Title: Transcription regulation of complex loci
1Transcription regulation of complex loci
- David Arnosti
- Dept. Biochemistry Molecular Biology
- Michigan State University
2Pioneers of the 19th century
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5Pioneers of the 21st century
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8- A biologists wish list
- Parts list operational system description
9- A biologists wish list
- Parts list operational system description
- Predict function of cis regulatory sequences
10- A biologists wish list
- Parts list operational system description
- Predict function of cis regulatory sequences
- Build picture of transcriptional regulatory
networks
11- A biologists wish list
- Parts list operational system description
- Predict function of cis regulatory sequences
- Build picture of transcriptional regulatory
networks - Understand dynamic properties of system effect
of - changes/mutations on output
12Tuesday Transcriptional regulation of complex
loci Wednesday Transcriptional logic machines
for developmental patterning
13Study the Form or the shadows on the cave wall?
14Compact regulatory regions in yeast
db.yeastgenome.org/cgi-bin/gbrowse/yeast/
15Dispersed regulatory regions in animals
Merli et al. (1996) Genes Dev. 101260
16Three lenses
Biochemistry
general, quantitative
17A word about genetic information
18Protein Coding
M P Q Q
5
3
AUGCCCCAGCAG
- Information content dictated by
- 5-3 orientation
- Position with respect to an AUG
- Phase (reading frame)
- Location distal to a transcriptional start site
19Regulatory
Regulatory regions are bound by transcription
factors
Complexity stems from information being
read out as nucleoprotein complexes of various
structure and function.
20Regulatory
- Move gene to particular nuclear compartment
21Regulatory
- Move gene to particular nuclear compartment
- Modify the chromatin structure of the gene
22Regulatory
- Move gene to particular nuclear compartment
- Modify the chromatin structure of the gene
23Regulatory
- Move gene to particular nuclear compartment
- Modify the chromatin structure of the gene
- Directly contact components of the basal
machinery
24Regulatory
- Move gene to particular nuclear compartment
- Modify the chromatin structure of the gene
- Directly contact components of the basal
machinery - 4. Influence the binding of cofactors
25Outline 1. Definitions 2. eve - one
gene/multiple enhancers 3. Globin locus - one
enhancer/multiple genes 4. HOX genes - boundaries
memory modules 5. Enhancer-promoter trafficking
and boundary elements
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27Promoter
Enhancer
Silencer
Boundary Element
Cis regulatory element
28Outline 1. Definitions 2. eve - one
gene/multiple enhancers 3. Globin locus - one
enhancer/multiple genes 4. HOX genes - boundaries
memory modules 5. Enhancer-promoter trafficking
and boundary elements
29Body segmentation is presaged by segmental gene
expression.
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317
6
3
4
5
2
1
figure from Steve Small, NYU
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34eve expression pattern evolves from broad pattern
to stripes
35Generalized activation
36Positional specification is dictated by
transcriptional repressors
Refinement through repression
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38Short-range repressors Long-range
repressors
39Short-range repressors Long-range
repressors
giant knirps Kruppel snail
lt100 bp
40Short-range repressors Long-range
repressors
giant knirps Kruppel snail
hairy Dorsal repression complexes
lt100 bp
gt1,000 bp
41hair
y
knirp
s
Short-range Long-range
42CtB
P
groucho
hair
y
knirp
s
Short-range Long-range
43 Histone
Deacetylases
CtB
P
groucho
hair
y
knirp
s
Short-range Long-range
44 Histone
Deacetylases
CtB
P
groucho
hair
y
knirp
s
Short-range Long-range
45 Histone
Deacetylases
CtB
P
groucho
hair
y
knirp
s
Short-range Long-range
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47Two Models for Enhancer Design
Enhanceosome - smart but high-strung IFN-ß
enhancer
Billboard - dumb but flexible developmentally
regulated enhancers
48- Enhanceosome
- - extensive cooperative interactions
- constrained placement of binding sites
- monolithic activation (repression) complex
Kulkarni and Arnosti, Development 130, 6569.
49- Billboard (information display)
- - cis element provides loose grouping
- multiple subelements - apparent redundancy
- - overall output - integration over time of
enhancer sampling
Kulkarni and Arnosti, Development 130, 6569.
