6 - Higher order DNA organization Flashcards
Give the hierarchical sussessions of DNA wrapping in chromatin
Interphase nucleus
- beads on a string
- 30 nm helical wrap on protein scaffold
Mitosis
- Solenoid
- Angle around histone, distance between one nucleosome and another and proportion of wrapped/unwrapped DNA is very precise
How did people figure out the structure of chromatin?
A big part of it was using cross linking. Treating DNA in a way that makes covalent bonds then visualizing with electron microscopy. You expect that adjacent nucleosomes would become bound by covalent bonds, with this you can predict which one it came from.
In this case, we fuond the solenoid model to be true. Although there are now alternative situations that can happen under non-physiological conditions.
How is the condensed state of chromatin at mitosis achieved?
Action of cohesin and condensin proteins
- Family of proteins that forms complexes
Cohesins: Holds together sister chromatids (eg during prophase).
Condensins: Chromatin condensation (and to keep a particular region of DNA together). Eg. during metaphase. Found in core of chromosome.
How are condensins like cord-stoppers?
They can allow DNA to slide through OR lock and act as a clamp to keep DNA from sliding.
Yeast that express these proteins show that these protiens were kept open during division and chromosomes were pulled from centromeres. But the rest of the arm was left intact because of condensins.
Condensins allow the molecule to be handled during cell division (Christian Häring).
True or false? Modulations in cohesins can influence the longitudinal compaction of chromosomes?
False.
Different CONDENSINS and number of them can influence longitudinal compression (eg. tighter or looser). It can do this through it’s different conformations, acting as a loop fastener (DNA can’t slide) or or light embracer (DNA can slide).
How is hetero and euchromatin DNA distributed through the nucleus?
Heterochromatin: Periphery
Euchromatin: Througout
Are chromosomes separated from each other?
Yes, by an interchromatin compartment
The interchromatin (interchromosomal) compartment is best viewed as a series of channels in and around the individual chromosomal territories that are in direct connection with the nuclear pores of the nuclear envelope. It is filled with nucleoplasm containing subnuclear bodies, nuclear proteins, and RNAs, which move rapidly through its channels. It is thought that as RNA is transcribed from genes along the periphery of the chromosomal territory, it drops into the interchromatin compartment for processing, packaging, and transport out of the nucleus through the nuclear pores.
Each chromosome occupies a distinct territory in the nucleus that is separated from the others by the interchromatin compartment.
Do each copy of a chromosome occupy the same territory?
No! During interphase they can occupy totally different territories.
Each chromosome kind of makes its own territory.
Although the relationship between chromosomes in the space of the cell appears to be consistent (eg. pattern of distribution). THis is variable between cell-types. The purpose of this is to facilitate proper gene expression!
How were chromosomal territories discovered?
By using a laser to induce genome damage. Damage was only localized to a small subset of chromosomes (eg. the laser only hit a territory with a chromosome one it).
What are some characteristics of DNA that indicate expression (in terms of territory location)?
- Loops of DNA sticking into interchromatin space are more transcriptionally active.
- More transcription factors and such stuff in the interchromatin space
- Actively transcribed genes that are put close to heterochromatin are silenced due to lack of transcription factors and other.
How are chromosome territories density wise?
Density is variable. Eg. you often see loose chromatin expanding into the interchromatin compartment. But dense chromatin is hidden away from interchromatin compartment.
How are chromatin territories distributed in relation to gene density?
Gene poor domains are located closer to the nuclear periphery.
Gene dense domains are located between gene poor compartments and the interior of the nucleus.
What are speckles?
Structures in the nucleus (aggregates of protein) that have difference functions depending on protein composision and different distributions through the nucleus.
The nuclear speckles are small subnuclear membraneless organelles or structures, also called the splicing factor (SF) compartments that correspond to nuclear domains located in interchromatin regions of the nucleoplasm of mammalian cells. Protein found in speckles serves as a reservoir of factors that participate in transcription and pre-mRNA processing.
Eg. more speckles are associated with splicing, which would be near intronic genes.
How are things like transversions effected by chromosome territories?
It is entirely possible for an gene to be moved to a dead territory (cause problems) or vice versa (potentially causing cancer)
