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Code biology: Does it apply to
histones?
Stefan Kühn
University of Stellenbosch
Dept. Biochemistry
What is a code?
A sign? A meaning? An adaptor?
Organic codes
Copying vs. coding
Natural selection vs. Natural conventions
The Histone code?
What is a code?
A code establishes a conventional
relationship between two
independent worlds
Two independent worlds:
A set of signs
A set of meanings
A code consists of:
A convention (a set of arbitrary rules)
that relates the signs to the meanings
Arbitrariness does not mean randomness
A third entity, the code-user or adaptor
that implements the code
This is not necessarily a mind
A code is a three-part system
MeaningSign
Adaptor
Code
The highway
code
World 1 (signs) World 2 (meanings)
establishes a relation between
Traffic signs Driving behaviours
STOP!
The genetic
code
is an
organic code
U
A
C
A
U
G
Organic
sign
Organic
meaning
(methionine)
Adaptor
Transfer-RNA
the adaptor of the
genetic code
Adaptors are the
“fingerprints”
of organic codes
Phenylalanine
(amino acid)
anticodon
two different,
physically separate
recognition sites
no necessary
connection between
the two sites
Phenylalanine
(amino acid)
anticodon
Phenylalanine
(amino acid)
that forms a
natural convention
What is connected
to what is an
arbitrary choice,
anticodon
Sign
(first messenger)
Meaning
(second messenger)
Adaptor
Copying
Coding
Two fundamental processes underlie
the evolution of life
and replication)
Catalysed assembly (replication and transcription)
Codified assembly (translation)
Copying creates organic information
DNA  mRNA
Information can evolve
(without changing meaning)
Mater  Madre, Mère, Mutter, Mother, Mamma
DNA  DNA
Coding creates organic meaning
UGG  tryptophan
Meaning can evolve (without changing information)
Ape
in English: “a hairy, anthropoid mammal”
in Italian: “a flying, stinging insect”
What’s the point?
A new code establishes
relationships that never before
existed in the world
Evolution by natural conventions vs.
natural selection
Absolute vs. relative novelties
Codes provide explanations for the major
evolutionary transitions and increases
in biocomplexity
The Genetic Code
Cultural Codes
3.8 billion
years
Nothing?
No more codes?
Yes, lots of them!
Code
Biology
Is the “Histone Code” an organic code?
Histones
Post-translational modification
Histones can be modified on their N-termini:
• Acetylation
• Methylation
• Ubiquitylation
H3 H4
K9
K12 ac
met
For a post-translational modification to act
as an organic sign
there must be an adaptor that translates it
into a unique effect (its organic meaning)
Modification as an organic sign
A structural motif (domain) on a
chromatin-associated protein acts as
an adaptor
• Bromodomain
• Chromodomain
• Tudor domain
H4H3
K9met
Effect as organic meaning
Modification (sign) Domain (adaptor) Effect (meaning)
H3K4met1/2 Tudor histone de-
acetylation
H3K4met2/3 PHD finger transcription
initiation
H3K9ac bromo transcription
initiation
H3K14ac bromo transcription
repression
H2BK120ac bromo ubiquitination of
H2BK120
H2BK120q Cps35 H3K4 methylation
Does it form a code?
Effect
Modifica
tion
Domain
Code
Yes:
• Post-translational modifications satisfy
criteria for sign
• Structural domains are suitable adaptors
• Effects on
histones, chromatin, chromosomes and
transcription qualify as meanings
Does it form a code?
Importance
Re-interpretation of existing biochemical knowledge in
terms of organic codes
Search for new codes
Understand evolution by natural conventions
Future work
Investigate degeneracy of the histone code
Function of the histone code
Investigate the proposed ubiquitin code
Thanks
Prof
Marcello Barbieri
Joachim De Beule
NRF
Office
1. GENETIC CODE (1952–1966) Dounce, Gamow, Niremberg,
Matthaei, Ochoa, Khorana
2. METABOLIC CODE (1975) Tomkins
3. SEQUENCE CODES (1988–1999) Trifonov
4. ADHESION CODE (1996) Redies and Takeichi
5. SPLICING CODES (1998, 2003) Barbieri
6. SIGNAL TRANDUCTION CODES (1998, 2003) Barbieri
7. SUGAR CODE (2000) Gabius
8. HISTONE CODE (2000) Allis, Turner
9. CYTOSKELETON CODES (2003) Barbieri
10. COMPARTMENT CODES (2003) Barbieri
11. APOPTOSIS CODES (2003) Barbieri
12. TUBULIN CODE (2007) Verhey and Gertig
13. NUCLEAR SIGNALLING CODE (2008) Maraldi
14. UBIQUITIN CODE (2012) Komander and Rape
Organic Codes

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Editor's Notes

  1. H3k14/h3k9 acetylation switchH2bk120ac hot-seath2bk119