Histone Modifications and Chromatin States

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Questions and Answers

What is the primary function of histone tail modifications?

To block access to chromatin DNA

To create binding sites for transcription factors (correct)

To facilitate histone-histone interactions

To increase chromatin compaction

What is the correlation between chromatin packing and gene expression levels?

Highly packed chromatin is associated with low gene expression

Loosely packed chromatin is associated with high gene expression (correct)

Loosely packed chromatin is associated with gene repression

Highly packed chromatin is associated with high gene expression

What is the term used to describe the process of histone modifications regulating gene expression?

Chromatin remodeling

Epigenetic regulation (correct)

Post-translational modification

Histone code hypothesis

Why must chromatin be made 'relaxed' before cellular machineries can access chromatin DNA?

To allow access to chromatin DNA Signup and view all the answers

What is the primary role of histone N-terminal tails?

To recruit transcription factors Signup and view all the answers

What was the prevailing view of histones before the discovery of histone modifications?

As structural proteins for chromatin compaction Signup and view all the answers

What histone modification is associated with transcribed gene bodies?

H3K36me3 Signup and view all the answers

Which histone modification is a mark of Polycomb-silenced promoters?

H3K27me3 Signup and view all the answers

What is the role of chromatin remodelers in the regulation of gene expression?

To regulate the transition from closed inactive to active chromatin Signup and view all the answers

Which histone modification is associated with active promoters?

H3K9Ac Signup and view all the answers

What is the result of densely populated nucleosomes on transcription factor binding?

They prevent transcription factor binding Signup and view all the answers

What is the characteristic of active enhancers?

They are marked by H3K4me1 and H3K27Ac Signup and view all the answers

What is the function of histone proteins in epigenetic regulation?

To help DNA condense into chromatin Signup and view all the answers

What is the effect of DNA methylation on gene expression?

It silences gene expression Signup and view all the answers

What is the role of histone modifications in epigenetic regulation?

They can either silence or activate gene expression depending on the tag Signup and view all the answers

What is the function of epigenetic writers, erasers, and readers?

To add, remove, or recognize epigenetic marks on histones Signup and view all the answers

What is the consequence of deregulation of histone modifications in diseases?

It leads to both cancer and autoimmunity Signup and view all the answers

What is the effect of environmental factors on epigenetic marks?

They can influence epigenetic marks Signup and view all the answers

Study Notes

Nucleosome Structure

Histone tails protrude out of the nucleosome, having a positively charged nature
Histone tails play a crucial role in chromatin folding and co-factor recruitment
N-terminal histone tails are the most accessible regions, possessing no specific structure

Histone Tail Modifications

Histone tails are subjected to various post-translational modifications (m, methylation; a, acetylation; p, phosphorylation; u, ubiquitination)
These modifications create sites for the recruitment of specific factors or modify existing sites to abolish previous interactions
Chromatin must be first made "relaxed" to allow the access of cellular machineries to chromatin DNA

The Histone Code Hypothesis

A core set of histone modifications define chromatin states
7 core histone modifications are associated with specific transcription events across the genome:
- H3K9Ac: active promoters
- H3K4me3: active promoters
- H3K4me1: enhancers and promoters
- H3K27Ac: enhancers and promoters
- H3K36me3: transcribed gene bodies
- H3K27me3: Polycomb-silenced promoters
- H3K9me3: Heterochromatin

Epigenetic Genome Annotation

Chromatin accessibility and nucleosome position play a critical role in transcription factor binding and enhancer activity
Densely populated nucleosomes are inaccessible and prevent the binding of transcription factors and cofactors
Accessible, nucleosome-free regions are available for the binding of transcription factors
Nucleosome positioning is a highly dynamic process, regulated by chromatin remodelers and pioneer transcription factors

Epigenomics

Epigenomics help annotate regulatory elements
Active enhancers are marked by H3K4me1 and H3K27ac, and are associated with the binding of transcription factors

Layers and Players in Epigenetic Regulation

Modification of histone proteins involved in packaging DNA
Methylation of DNA template
Non-coding RNAs can influence both histone and DNA modifications
Epigenetic layers: DNA methylation and histone modifications
Both tagging systems are conserved and critical for development
Tags are often deregulated in diseases (cancer, autoimmunity)

Epigenetic Writers, Erasers, and Readers

Histones mediate chromatin compaction
Histones are the template for PTM epigenetic modifications
Histones are a group of basic proteins that associate with DNA and help the DNA to condense into chromatin

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Description

Learn about the histone code nomenclature and how specific histone modifications are associated with transcription events across the genome. Understand the role of chromatin accessibility and nucleosome position in epigenetic genome annotation.