Genomics and Chromosome Organization

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Questions and Answers

What is the result of acetylation of lysine side chains by histone acetyl transferases?

Complete removal of positive charge from nucleosomes

No change in the charge of nucleosomes

Increased positive charge on nucleosomes

Reduced positive charge on nucleosomes (correct)

What is the effect of histone deacetylases on gene transcription?

It activates transcription by loosening nucleosomes

It inhibits transcription by compacting nucleosomes (correct)

It has no effect on transcription

It activates transcription by compacting nucleosomes

Which histone modification is associated with gene activation?

H4 phosphorylation

H2A ubquitination

H3K9me

H3K4me (correct)

What is the function of histone demethylases?

To remove methyl groups from histones Signup and view all the answers

What is the result of histone H3 lysine 9 methylation?

Inhibition of gene transcription Signup and view all the answers

What is the role of enzymes in chromatin structure regulation?

They actively regulate chromatin structure by modifying histones Signup and view all the answers

What is the primary function of bromodomains in HATs?

To recognize acetylated histone marks Signup and view all the answers

What is the result of competition between histone acetylation and histone methylation?

The specific histone modification that occurs depends on the specific amino acid position Signup and view all the answers

How are histone modifications inherited by daughter cells?

Through the inheritance of modified histone proteins Signup and view all the answers

What is the function of MeCP2 in DNA methylation?

To recognize methylated cytosine residues Signup and view all the answers

What is the result of DNA methylation in the context of CpG islands?

The inhibition of gene expression Signup and view all the answers

How are histone deacetylation and DNA methylation coordinated?

Through the recognition of methylated cytosine residues by MeCP2 Signup and view all the answers

What is the primary function of histone H3 lysine 9 methylation in chromatin compaction?

To drive local chromatin compaction Signup and view all the answers

Which type of elements is subject to high levels of DNA methylation?

Repetitive elements Signup and view all the answers

What is the role of histone deacetylases in chromatin compaction?

To remove acetyl groups from histones Signup and view all the answers

What is the function of insulators in chromatin compaction?

To attenuate the lateral spread of modifications Signup and view all the answers

How is the initiation of heterochromatin formation driven?

Through DNA binding proteins that recognize specific DNA sequences Signup and view all the answers

What is the effect of cytosine methylation on gene expression?

It represses gene expression Signup and view all the answers

Study Notes

Pseudogenes and Genome Instability

Pseudogenes originate from genic sequences and are typically inserted into new locations via transposons.
Repetitive sequences can cause genomic instability, leading to errors in DNA repair, which may result in inversions and deletions.
An example of genome rearrangement is Williams Syndrome, which exhibits specific physical traits and sociable behavior.

Epigenetic Modification of Histones

Enzymatic regulation of chromosome structure involves modifying histone N-terminal tails through acetylation, methylation, phosphorylation, and ubiquitination.
Histone acetyl transferases (HATs) acetylate lysine side chains, reducing their positive charge. This promotes an open chromatin conformation, facilitating transcription factor access.
Acetylation of lysines forms an amide bond, similar to peptide bonds.
Histone deacetylases (HDACs) remove acetyl groups, leading to compact nucleosome packaging and repression of transcription.
Histone methyltransferases (HMTs) add methyl groups to lysines, resulting in activating (e.g., H3K4me) or inhibiting (e.g., H3K9me) modifications.
Lysines can be modified by mono-, di-, or tri-methylation, and specific enzymes demethylate these sites.
Many HATs and HMTs must recognize their modification products, with HATs often containing bromodomains that specifically recognize acetylated histones.
Competition exists between acetylation and methylation at specific histone positions, creating a complex regulatory landscape.
Histone modifications can be epigenetically inherited by daughter cells, thus not being encoded in the DNA sequence.

DNA Methylation

DNA can undergo methylation, primarily at cytosines, which is considered an epigenetic modification due to its heritable nature.
Cytosine is often methylated at the 5' position within CpG sequences, typically clustered into "CpG islands."
Proteins like methyl-cytosine binding protein (MeCP2) bind to methylated cytosines and recruit DNA methyltransferases (DNMT) to propagate the modification.
DNA methylation is interrelated with histone modifications; for example, MeCP2 also recruits histone deacetylases.
Methylation is commonly found in gene promoter regions and is associated with gene repression.
Repetitive elements, particularly transposable elements, experience high levels of methylation, contributing to their repression.

Chromatin Compaction and Epigenetic Modifications

Heterochromatin compaction is reliant on specific epigenetic modifications, particularly H3K9 methylation.
H3K9me serves as a binding site for heterochromatin protein 1 (HP1), a reader protein that recruits various modifying enzymes.
The spreading of these modifications can lead to local chromatin compaction and inactivation of adjacent genes.
Insulators located at topologically associating domain (TAD) boundaries can suppress the lateral spread of modifications through steric disruption.
Heterochromatin formation can be initiated by DNA binding proteins or the production of double-stranded RNA from repeats, leading to recruitment of H3K9 methylases.

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Description

Learn about pseudogenes, repetitive sequences, and their impact on genome instability. Discover how errors during DNA repair can lead to genetic disorders like Williams Syndrome. Explore epigenetic modification of histones and enzymes.