Chromatin structure

The DNA in eukaryotes is very long, around 2 meters in humans! Chromatin must tightly pack all of that DNA inside the cell while still being dynamic enough to facilitate transcriptional regulation.

Core Histones

Core histones provide much greater compaction when compared to the equivalent structures in bacteria. They are very highly conserved across species when compared to linker histones.

The globular domain of the core histones have many charged amino acid near the surface. Non-polar amino acids form the interior of the globular domain. Core histones have tails on the N-terminal between 20 and 30 amino acids long. These tails are disordered or unstructured and contain many lysine and arginine residues. The tails are highly conserved, indicating some important function.

Chaperone chromatin assembly factors catalyze core histone assembly in the S phase. Histone tails are very positively charged making them interact with the negatively charged DNA backbone. A core nucleosome consists of 8 histone proteins: H2A, H2B, H3 and H4.

linker histones

A linker histone is an H1 protein and links groups of core histones together. Linker histones also stabilize nucleosomes when they are in a compact conformation.

Linker histones have a tripartite structure consisting of an N-terminal tail, a globular domain, and a C-terminal region which may play a role in protein stability.

Heterochromatin

Heterochromatin is the inactive form of chromatin and is typically inaccessible to transcription factors. Usually, heterochromatin is composed of highly repetitive DNA sequences.

Euchromatin

Euchromatin is condensed only at metaphase, genes may be active or inactive. Inactive chromatin may be referred to as silent chromatin. Euchromatin is usually modified via acetylation.

Pioneer TFs

The cell needs some way to open closed chromatin. It does so using proteins called pioneer transcription factors. FOXA and GATA are two examples. Pioneer transcription factors have a high affinity to nucleosomes and a slow nuclear mobility.

Histone code hypothesis

The histone code refers to epigenetic modifications like methylation and acetylation.

Gene regulation

Gene regulation allows cells to change their phenotype based on their environment. This allows cells to differentiate into different cell types.

Gene profiling techniques

• Northern blot is a classic technique that was able to detect a single transcript
• qPCR is a technique first converts the mRNA to a cDNA library before performing quantitative PQR. Quantitative PCR measures the rate of replication of cDNA transcripts, allowing for quantification of relative expression levels.
• Microarray tiles sequences to a known set of genes
• RNA-sequencing first converts mRNA to cDNA then directly sequences the cDNA, no reference necessary.

Major control points in gene regulation

• Transcription
• RNA processing
• Translation
• Post-translational modifications