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51D. Tautz, U. Cologne
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53Enhanceosome
Senger et al., (2004) Mol. Cell 13, 19
54Billboard
Clustered, but not necessarily conserved
Emberly et al., (2003) BMC Bioinformatics 457
55Berman et al. (2002) PNAS 99, 757-762
56Berman et al. (2002) PNAS 99, 757-762
57System modeling
58Quantitative Measurements
Janssens et al. (2005) Dev Genes Evol 215374-81
59Reinitz gene circuit dynamic model for
calculating the changing concentrations of
transcriptional regulatory proteins in the
embryo - involving 348 ordinary differential
equations for the matrix of nuclei in the field
of cell expressing eve.
Jaeger et al. (2004) Nature 430, 368.
60eve lessons
Regulatory regions can be divided into modular
units. Modularity of enhancers depends on local
activity of repressors. eve (and other) enhancer
sequences are subject to evolutionary
drift. Premier system for quantitative analysis.
61Outline 1. Definitions 2. eve - one
gene/multiple enhancers 3. Globin locus - one
enhancer/multiple genes 4. HOX genes - boundaries
memory modules 5. Enhancer-promoter trafficking
and boundary elements
62Enhancer 2
Enhancer 1
Locus control region (LCR)
63Beta globin genes in man mouse
embryonic fetal adult
Fu et al. (2002) Exp Cell Res 278, 1-11
64Binding of tissue-specific and general transcripti
on factors create altered chromatin structure
(DNAseI hypersensitivity)
Dekker (2003) TIBS 28, 277.
65Spreading model
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69 Dekker (2003) TIBS 28, 277.
70 Dekker (2003) TIBS 28, 277.
71Carter (2002) Nat Gen 32623.
72Stochastic regulatory switching
Wijgerde et al. (1995) Nature 377, 209.
73Beta globin lessons
Regulatory regions can be very large Roles in
chromatin modification and direct gene
activation Transcription of noncoding regions -
cause or effect? Sequential activation of gene
cluster
74Outline 1. Definitions 2. eve - one
gene/multiple enhancers 3. Globin locus - one
enhancer/multiple genes 4. HOX genes - boundaries
memory modules 5. Enhancer-promoter trafficking
and boundary elements
75Homeosis - William Bateson
76Genetic and molecular identification of HOX genes
77Evolutionarily conserved (duplications,
losses) Role in specification of segmented
tissues Anterior-posterior expression colinear
with gene order 5-3 Link to morphological
diversification
78Multiple, complex regulatory regions controlling
Hox genes. Drosophila
79Expression of homeotic genes of the bithorax
complex
80Functional elements in transcriptional control
region
Abd-B
iab-5 iab-6 iab-7 iab-8
81Functional elements in transcriptional control
region
Abd-B
iab-5 iab-6 iab-7 iab-8
82Functional elements in transcriptional control
region
Boundary Elements
Mcp Fab-6 Fab-7 Fab-8
Abd-B
iab-5 iab-6 iab-7 iab-8
83Functional elements in transcriptional control
region
Boundary Elements
Mcp Fab-6 Fab-7 Fab-8
Abd-B
iab-5 iab-6 iab-7 iab-8
84Functional elements in transcriptional control
region
Promoter-targeting sequences
Mcp Fab-6? Fab-7 Fab-8
Abd-B
iab-5 iab-6 iab-7 iab-8
85Memory Modules
Transient activation or repression, followed
by action of Polycomb or Trithorax group proteins
Arnosti (2002) Insect Biochem Mol Bio 32 1257
86Blue lines indicate predicted genes
This cluster of genes is situated in an island
lacking junk DNA.
87Expression of HOX genes in crustaceans
Levine, Carroll
88HOX lessons Linear order of genes and regulatory
sequences important Enhancers, boundary
elements, promoter targeting sequences, and
memory modules combined to achieve fine
regulation Colinearity between physical layout
and anterior-posterior expression is still not
understood Variation in HOX expression linked to
evolutionary changes
89Outline 1. Definitions 2. eve - one
gene/multiple enhancers 3. Globin locus - one
enhancer/multiple genes 4. HOX genes - boundaries
memory modules 5. Enhancer-promoter trafficking
and boundary elements
90Traffic problems
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92Enhancer-promoter specificity
Merli et al. (1996) Genes Dev. 101260
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95rhomboid NEE
TATA
DPE
(nonselective)
ftz AE1, abdB IAB5
TATA
DPE
(selective)
Ohsutki and Levine
96Promoter-Enhancer specificity - is fidelity the
rule?
97Enhancer-promoter specificity lessons Cis-regulat
ory elements have a limited range, generally
preventing widespread cross-regulation Boundary
elements may contribute to enhancer-promoter
specificity- few documented cases Examples of
enhancer-promoter specificity exist Perhaps
cross-regulation is tolerated in many cases
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