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[Bejerano Fall09/10]
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Lecture 12
Cis-Regulation
Cellular Signaling
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[Bejerano Fall09/10]
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Big Picture Context
We are surveying the functional classes of elements
encoded by the human genome.
We have previously discussed:
• Protein coding genes
• Repetitive sequences
• Non coding RNAs
Today we’ll cover the last (known :) large class of functional
elements.
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Unicellular vs. Multicellular
unicellular
multicellular
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Vertebrate Transcription Regulation
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Pol II Transcription
Key components:
• Proteins
• DNA sequence
• DNA epigenetics
Protein components:
• General Transcription factors
• Activators
• Co-activators
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Activators & Co-Activators
Protein - Protein
Protein - DNA
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The Core Promoter
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Chromatin Remodeling
“off”
“on”
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CpG islands
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Nucleosome tail
modifications
Lysine acetylations. •
Histone Acetyl-Transferases (HAT) & Histone Deacetylases (HDAC). •
Lysine and Argenine Metylations. •
Modified by histone- –
metyl-transferase.
Phosphorilation. •
Ubiquitination. •
H2A ubiquitination affects –
10-15% of this histone in
most eukaryotic cells
ADP-ribosylation. •
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Transcription Factor (TF) Binding Sites
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TFs in the Human Genome
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Combinatorial Regulatory Code
2,000 different proteins can bind specific DNA sequences.
Proteins
DNA
Protein binding site
Gene
DNA
A regulatory region encodes 3-10 such protein binding sites.
When all are bound by proteins the regulatory region turns “on”,
and the nearby gene is activated to produce protein.
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Enhancers
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Enhancers: action over very large distances
Basal factors
promoter
RNAP II
Enhancer with bound protein
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Transient Transgenic Enhancer Assay
in situ
Conserved
Element
transgenic
Minimal Promoter
Reporter Gene
Construct is injected into 1 cell embryos
Taken out at embryonic day 10.5-14.5
Assayed for reporter gene activity
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Vertebrate Enhancer Combinatorics
limb
neural
tube
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brain
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Sall1
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Vertebrate Enhancer Combinatorics
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What are Enhancers?
What do enhancers encode?
Surely a cluster of TF binding sites.
[but TFBS prediction is hard, fraught with false positives]
What else? DNA Structure related properties?
So how do we recognize enhancers?
Sequence conservation across multiple species
[weak but generic]
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Gene Expression Domains: Independent
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Vertebrate Gene Regulation
distal: in 106 letters
gene (how to)
control region
(when & where)
DNA
DNA binding
proteins
proximal: in 103 letters
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Most Non-Coding Elements are likely cis-regulatory
“IRX1 is a member of the Iroquois homeobox gene family.
Members of this family appear to play multiple roles
during pattern formation of vertebrate embryos.”
gene deserts
regulatory jungles
9Mb
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Many non-coding elements tested are cis-regulatory
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Gene Expression Domains: Dependent
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Distal Transcription Regulatory Elements
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Repressors / Silencers
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What are Enhancers?
What do enhancers encode?
Surely a cluster of TF binding sites.
[but TFBS prediction is hard, fraught with false positives]
What else? DNA Structure related properties?
So how do we recognize enhancers?
Sequence conservation across multiple species
[weak but generic]
Verifying repressors is trickier [loss vs. gain of function].
How do you predict an enhancer from a repressor? Duh...
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Insulators
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Disease Implications: Genes
gene
genome
protein
Limb Malformation
Over 300 genes already
implicated in limb malformations.
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Disease Implications: Cis-Reg
gene
genome
NO protein
made
Limb Malformation
HANDFUL of cases known (limb, deafness, etc).
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Transcription Regulation & Human Disease
[Wang et al, 2000]
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Critical regulatory sequences
Lettice et al. HMG 2003
12: 1725-35
Single base changes
Knock out
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Other Positional Effects
[de Kok et al, 1996]
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Genomewide Association Studies point to non-coding DNA
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WGA Disease
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Rapid TFBS turnover
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Cis-Regulatory Components
Low level (“atoms”):
• Promoter motifs (TATA box, etc)
• Transcription factor binding sites (TFBS)
Mid Level:
• Promoter
• Enhancers
• Repressors/silencers
• Insulators/boundary elements
• Cis-regulatory modules (CRM)
• Locus control regions (LCR)
High Level:
• Epigenetic domains / signatures
• Gene expression domains
• Gene regulatory networks (GRN)
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Cis-Regulatory Evolution: E.g.,
obile Elements
Gene
Gene
Gene
Gene
What settings
make these
“co-option” events
happen?
[Yass is a small town in
New South Wales, Australia.]
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Britten & Davidson Hypothesis: Repeat to Rewire!
[Davidson & Erwin, 2006]
[Britten & Davidson, 1971]
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Modular: Most Likely to Evolve?
Chimp
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Human
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Human Accelerated Regions
• Human-specific substitutions in conserved
sequences
Human
[Pollard, K. et al., Nature, 2006]
Chimp
[Beniaminov, A. et al., RNA, 2008]
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[Prabhakar, S. et al., Science, 2008]
Signal Transduction
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Cell Communication
Lodish, 20-1
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Wnt and Hedgehog signaling
Jacob & Lum Science 2007
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Signaling Pathways Important in
Developmental Biology
•
•
•
•
•
•
•
Wnt/Frizzled through b-catenin
Hedgehog
TGF-b family through Smads
Growth factors via JAK-STATs
Notch
Integrin
TNF
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