Chromatin Structure and Function

A comprehensive set of flashcards focusing on chromatin structure, function, and modifications based on the lecture notes.

What is transcription reliant on in regard to the DNA template?

Accessibility of the DNA template.

What is chromatin primarily composed of?

DNA and nucleosomes, which are made of histone proteins.

How does chromatin assist in DNA organization?

It packages DNA to fit into the nucleus and regulates various processes.

What proportion of eukaryotic chromosomes consists of DNA and proteins?

Approximately half DNA and half proteins by weight.

What are the four types of histones found in nucleosomes?

H2A, H2B, H3, and H4.

How is DNA wrapped around histone proteins in nucleosomes?

146 base pairs of DNA twist approximately 1.3 times around the histone core.

What is the structure formed by nucleosomes called?

The 10 nm fiber, which is the initial level of DNA packaging.

What distinguishes euchromatin from heterochromatin?

Euchromatin is loosely compacted and accessible for transcription, while heterochromatin is densely compacted and inhibits transcription.

What is position effect variegation (PEV)?

A phenomenon where a gene is partially silenced due to its proximity to heterochromatin.

What are the main regulators that control chromatin activity?

Chromatin remodelers, chromatin modifiers, and DNA methylation.

What is the function of chromatin remodelers?

They are enzymatic complexes that move nucleosomes to change the compaction state of chromatin.

What do chromatin modifiers do to histones?

They chemically modify histones by adding or removing chemical groups.

What is the Histone Code hypothesis?

Histone post-translational modifications help specify the activity of genes.

Which specific chemical modifications are commonly studied regarding gene expression?

Acetyl and methyl groups.

What role do enzymes known as 'writers' play in chromatin modification?

They add chemical groups to histones.

How do histone acetyltransferases (HATs) affect chromatin?

They add acetyl groups, making chromatin more open.

What is the role of histone deacetylases (HDACs)?

They remove acetyl groups, promoting a tighter binding of nucleosomes to DNA.

How does histone methylation differ from histone acetylation?

Methylation does not affect nucleosome-DNA interactions but creates binding sites for regulatory proteins.

What is the significance of different lysine methylation states?

They can promote either euchromatin or heterochromatin based on the specific site of methylation.

What enzymes remove methyl groups from histones?

Demethylases.

What important proteins were identified in the study of heterochromatin in Drosophila?

Su(Var)3-9, which is the HMT for H3 K9 methylation, and HP1, the reading protein.

What does ChIP-seq stand for and why is it used?

Chromatin Immunoprecipitation followed by sequencing; used to study histone modifications.

What is the outcome of ChIP-seq analysis in terms of gene activity?

It helps identify which genes are active versus repressed based on histone PTMs.

What do methylation levels at histone H3K4 indicate?

Active promoters in euchromatin.

What is the basic structure of a nucleosome?

DNA wrapped around a histone octamer consisting of H2A, H2B, H3, and H4.

What is the function of linker DNA in chromatin structure?

It connects nucleosomes and is important for higher-order chromatin organization.

What composes constitutive heterochromatin?

Regions of the genome that are always heterochromatic and are not transcriptionally active.

What happens to chromatin when it is in an 'open' state?

It allows access for transcriptional machinery.

What is the role of histone methyl transferases (HMTs)?

They add methyl groups to histones, affecting gene expression.

Why is DNA packaging into chromatin crucial for cellular function?

It regulates DNA accessibility for transcription, replication, and processing.