DNA 3D structure

DNA compaction hierarchial levels of chromatin organization

1. nucleosomes

2. Histone H1 binding

3. Additional compaction

the first level of DNA compaction is achieved by

wrapping about 147 base pairs of DNA around a histone octamer

histone octamers are composed of

• two H₂A proteins

• two H₂B proteins

• two H₃ proteins

• two H₄ proteins

How many times does DNA wrap around the histone octamer

about 1.7 times

DNA wrapping around the histone octamer forms a

nucleosome

Histones are ___ charged

positively

The positive charge of histones promotes

interactions with negatively charged DNA

Histones bind largely independent of

sequence

Histones interact with DNA through non-covalent interactions, allowing

dynamic chromatin remodeling

Level 2 of DNA compaction occurs when

Histone H1 binds linker DNA located between nucleosomes and promotes additional compaction

Additional DNA compaction occurs through

• chromatin looping

• interactions with structural proteins

• higher-order chromosomal organization

Topologically Associating Domains (TADs)

large chromatin domains in which DNA sequences interact more frequently with one another than with sequences outside the domain

Topologically Associating Domains (TADs) are generated in part through

loop extrusion

loop extrusion is a process involving

cohesion complexes and CTCF proteins

organization of Topologically Associating Domains (TADs) is biologically important because it

• helps compact chromosomes

• organizes enhancer-promoter communication

• regulates gene expression

• contributes to cell differentiation

• can be disrupted in cancer and developmental disorders

functions of chromatin organization

• compaction

• chromosome segregation during mitosis

• regulation of gene expression

highly condensed chromosomes are essential for ___ during mitosis

accurate chromosome movement and segregation

poorly condensed chromosomes can become ___ and __ during mitosis

entangled and segregate improperly

chromatin structure strongly influences

transcriptional activity

euchromatin

chromatin that is loosely compacted, transcriptionally active, and accessible to RNA polymerases and transcription factors

heterochromatin

chromatin that is highly compacted, transcriptionally suppressed, and less accessible to RNA polymerases and transcription machinery

chromatin states are regulated by

• histone modifications

• chromatin-remodeling complexes

• DNA methylation

• higher order chromatin interactions

DNA methylation commonly occurs at

cytosine residues with CpG dinucleotides

Hi-C

a chromosome conformation capture technique used to study the 3D organization of genomes

Hi-C method measures

how frequently genomic regions physically interact in 3D space, even when they are far apart along the linear chromosome

General workflow of Hi-C

• crosslinking nearby chromatin regions

• DNA fragmentation

• ligation of crosslinked fragments

• reversal of cross links

• DNA sequencing

• computational reconstruction of chromatin interaction maps

Data from Hi-C technology is represented as

2D matrices called Hi-C maps

Do Hi-C and FISH technologies generate identical results?

NO

Hi-C analyzes how many cells at once?

millions

FISH analyzes how many cells at once?

one

Hi-C may obscure

cell-to-cell heterogeneity

Hi-C produces an

averages interaction map

FISH captures

single cell variability

FISH suggests that

chromatin architecture can vary substantially between cells

Chromosome organization is dynamic and sensitive to

developmental and environmental conditions

4D Nucleosome Program

a large NIH-funded research initiative

The 4D Nucleosome Program aims to understand how

• genomes are organized in 3D nuclear space

• chromatin organization changes over time (4th dimension)

• Nuclear architecture regulates gene expression and cell function

• defects in genome organization contribute to diseases such as cancer and developmental disorders

30 nm fiber

a higher-order structure of chromatin formed by coiling the 10 nm nucleosome array into a thicker, roughly 30 nm diameter fiber

chromatin

the complex of DNA, histone proteins, and non-histone proteins that makeup eukaryotic chromosomes

cohesion

the physical holding together of sister chromatids after DNA replication

CpG island

a genomic region with a high density of CG dinucleotides

What does the p stand for in CpG

the phosphodiester bond between C and G

CTCF

CCCTC binding factor, a highly conserved Zinc protein that functions as a master organizer of chromatin architecture

histone tail

the flexible, unstructured N-terminal (and sometimes C-terminal) extensions of core histones that protrude from the nucleosome core

nucleosome

fundamental repeating unit of chromatin

phosphorylation

post-translational modification on histones that results in the addition of a phosphate group to serine, threonine, or tyrosine residues

acetylation

post-translational modification on histones that results in the addition of an acetyl group (COCH₃) to the ε-amino group of lysine residues

methylation

post-translational modification on histones that results in the addition of 1-3 methyl groups (CH₃) to lysine or arginine residues