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Chromosome Chemistry and Packaging
Terms in this set (26)
Name the main components of chromatin
Composed of DNA and proteins such as histones
Why is chromatin packaging needed? Discuss both physical and functional aspects
Physical: Physico-chemical properties of DNA: negatively charged phosphate groups stiffen the DNA so that it cannot fit into the nucleus
Functional: It allows the DNA to be highly condensed at times when there is no transcription occurring, and it is more open in interphase when it is functionally active (dynamic)
Describe the organization of the fundamental levels of chromatin packaging: nucleosome core, nucleosome and folded nucleosomes
1. Nucleosome core is 8 histone molecules forming a 2x2x2 cube which DNA is wrapped around. this is the most fundamental component
2. Nucleosome cores are linked together by a DNA linker, and histone H1 attaches at the linker position, and twists nucleosomes together in a more compact structure
Discuss higher orders of packaging based on hierarchical model and more recent models
The classical hierarchical model is that the DNA and histones may form a 'scaffold' structure which is just loops of DNA that are varying in size from that it condenses to form the traditional chromosome.
- More recent models find that the metaphase chromosome is best described as a linearly organized longitudinally compressed array of consecutive chromatin loops
Regarding protein content, what is the main difference between lower and higher (scaffold based) levels of chromatin packaging?
Lower levels: just histones
Higher levels: Topoisomerase II, Scaffold protein SC2, high mobility group proteins, metaphase chromosome protein, centromeric proteins, cohesin protein complex
Describe chromosome scaffold and the scaffold attachment regions. which proteins are involved?
chromatin loops have specific scaffold associated regions which are DNA segments that define the bases of the DNA loops
- scaffold protein SC2?
which experiments proved the existence of chromosome scaffold?
evidence suggested that there were other proteins involved in making the chromosomes other than histones, and if DNA was not digested, loops of DNA protruded from the proteins
Compare chromatin packing in interphase and metaphase chromosomes. what is the functional significance of the observed difference?
Metaphase is likely the scaffold structure, while in interphase the chromosomes fold to form territories and individual chromosomes form compartments A (active) and B (silent), within each compartment it is packaged to form topologically associated domains (TADs) and then into sub-TADs
Is metaphase chromosome organization essentially different between different cell types?
no, it is consistent among cell types
Mitotic chromatin loops carry so called structural bookmarks. what is their function?
Structural bookmarks retain epigenetic memory about TADs present in interphase. tells how to reassemble the chromosome in different times of the cell cycle
is interphase chromosome organization different between different cell types?
yes, the TAD positions and compartments are generally conserved across species
Characterize different levels of chromosome/chromatin organization in interphase chromosomes: Chromosome territories, A and B compartments, TADs. Which methods are used to study these
- Chromosome territories: locations of individual chromosomes during interphase (banding)
- A and B compartments: A is open/active compartments with high GC content enriched in genes, B are silent, late replication timing (studied thru banding)
- TADs: blocks of dense chromatin that interact more frequently within themselves than with neighboring regions (studied thru Hi-C)
Characterize chromosome territories? can they be observed during the entire cell cycle or only at certain stages? how are chromosome territories associated with gene/chromatin/chromosome functions?
Chromosome territories are defined locations of individual chromosomes in nuclei during interphase, they are dynamic.
- only at interphase
- territories depend on chromatin type where heterochromatin is close to the nuclear membrane and euchromatin is close to the center and inter-chromosomal channels. Gene rich chromosomes are in the center, and gene poor chromosomes are in the periphery
are chromosome territories usually separated or overlapping?
generally separated? or overlapping with immediate neighbors
Describe interphase chromosome compartments A and B with regards to chromatin conformation, transcriptional activity, gene content, type of chromatin, centromeres, telomeres.
A has open chromatin, is transcriptionally active, gene rich, high GC
B has more chromatin interaction, late replication, close to nuclear periphery, gene poor, telomeres and centromeres
Describe inter-chromosomal contacts like the one known as chromosome kissing? relate it to chromosome territories and regulation of gene functions.
Chromatin loops out from a chromosome territory, and two or more genes get in touch, may have function in coordinating gene expression
Describe chromatin dynamics in cell differentiation from stem cells to differentiated adult cells
Differentiation restricts the expression profile and dynamics of the cell's interphase chromatin. Totipotent stem cells nuclei are large and have fully dynamic chromatin, as transcription patterns become increasingly defined the nuclei gets smaller and less of the chromatin remains mobile
What is chromatin remodeling and why is it needed?
Changes in chromatin structure that allow protein-DNA interactions during replication and transcription. allows for spatio-temporal regulation of gene expression at different developmental stages in different cells, tissues, and organs.
Name the main mechanisms of chromatin remodeling, and their impact on gene activity
DNA-histone contacts may be loosened, the path around a nucleosome core may be altered, the composition of the nucleosome core may be altered
Chromatin remodeling is an epigenetic process. Explain
Epigenetic: changes in chromatin and DNA that do not involve changes in DNA sequence. The histones may be methylated which may induce alterations in chromatin architecture, either condensing or relaxing its structure.
What does chromatin modification H3K9me3 mean? is it a repressing or an activating modification?
H3 = histone 3
K9 = lysine 9
me3 = trimethylation
It is a repressing modification
How is histone methylation correlated with gene density and DNA base composition? Use the example of H3K4me3 in human chromosomes.
histone methylation is associated with gene density and transcriptional activity. Where H3K4me3 is often found where there is a high gene density and high transcriptional activity and a higher GC content
Use HSA18 and 19 as examples for chromosome territories and chromatin remodeling
in chromosome territories, the more gene rich and transcriptionally active chromosomes are found in the center, which is where HSA19 is, and the less active gene poor chromosomes such as HSA18 are found in the periphery. These transcriptionally active and gene rich chromosomes have more activating methylation and chromatin remodeling, while the less active may have more repressing modifications?
Know the main concepts of molecular hybridization and fluorescence in situ hybridization: know the underlying properties of DNA/nucleic acids
Molecular hybridization: relies on the denaturation and renaturation property of RNA/DNA, as well as the base-pairing principle. permits the location of DNA markers in their original place. the probes are labeled with fluorochromes and bind to the target sequence
Know the main principles of Chromatin Conformation Capture Hi-C.
1. cell populations are fixed with formaldehyde
2. Digested with a restriction enzyme
3. sticky ends are filled in with dNTPs
4. blunt-end ligation with a ligase
5. DNA is purified and sheared
6. interacting fragments are identified by paired end sequencing
How does Chromatin Conformation Capture advance our understanding about chromosome organization and functions?
it allowed us to see specific interactions between genes and genomic elements located on different TADs or on different chromosomes
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