Download No Slide Title

All Wrapped Up
Chromatin-Level Gene Regulation
GENETIC
Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman.
EPIGENETIC
Genes can be regulated by chromatin
organization
Chromatin Packaging
• Chromatin is the combination of DNA and
proteins found in eukaryotic chromosomes.
• Proteins in chromatin are:
– histones: small, positively charged
– non-histone proteins: transcription factors,
enzymes
• Packaging of DNA with proteins leads to
compacted structure, which facilitates fitting
the DNA into the nucleus
Nucleosomes: the basic chromatin unit
• Nucleosomes are formed by winding about
200 base pairs of the DNA duplex around a
core of histone proteins.
• The histone core is made of:
–
–
–
–
2 molecules histone H2A
2 molecules histone H2B
2 molecules histone H3
2 molecules histone H4
• Another histone, H1, binds outside the core.
http://www.cbs.dtu.dk/staff/dave/roanoke/genetics980218.html
Nucleosome organization
1.
2.
3.
4.
5.
Nucleosome (11 nm)
Solenoid (30 nm)
Loops (300 nm)
Coiled loops (700 nm)
Metaphase chromosome (1400 nm)
1
3
4
2
5
Pierce, B. 2005. Genetics, a conceptual approach. 2nd Ed. WH Freeman.
Higher orders of chromatin packing produce
fibers with wider diameters
The DNA component of chromatin
can be covalently modified
• DNA methylation of cytosines
CH3
CH3
CH3
CH3
CH3
• Only certain cytosines can be methylated.
• Sequence context matters.
– In animals, CG
– In plants, CG and CNG
Core histones can be covalently modified
• Example: Histone acetylation
H O
––N–C–C––
(CH2)4
NH3
+
Lysine
H O
––N–C–C––
N-ARTKQTARKSTGGKAPRKQLATKAARKSAP
(CH2)4
H-N-CH2-CH3
9
14
18
Acetylation
23
H3
Acetylated Lysine
Acetylation
Pierce, B. 2005. Genetics, a conceptual approach. 2nd Ed. WH Freeman.
Acetylation causes histones
to lose some of their positive
charge. This causes them to
bind less tightly to the
negatively charged DNA
backbone.
Consequences of chromatin modificaton
• Histone modification can reduce the positive charge on
the proteins, thus altering their attraction for negatively
charged DNA and loosening chromatin packing.
Acetylation
Pierce, B. 2005. Genetics, a conceptual approach. 2nd Ed. WH Freeman.
• Modification of both histones and cytosines can provide
recognition sites for binding of other regulatory proteins,
which in turn can alter chromatin packing.
Relationship of chromatin organization
and gene expression
Transcriptional
Activity
Chromatin
Configuration
Histone
Modification
DNA
Methylation
On
Active
Expressed
Open
Loosely packed
Accessible to
transcription
machinery
Acetylated
Low
Off
Inactive
Silent
Closed
Tightly packed
Not accessible
to transcription
machinery
Deacetylated
High
Chromatin-level regulation of gene expression
is called “epigenetic”
• Altered chromatin structure
• Altered expression
• Potentially reversible
• Independent of DNA sequence changes
• Frequently developmentally regulated
• Mitotically and / or meiotically heritable
Example:
X-inactivation in mammals
• In mammals, there are many genes on the X
chromosome.
• Females have two X chromosomes and males
have only one.
• To compensate for possible differences in
gene expression, due to the differences in Xchromosome number in females and males,
one of the X’s in females is transcriptionally
silenced by tightly packing the chromatin of
one X.
Example:
X-inactivation in mammals
• In cats, the gene for fur
color is on the X.
• There are two alleles, for
orange and black.
XX
XX XX
XX XX XX
XX XX XX
•X X•
X• •X •X
X• X• •X
X-inactivation fits the criteria for
epigenetic regulation
• It is an example of altered gene expression
(silencing) due to altered (more tightly packed)
chromatin structure, not change in DNA sequence.
• It is developmentally imposed early in embryo
formation.
• The new chromatin configuration is mitotically
heritable, in that daughter cells maintain the
chromatin state of the cell from which they came.
• It is reversible; during meiosis, the inactive X is reactivated, so that gametes inherit fully active X
chromosomes.
Non-reversible epigenetic change in gene
expression: paramutation
• In corn, synthesis of purple anthocyanin pigments
requires a gene called booster (b), which codes for a
transcription factor that activates the enzyme-coding
genes in the pigment pathway.
• A strong allele, called B-I, is
expressed at high levels and
B-I
activates the pathway very well to
produce deep purple coloration.
• Another allele, called B’, is
B’
expressed at lower levels and leads
to weaker coloration.
Paramutation exhibits non-Mendelian
inheritance
X
B’/B’
B-I/B-I
X
B’/B-I
B-I/B-I
Non-Mendelian
pattern of inheritance
all B’
Images courtesy of Vicki Chandler, Univ of Arizona
Molecular explanation for paramutation
• Allelic interaction.
• One allele (B’) transfers its low expression state
to another allele (B-I), converting B-I to B’.
• The conversion is chromatin-based.
– B’ has a more closed chromatin configuration than B-I.
– After association with B’, B-I assumes a closed
chromatin configuration and is expressed at low levels
like B’.
• The B-I-to-B’ conversion is permanent. B’ never
reverts to B-I.
Chemically-induced transgenerational
alterations in sexual function
• Many chemicals are related to estrogens and
can disrupt endocrine function.
• Developing fetuses are especially sensitive to
these so-called endocrine disrupting
chemicals (EDCs).
• Treatment of pregnant mothers with EDCs
can lead to changes in sexual development in
their male offspring.
• The males can then transmit the changes to
their offspring.
Chemically-induced defect can be passed
to offspring
F1
transient exposure
to EDC
pregnant mouse
X
males; low
sperm count
normal female
F2
X
F4
males; low
sperm count
males; low
sperm count
F3
X
normal female
Reference:
Science (2005) 308:1466
males; low
sperm count
normal female
Chemically-induced change is epigenetic
• Analysis of genes in sperm of the defective
male mice revealed changes in DNA
methylation of several genes.
• This altered pattern of DNA methylation was
seen in mice from multiple generations (F1,
F2, F3).
• Interpretation is that EDC induced a DNA
methylation change in the germ line of male
mice, and this change can be transmitted to
offspring.
What we don’t know
about chromatin-level regulation
• How many genes are targets for this level of
regulation?
• How are those genes targeted?
• How are the chromatin modifications
accomplished?
• What determines whether chromatin changes
will be transient or permanent?
Summary
• DNA is packed into the nucleus by
association with histone and non-histone
proteins to form chromatin.
• Both the DNA and histone components of
chromatin can be modified.
• Modifications change the configuration of
chromatin and this in turn alters accessibility
of genes for transcription.
• Some chromatin modifications can have
transgenerational effects on gene expression.