D7 Eukaryotic transcription

What is chromatin made of?

DNA, RNA, and proteins.

When is chromatin most open and accessible during the cell cycle?

During interphase (all stages except mitosis).

Why must chromatin be open during interphase?

To allow transcription, replication, and access to DNA.

What is heterochromatin?

Highly condensed chromatin that is transcriptionally silent and inaccessible to transcription machinery.

. What is constitutive heterochromatin? Give examples.

Regions that are always heterochromatin in every cell type.
Examples: Centromeres and telomeres.

What is facultative heterochromatin?

Regions that are heterochromatin in some cell types or conditions but can become euchromatin in others.

What is euchromatin?

Lightly stained, open chromatin where transcription is active because DNA is accessible.

What is the repeating structural unit of chromatin?

The nucleosome.

What components make up a nucleosome?

A histone core of 8 histone proteins (2 each of H2A, H2B, H3, H4)

• ~200 base pairs of DNA (including ~50 bp linker DNA)

What is the “beads on a string” structure?

The 10-nm fiber of euchromatin where nucleosomes (beads) are separated by linker DNA (string).

What is the role of histone H1?

Not part of the core but binds linker DNA to “lock” DNA onto the nucleosome and promote compaction.

Why are histone proteins positively charged?

Because they contain many positively charged amino acids, enabling them to interact with the negatively charged DNA backbone.

What are histone tails?

Unstructured N-terminal (and some C-terminal) extensions that interact with neighboring nucleosomes and are sites of epigenetic modification.

What are epigenetic modifications?

Covalent modifications to DNA or histone proteins that alter chromatin accessibility without changing DNA sequence.

What does histone acetylation do?

• Acetyl groups (added to lysines) neutralize positive charges

• Reduces nucleosome interactions

• Opens chromatin (euchromatin)

  • Promotes transcription

Which enzyme adds acetyl groups to histone tails?

Histone acetyltransferase (HAT)

Which enzyme removes acetyl groups?

Histone deacetylase (HDAC).

What does histone methylation do?

• Adds 1–3 methyl groups to lysines or 1 to arginines

• Does not change charge

• Can activate or repress transcription depending on context

  • Hypermethylation (especially trimethylation) often → repression / heterochromatin

Which enzyme adds methyl groups?

Histone methyltransferase.

What genomic sequence is targeted for DNA methylation in eukaryotes?

CpG sites (cytosine-phosphate-guanine).

What enzyme methylates DNA?

DNA methyltransferase (DNMT).

Where does the methyl group sit on cytosine, and where does it project into DNA structure?

Added to carbon 5 → Projects into the major groove.

What is the effect of CpG methylation on transcription?

Typically represses transcription by blocking transcription factor binding.

What are CpG islands?

: CG-rich regions near promoter regions that can be methylated to regulate transcription.

What does hypermethylation of a CpG island usually cause?

Transcriptional silencing.

What are cis-acting regulatory elements in eukaryotes?

• Promoters

• Promoter proximal elements

  • Enhancers (unique to eukaryotes)

What are enhancers?

Promoter-distal DNA sequences that can be thousands of base pairs away (upstream or downstream) and increase transcription by binding activators.

How can enhancers regulate a promoter so far away?

DNA looping allows enhancer-bound proteins to interact with the promoter