MARCO - histone modification Flashcards
Histone methylation
- Addition of methyl groups (CH3) to lysine residues of histone tails
- Deposited by histone methylases & removed by histone demethylases
Histone acetylation
- Addition of acetyl groups (COCH3) to lysine residues of histone tails
- Deposited by histone acetylases (HAT)
o Weakens the association of DNA with histones making the DNA more accessible to transcription. Transcription is up-regulated - Removed by histone deacetylases (HDAC)
o Strengthens the association of DNA with histones making the DNA less accessible to transcription. Transcription is down-regulated
Identifying chromatin state by histone modifications:
- The genome is compacted by coiling around histones.
- DNA and histone form Nucleosomes.
- Repetition of nucleosomes form chromatin
- Histone modifications determine packing of nucleosomes (tight/ loose)
- Difference in packing of nucleosome can result in different physical structures in different regions of chromatin
o some = accessible while some = inaccessible, affecting TF binding thus gene expression
Therefore, regions of chromatin = marked by histone modification as active/inactive & those histone modifications are recognized by TF to locate active/ inactive chromatin, indicating where it is able to perform its function.
Studying histone modification is useful to
make a catalogue of the different regions to better understand gene expression.
Euchromatin
– regions where most of the nucleosomes are depleted, so the DNA is stretched and open, accessible, transcriptionally active. – always allow for binding of TF
* usually where house-keeping genes are located in
Heterochromatin
– regions where chromatin is closed, compacted, transcriptionally inactive due to tight packing of nucleosomes
Constitutive heterochromatin –
permanent heterochromatin which was assigned a specific set of histone modification after DNA replication to keep it compact, inactive
* Important for structural support or silencing of transposable elements
* Histone modification that leads to constitutive heterochromatin = di or tri-methylation
of lysine 9 of histone H3 (H3K9me2/3)
- In aging, the older age, there will be weaker methylation of these histones, so the regions that are supposed to be heterochromatic can get aberrantly expressed, leading to diseases (ex. Alzheimer’s, ALS)
Facultative heterochromatin
– regions of chromatin that can be turned on and off, depending on when the genes are needed. Ex. promotors for developmental genes that are needed during developmental period/ other specific times in life but not all the time
* Histone modification that leads to facultative chromatin = di or tri-methylation of lysine 27 of histone H3 (H3K27me2/me3) – a repressive methylation that can be countered by other modifications that cause chromosome remodeling to active form
- H3K27 methylation is deposited by PRC2, a complex consisting of:
- EED
- SUZ12 (for accessory/ structural subunits)
- EZH2 performing the enzymatic activity
- And other proteins that may or may not be present,
depending on the cell type it is functioning in (have cell- type specific composition)
activating facultative heterochromatin
- To be activated, require pioneer transcription factors that will first bind to inactivated regions of chromosome to signal arrival of activating machinery – ex. activating methylation: H3K4me1 & acetylation: H3K27ac which are always observed to flank active enhancers.
Those modifications then cause chromatin remodeling so nucleosomes are removed/ less packed & allow binding of other TF & gene expression
Ex. of histone modification:
X-inactivation
- the silencing of one of the X chromosomes in all female mammals
- Required for dosage compensation to avoid over expression of genes on the extra X chromosome
o females have XX chromosomes while males only have 1X and 1Y. For most genes, expression from 1 X chromosome is enough, but females have 2 copies of X chromosomes; therefore, there will be double the amount of expression if one of the X chromosomes is not silenced. - brought about by chromosome wide histone methylation – H3K27me3
- Inactivation carried out by Xist gene, which is a long non-coding RNA (lncRNA)
Long non-coding RNA (lncRNA)
- RNA that does not get translated by ribosomes into proteins, but perform their functions in the form of RNA. They are longer than 200 nucleotides.
- They can function as co-regulators to modify transcription factor activity & can also control other co-regulators or transcription factors
- Can act in cis – regulate gene expression on same chromosome they are transcribed from, or in trans – regulate gene expression on another chromosome
- Many thousands identified but function largely unknown
Xist
- 17Kb long lncRNA
- Expressed from only one of the 2 female X chromosomes and acts in cis – silences the X chromosome that it is transcribed from
- Performs function early on in the developmental stage & every time cells duplicate DNA
- Xist contains many repeats in the transcript – important = Repeat A (RepA) required for the silencing function of Xist
- Rep A forms 2ndary structure to recruit and bind the histone methyltransferase complex (PRC2) which has the enzyme EZH2 whose function is to lay down H3K27me histone modification, making the chromosome inaccessible by transcription factors.
- Xist has sequence specificity for the X chromosome which “guides” the inactivation complex along the chromosome, resulting in complete repression.
HOTAIR
- Acts in trans on HOX genes which are important for development – expressed by HOXC locus on chromosome 12 and represses the HOXD locus on chromosome 2
- Acts as both a guide and a scaffold – bringing together several complexes
- Form 2ndary structures to bind to:
o PRC2 which adds repressive H3K27me histone methylation
o LSD1 (demethylase) which removes active H3K4me histone methylation
o This combined function results in a repressive chromatin structure & repression of HOXD.
In cancer, HOTAIR acts on regions other than HOXD, causing aberrant gene repression
