Chromosomes and chromatin Flashcards
What are euchromatin and heterochromatin?
2 different packaging states of chromatin. Heterochromatin is much more compact and can be either facultative or constitutive. Genes in heterochromatic regions are repressed. No room for transcription factors and RNA polymerase to bind. Euchromatin is a looser form om chromatin and genes that are actively transcribed can be found in these regions.
Constitutive vs facultative heterochromatin.
Constitutive: same for all cells: chromosomes 1, 6, 9 and Y for intance. Also often centromers (and telomers). Low desity of genes. Often contains repetitive sequences. Replicates late in S-phase. Low frequency of recombination. Permanently condensed
Facultative: varies between cells in the same organism. Dosage compensation X chromosomes. Can be converted to euchromatin.
G-bands
- stained with giemsa
- lower GC content than interband regions
- large structures that may contain hundreds of genes
- gives a unique banding pattern for each condensed chromosome
- genes are often found in interband regions
Polytene chromosomes
Giant chromosome in interphase nuclei in some tissues/cells in certain flies. Form when repeated rounds of DNA replication happens without cell division and the sister chromatids stay synapsed together. They are highly extended and thick. Chromosoe puffs can be seen in regions where there is active transcription of genes. Useful for mapping individual genes on the chromosome.
What is the philadelphia chromosome?
Reciprocal translocation between chromosomes 9 and 22 - leads to a fusion protein with the genes bcr and abl. Leads to a constitutively active tyrosine kinase (Abl)
Found in various leukemias
What is the function of centromeres?
Proper segregation during mitosis
Has specific histone varinat CENP-A/CenH3 and nucleosomes containing these protrude from the chromatin, binds to the kinetochore, which again binds to the spindle apparatus
Centromeres in humas and yeast?
Yeast:
- point centromeres
- very short, around 120 bp
- a single mictotubule attach point per chromosome
- can give stability to plasmids - YACs centromere, telomrere, replication origin
- cosists of two short conserved sequences, CDE-I and CDE-III, which flank an AT-rich region CDE-II
Humans:
- regional
- a lot of repetitive DNA
- many attachpoints
- CENP-A
- up to 5 Mb
What is the function and structure of telomers?
- needed for protection of the ends of linear chromosomes
- long stretch of tandemly repeated sequences (100-1000 repeats)
- generall form: Cn(A/T)m n>1 and m = 1-4
- solution needed fr shortening of telomers
- ## has a g-tail which loops back and invades and upstream sequence where it base pairs with the c-rich strand –> catalyzed by TRF2 and leads to the T-loop structure
How are the repeated elements in the telomeres synthesized?
- Specialized protein - telomerase
- Telomerase is a ribonucleoprotein
- -> has RNA template, reverse transcriptase and protein with enzymatic activity
- Telomerase often not expressed in cells - leads to telomere shortening
- After telomerase has done it’s job DNA poly alfa which has a DNA primer as it’s subunit finishes the 5’ strand
Describe the different levels of DNA packaging
2 nm - DNA DS
10 nm - DNA wrapped around histone octamers - beads on a string
30 nm - helical arrangement of nucleosomes - helped by linker histones H1. Packing ratio of 40.
60-300 nm - chromonema fibers. further levels of compaction - structure unknown.
What are DNA hypersensitive sites?
siites more sensitive to DNAase I than the bulk of chromatin. Found in areas around promoters of actively transcribed genes and the loose arrangement of chromatin (necessary for the binding of transcription factors and RNA pol) makes is more suspectible to DNAase I. Also for instance the LCR
What happens to nucleosomes during replication and transcription?
Displaced druing replication. New nucleosomes, old and new subunits, for rapidly after replication. H3-H4 tetramers, H2A-H2B dimers.
Transcription: RNA pol displaces octamer, which then reassociates with the DNA immediately after RNA pol has passed
Histone variants: What are they and examples.
In addition to the canonical histones H2A, H2B, H3 and H4 there are (more specialized) histone variants. These are also incorporated into the DNA and are often associated with specific chromatin states.
H2AX - gets phosporylated when there are DS. Recruits DDR machinery.
H2AZ - transcriptional repression and activation
MacroH2A - long C-terminal tails that possibly interferes with binding of transcription factors. Repression.
CENP-A - centromeres
H3.3 - associated with sites of active transcription
