Epigenetics and Chromatin Overview

Tightly packed eukaryotic DNA and proteins.

Fundamental subunits of chromatin, DNA wrapped around histone proteins.

Highly condensed form of chromatin, typically found near chromosome ends.

Less condensed form of chromatin; contains many active genes.

Small proteins around which DNA wraps to form nucleosomes.

Study of how environment affects gene function.

Chemical changes to histone proteins that can affect gene expression.

Enzyme used to study nucleosome structure, by preferential digestion of DNA outside nucleosome.

147bp of DNA wrapped around an octamer of histone proteins.

Adding an acetyl group to a lysine residue on a histone protein, which removes its positive charge and loosens the nucleosome structure.

Adding a methyl group to a lysine or arginine residue on a histone protein. Can be mono-, di-, or trimethylated.

Enzymes that catalyze acetylation of histone proteins, adding acetyl groups and loosening the DNA.

Enzymes that remove acetyl groups from histone proteins, tightening the DNA structure.

Enzymes that add methyl groups to histone proteins, causing a variety of effects.

Enzymes that remove methyl groups from histone proteins, reverting the modification.

The idea that specific patterns of histone modifications act like a code, dictating gene expression and other cellular processes.

A protein that binds to trimethylated histone tails, contributing to the spread of heterochromatin.

The dynamic process of changing the structure of chromatin to regulate gene expression, often involving histone modifications.

Histone modifications can attract other proteins to the modified chromatin, influencing various cellular processes.

Protein domains that specifically recognize methyl modifications on histones. They are often found within proteins involved in chromatin regulation and gene expression.

Protein domains that bind to methylated histone tails, specifically targeting lysine residues. They play roles in gene regulation and heterochromatin formation.

Protein domains that bind to methylated histone tails, particularly arginine residues. They are often part of complexes involved in transcriptional regulation and DNA repair.

Protein domains that recognize methylated lysine residues on histone tails, particularly those involved in transcriptional regulation and chromatin compaction.

Protein domains that specifically recognize acetylated lysine residues on histone tails, which are linked to gene activation and chromatin remodeling.

Enzymes that add modifications to histones, such as acetylation, methylation, or phosphorylation. They ultimately influence gene expression.

Enzymes that remove modifications from histones, counteracting the effects of writers. They play crucial roles in resetting the histone code.

Protein domains that specifically recognize and bind to certain histone modifications, interpreting these modifications and influencing gene expression.

A multi-protein complex that acts as a histone modifying enzyme, modifying histones through acetylation and deubiquitination, influencing gene expression.

A model where writers add modifications to histones, which are then recognised by readers. The interactions between these can create a feedback loop, ultimately affecting gene expression.

A sequencing method that reads both ends of a DNA fragment, providing information about interacting regions within the genome.

A point on a Hi-C map representing a physical interaction between two regions of the genome.

Regions of the genome organized into self-interacting loops, where genes within a TAD often share similar activation patterns.

Genes within the same TAD tend to be regulated together; they are turned on or off at the same time due to their physical proximity.

Hi-C provides a genome-wide map of chromatin interactions, capturing interactions across all chromosomes simultaneously.

A technique used to study long-range interactions within the genome by crosslinking DNA and associated proteins, then digesting, ligating, and analyzing the resulting fragments.

Fragments of DNA that were physically close in the 3D space of the cell are more likely to be ligated together during the 3C process.

3C can be used to study how genes are regulated, how chromosomes are compartmentalized, and to map structural domains within the genome.

A specialized type of 3C technique that specifically investigates interactions between DNA and proteins.

ChiA-PET uses antibodies specific to a protein of interest to pull down chromatin regions bound by that protein. This allows for the enrichment of DNA interactions mediated by the targeted protein.

ChiA-PET is helpful in determining the 3D structure of transcriptional regulation, by identifying DNA regions that interact with specific regulatory proteins.

ChiA-PET uses antibodies to specifically isolate protein-bound DNA regions, while 3C analyzes all DNA interactions within the cell.

3C can reveal how distant enhancers regulate genes by physically looping to their promoters.

3C can help identify regions of euchromatin (active) and heterochromatin (inactive) within the chromosome, providing insight into how the chromosome is compartmentalized.

Topologically associating domains (TADs) are regions of the genome that are physically interacting more with themselves than with other regions. These domains represent functional units of the genome.