yeast)

Enhancer

(activator)

DNA loop Promoter-proximal Mediator complexes connect

200 bp - 200 kb DNA elements enhancer-binding proteins to Pol II
GTFs
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FEBS Letters 579:909-915 (2005)
221.S16
 Mediator protein complexes

Mediator complexes are large,

containing at least 30 proteins, but
does NOT bind DNA. Rather, they
form a bridge between Pol II and
enhancer binding proteins, which
are often at a considerable
distance from the promoter. MED
complexes serves as co-
activators for Pol II transcription.

Subtly different versions, differing

in one (or a few subunits) have
been identified, and may have
different functions.

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221.S16 B. Keith
 Eukaryotic promoters: cis-acting elements

cis-acting element Location trans-acting factors

• includes TATA-box and

Initiator sequence (Inr)
Promoter RNA polymerase
• Orientation dependent
• Position dependent
• Usually within 200 bp from General
start-site Transcription
Promoter-proximal elements
• Orientation dependent Factors
• Position dependent (TFII factors)
• Usually beyond 200 bp
Promoter-distal elements from start-site Many enhancer-
Enhancers • Orientation independent binding proteins
Silencers • Position independent known
• DNA sequence-specific

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 The Encyclopedia of DNA Elements (ENCODE)

Public research project launched by the US National Human Genome Research Institute (NHGRI) in
September 2003. Intended as a follow-up to the Human Genome Project (Genomic Research), the
ENCODE project aims to identify all functional elements in the human genome. The project involves a
worldwide consortium of research groups, and data generated from this project can be accessed through
public databases.
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221.S16 PNAS (2014) 111: 6131–6138
 The Encyclopedia of DNA Elements (ENCODE)

Transcription factor binding sites

Genome size ~3.1 x 109 bp

Gene number (protein-coding) 20,687
Transcription factor proteins tested 119
Cell types tested 72
Transcription factor binding sites discovered 636,000 (8.1% of genome)
Transcription factor proteins known ~1,800
Transcription factor binding sites (total) TBD

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221.S16 http://www.genome.gov/ENCODE/
 Gene co-regulation with trans-acting factors
The galactose catabolism GAL4 homodimer protein
pathway in yeast binds to UAS elements

UAS: Upstream Activating Sequence

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