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Summary Chapter 16 genetics
- Vak
- Genetics
- Instelling
- Vrije Universiteit Amsterdam (VU)
Chapter 16 genetics vu biomedical sciences
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CHAPTER 16 Open chromatin- active gene16.1 OVERVIEW OF EPIGENETICS Closed chromatin – gene not active
Epigenetics is the study of mechanisms that lead to changes in gene expression that can be
passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA.
Epigenetic inheritance involves epigenetic changes that are passed from parent to
offspring. Examples include X-chromosome inactivation and genomic imprinting.
The molecular mechanisms that promote epigenetics gene regulation: DNA methylation,
chromatin remodeling, covalent histone modification, histone variants and feedback loops.
- In some cases, transcription factors recruit proteins which leads to epigenetic changes.
- In other cases, ncRNAs act as bridges between specific sites in the DNA and proteins,
altering chromatin/DNA structure.
Cis-epigenetic changes:
Maintained at a specific site.
It does not affect the expression of the same gene located elsewhere.
For example, a cis-epigenetic change may affect only one copy of gene but not the other copy
Trans-epigenetic changes:
Maintained by diffusible factors (transcription factors, proteins, ncRNAs).
Example: feedback loop.
A trans-epigenetic change affects both copies of a gene.
An epigenetic change is established by activating a gene that encodes a transcription factor.
They may have phenotypic effects.
Cis- and trans-epigenetic mechanisms can be distinguished from each other by cell fusion
experiments.
If one cell has gene B modified to be transcriptionally active and the same gene in another cell is
inactive. Cells fuse:
a) cis mechanism: the epigenetic modification will be maintained only for the copy of gene B
that was initially modified. The other copy will remain inactive.
b) Trans mechanism both copies will be expressed because the cell contains enough of the
transcription factor protein to stimulate both copies.
1. Epigenetic gene regulation may occur as a programmed developmental change
- Genomic imprinting
- X chromosome inactivation: during embryogenesis. One of the X chromosomes becomes
inactive and form a Barr body
- Cell differentiation
2. Epigenetic gene regulation that may be caused by environmental agents
- Temperature
- Diet
- Toxins (e.g. tobacco smoke)
16.2 HETEROCHROMATIN: FUNCTION, STRUCTURE, FORMATION AND MAINTENANCE
Chromatin composed of DNA, protein, non-coding RNAs.
Euchromatin – regions that are not stained during interphase
- Transcriptionally active (not always active, though)/competent
- Occupies a central position in the nucleus
Heterochromatin – regions that are stained throughout the cell cycle
- Greater level of compaction
- Inhibitory effect on gene transcription
- Localized along the periphery of the nucleus; attached to nuclear lamina
Roles of Heterochromatin
1. Gene silencing –the compact structure of heterochromatin silences the expression
of genes by limiting the access to DNA of DNA-binding proteins. Heterochromatin
inhibits transcription by recruiting general transcription factors.
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CAROLINA SANZ HERNÁNDEZ
, 2. Prevention of transposable element movement – The insertion of TEs inactivates
a gene’s function. The sites where TEs are located are converted to
heterochromatin, which silences genes needed for transcription.
3. Prevention of viral proliferation – genes needed to produce more viruses are
silenced.
Constitutive versus Facultative Heterochromatin
Allows silencing of genes in a cell-specific manner (it depends on the cell type that they are, they
silence some genes or not).
Constitutive Heterochromatin: heterochromatic at the same location in all cell types.
- Chromosomal locations: close to a centromere or telomere.
- Repeat sequences: the DNA within heterochromatin sequences is composed of short
tandemly repeated sequences.
- DNA methylation: highly methylated on cytosines in vertebrates and plants.
- Histone modifications: H3K9me3 common in constitutive heterochromatin in yeast and
animals; H3K9me2 in plants.
Posttranslational modifications (PTMs): the amino-terminal tails of histone proteins are
subject to this.
Specific proteins bind to PTMs in nucleosomes via protein domains called
reader domains; found in proteins that modify chromatin. These domains are
called:
Writer domains – catalyze addition of PTMs
Eraser domains – catalyze removal PTMs
Facultative heterochromatin: locations vary among different cell types.
Formation is reversible thanks to erasers.
The state depends on the stages of development or cell type.
The formation of it plays a role in genomic imprinting, gene silencing and X chromosome
inactivation.
- Chromosomal locations: discrete sites between the centromeres and telomeres.
- Repeat sequences: LINE-type repeats ~6500 bp.
- DNA methylation: more discrete than constitutive heterochromatin. methylation at CpG
islands in gene regulatory regions; silences genes.
- Histone modifications: H3K9me3 also found in facultative heterochromatin; animals also
often have H3K27me.
Pattern of heterochromatin before and after cell division
During interphase the chromosome contains facultative and
constitute heterochromatin in the pericentric and telomeric regions. Most
of the chromosome is composed of euchromatin (genes are not silenced).
During M phase euchromatic regions condense.
Following M phase, during interphase of the daughter cells, the
chromosome follow the same pattern of heterochromatin from the
mother cell.
Molecular Events Leading to Heterochromatin with Higher Order Structure
Heterochromatin formation thought to involve:
- Histone PTMs
- Binding of proteins to nucleosomes
- Chromatin remodeling (nucleosomes displacement/sliding)
- DNA methylation
- Binding of non-coding RNAs
The consequences of these molecular events are:
- Silence gene expression Closer, more stable contacts of nucleosomes
- Formation of higher-order structures in which heterochromatin is: Loop domains
Binding of heterochromatin to nuclear lamina
o Closer, more stable contacts of nucleosomes : the H3K9me3 histone modification is
recognized by HP1, HP1 bridges nucleosomes and makes them more compact.
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CAROLINA SANZ HERNÁNDEZ
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