Module 3 Section 8 Flashcards
Cellular processes that rely on the modification of chromosomes
- Regulation of gene expression
- DNA replication
- DNA editing and repair
- Recombination events
- The preservation of epigenetic tags
Epigenetic tags
-a specific modification on DNA or specific amino acids in the histone proteins that DNA is wrapped around
Chromatin remodelling complexes functions (3)
- repositions (slides) nucleosome to different position on DNA
- Eject nucleosome from the DNA
- Replace the nucleosome with one that contains a histone variant
Chromatin remodelling complexes mechanism
- latch around histone octamer, pull out DNA associated with the nucleosome
- “loop propagation,” slide DNA across, then tighten the histone around the new area of DNA
- requires ATP (the enzymes contain ATPase domains)
Questions answered by ChIP for studying chromatin remodelling or modification
- ChIP: chromatin Immunoprecipitation
1. Across genome: - which segments of DNA are incorporated in nucleosomes?
- What is nucleosome density in particular regions of the genome?
- Can we use this info to identify actively transcribed regions of the genome?
2. For gene of interest - is the promoter for my gene of interest associated with a nucleosome bearing a particular histone variant or histone modification?
- What does this tell us about the accessibility of of this gene under different conditions?
ChIP steps (4)
- Cells treated with formaldehyde (this covalently crosslinks the nucleosomes to DNA.
- The genomic DNA is fragmented using non-specific endonuclease or mechanically (sheared)
- an antibody to a specific modified histone is used to immunoprecipitate the nucleosome-DNA complex. Any DNA not bound to a histone is washed away
- The protein-DNA crosslinks are reversed by heating. Released DNA is analyzed with PCR, qPCR, NGS or microarray
H3 histone variants
H3.3
CENPA (centromere protein A)
H2A histone variants
H2AX
H2AZ
macroH2AZ
H2AX function
- associated with DNA repair/genetic recombination
- C-term has phosphorylation region, site for recruitment of proteins for DNA repair
H2AZ function
- associated with nucleosomes located at actively transcribed genes
- thought to stabilize the open state of chromatin to facilitate access of transcriptional machinery
macroH2AZ function
- abnormally large, unique C-term domain
- used for X-chromosome inactivation, keeps from double expression of X in females:
- XIST RNA expressed by X-chromosome
- macroH2AX substituted for normal H2A, serves as docking site for XIST RNA, capping off one of the X-chromosomes
- occurs at blastysis stage of development
H3.3 function
- found in transcriptionally active regions
- associated with transcriptionally active state
CENPA function
(centromere protein A)
-allows for kinetochore attachment (docking site for spindle fibres, separation of nucleosomes during cell division)
What do Histone Modification enzymes do?
- covalently modify histones, primarily on the N-term tail
- modifications are heritable
- There are cis acting and trans acting modifying enzymes
- NOT mutually exclusive, certain modifications can have both effects
Types of histone modifications (and the AA they happen on)
- phosphorylation of serine (S), threonine (T), tyrosine (Y)
- acetylation of lysines
- methylation lysines and arginines