Chromosome Organisation - Eukaryotes Flashcards
What do the labels refer to? * * ------A * * * -------B * * * * ---------C |/ D
A - Telomere
B - Centromere
C - Telomere
D - Sister Chromatids
How many chromosomes do humans have?
23 pairs:
22 pairs of autosomes
and
1 pair of sex chromsomes
Does chromosome number tell us anything about the organism?
No
How are autosomes numbered?
Largest to smallest
How are chromosomes classified?
Telocentric - no chromosome arm (p arm) above centromere (not in humans)
Arocentric - small chromosome arm (p arm) above centromere
Submetacentric - medium sized chromosome arm (p arm) above centromere
Metacentric - chromosome arms same length either side of centromere
What technique can be used to distinguish chromosomes?
G-banding
Uses Giemsa staining to produce dark bands (gene poor) and light bands (gene rich)
What technique can be used to map genes to chromosomal regions?
FISH (Fluorescence in situ Hybridisation)
Make fluorescent copy of probe sequence
Denature sequences
Probe and target sequences mixed
Probe hybridises to target sequence
Can detect presence of probe using a fluorescent microscope
Name the types of numerical abnormalities
Polyploidy - many copies of entire karyotype (not in humans)
Aneuploidy:
Monosomy, loss of one chromosome (not in humans except Turner Syndrome)
Trisomy, gain of one chromosome
What syndromes result from aneuploidy in humans?
Sex chromosomes: Turner syndrome - XO Trisomy X - XXX Klinefelter syndrome - XXY Autosomes: Down syndrome - +21 Edwards syndrome - +18 (lethal at infancy)
What are the 4 main classes of rearrangements?
Duplication, Deletion, Inversion, Translocation
What are the causes and consequences of rearranged chromosomes?
Causes: ds breaks Non-allelic homologous recombination (NAHR) Consequences: Change to gene dosage Unbalanced Gene disruption Centromere not preserved Meiotic pairing affected
What is a robertsonian translocation?
Centric fusion of arocentric chromosomes 13, 14, 15, 21, or 22
Can cause Down syndrome in progeny of carrier
What is a reciprocal translocation?
Exchange of parts between two non-homologous chromosomes
Can produce Philadelphia chromosome - exchange of 9q with 22q, causes Chronic myeloid leukemia
What condition can gene duplication cause and how is it detected?
Charcot-Marie-Tooth syndrome type 1 from duplication including PMP22
Detected using FISH on interphase nuclei
What are copy number variations? (CNVs)?
Duplications and deletions not microscopically visible
Main source of human variation
Associated with human phenotypes but can be neutral
Often fixed segmental duplications
How so segmental duplications allow for evolution?
Generate redundant genes free to evolve
Can also generate further de novo rearrangements
What is a syntenic block?
Collection of contiguous genes located on the same chromosome, traits by the genes inherited together
What does the number of conserved syntenic blocks indicate?
Larger number = more evolutionary arrangements
What is the average gene composed of?
Non-coding intervening sequences
Non-coding control sequences (promoters, enhancers, etc.)
CpG islands
Small coding sequence
What indicates the presence of genes?
High GC content signifies areas with more concentrated genes
Are genes dispersed evenly throughout the genome?
No
What is a Cot renaturation curve?
Measures how much repetitive DNA is in a DNA sample
Used to study genome structure and organisation
What is repetitive DNA?
A sequence present more than once in a haploid genome
What is a gene family?
Genes present in more than one copy in a haploid genome
What’s an example of gene families providing variant proteins?
Beta globin cluster, change of expression throughout development
All carry oxygen in blood but decrease in oxygen affinity as human ages
What’s an example of gene families making a large amount of gene product?
Histone repeating units in sea urchins
What are the 2 types of interspersed repeats?
SINEs (short interspersed nuclear element) - Alu most abundant
11% genome
LINEs (long interspersed nuclear element) - L1 most abundant
17% genome
Where can SINEs be interspersed?
Within and between genes
How do most interspersed repeats spread?
Retrotransposition
Integrated using reverse transcription - LINE encodes RT
What are negative effects of interspersed repeats?
Can cause insertional mutagenesis and genome rearrangements
What are VNTRs?
Variable number tandem repeats Can be: Satellite - >100 bp Minisatellite - 15-100bp Microsatellite - <15bp
Why are VNTR repeats variable in number?
Unequal crossing over
DNA replication slippage
DNA repair
What is genetic fingerprinting?
Detected repeat numbers in individuals eg. using minisatellites - generated 1st fingerprints
Microsatellite VNTRs now amplified by PCR so they can be detected, held as genetic profiles
Repeat number is reliably inherited throughout pedigrees
What causes triplet repeat diseases?
Length variation in specific unstable trinucleotide repeats (microsatellites)
Expansion beyond a critical number is associated with disease
Eg. neurogenerative disorders like Huntington’s disease
What does epigenetic mean?
Mitotically heritable states of gene expression that cannot be explained by changes in DNA sequence
What makes up chromatin?
The nucleosome, made up of a core histone ocatamer plus DNA
What is heterochromatin?
Tightly packed DNA, transcriptionally inactive
Constitutive and facultative forms
What is euchromatin?
Open and active DNA, nucleosomes look like a bead on a string
What part of the chromatin can be modified to alter its structure?
The histone tail
What does acetylation of lysine do?
Acetylated chromatin on H3 and H4 tails opens up chromatin making it transcriptionally active
HAT acetylises, HDAC deacetylises
What does methylation of lysine residues do?
Context specific:
H3K4 tri-methylation associated with active genes
H3K9 tri-methylation associated with chromatin condensation (recognised by HP1)
What is ChIP?
Chromatin Immunoprecipitation
Detects DNA sequences associated with specific chromatin modifications
Steps of ChIP
Cell lysis Sonication Fragmented chromatin Immunoprecipitation with antibody DNA purification Analysis - eg. sequencing
What are the 3 chromatin changes associated with gene activity change?
Histone modification
Histone re-modelling (moving nucleosomes)
Variant histones
How is specificity achieved for kinetochore assembly?
Centromeric chromatin contains CENP-A (variant H3) and is flanked by pericentromeric chromatin (H3K9 tri-methylated)
What causes Position Effect Variegation (PEV) in Drosophila?
Chromosomal inversion can result in the w+ gene being located close to the heterochromatic region - can cause gene silencing
What do Suvar genes do?
Have a role in forming heterochromatin with HP1
What are examples of highly methylated sequences?
Satellite DNAs, repetitive elements, intergenic DNA, exons of genes
What does DNA methylation usually signify?
Repression
Which sites are mostly methylated?
CG sites (70-80%)
What CG sites aren’t methylated?
CpG islands: Around 1kb long Mark promoters and 5' regions of genes Open chromatin Normally unmethylated even if not expressed
How does methylation lead to chromatin modification?
Methyl-CpG recognised by proteins with methyl DNA-binding domain
Recruit chromatin repressor complexes
Unmethylated CpG recognised by other proteins
Recruit chromatin activating complexes
Why and how does X inactivation occur?
Would have double gene expression in females (XX) so inactivated in dosage compensation
Inactivation occurs through heterochromatin formation
What happens to CpG island in inactivated X
Become methylated, except X inactive specific transcript (Xist), CpG island methylated on active X instead
What does Xist do?
Coats the inactive X chromosome and recruits chromatin modifications and DNA methylation
