mcb 134 final (lecs 13-18)

cellular metabolism, UV light exposure, ionizing radiation, chemical exposure

issues with fork-stalling and collapse can cause DSBs

homologous recombination (HR) and non-homologous end joining (NHEJ)

HR, it is regulated by many proteins and phospho-cascades

increase generic diversity

errors in crossovers can lead to chromosomal abnormalities; can also lead to hybrid sterility or inviability

NHEJ, the break ends are directly ligated without the need for a homologous template and errors occur when overhangs are not perfectly compatible; leads to mutagenesis

when the blunt end of a section of double-stranded DNA is modified by cutting away some nucleotides from the 5' end to produce a 3' single-stranded sequence

Ataxia telangiectasia (mutation in ATM), and bloom's syndrome (mutation in DNA helicase)

1. MRN recognizes DSB and coats with RPA polymers. 2. BRCA2 replaces RPA with Rad51. 3. Rad51 mediates strand invasion and homology search

stall the cell cycle, block replication, and facilitate repair

ATM: phosphorylates several key proteins (like p53) that initiate activation of the DNA damage checkpoint

apoptosis or genome instability, and diseases

ATM, prevents phosphorylation of H2A/variants critical for proper repair

access (chromatin remodelling factors), repair (repair machinery), restore (chromatin assembly factors)

must open chromatin and silence gene transcription for repair, then remove machinery and restore marks when repair complete

modifications can facilitate nucleosome removal and recruitment of resection proteins

keeping nucleosomes, recruiting NHEJ factors and blocking HR factors

membraneless condensates that form at the site of repair, multiple DSBs cluster

liquid fusion

53BP1 is recruited by phospho-gamma H2AX and its reader MDC1; 53BP1 recruits p53

concentrated at DSBs

repeats on non-homologous chromosomes can cause abberant recombination, resulting in acentric, dicentric, and/or translocations

loop extrusion brings rest of TAD into contact WITH ATM/ATR

uses spatial-temporal dynamics to ensure repeat stability

inside: MRN recognition, resected DNA coated with RPA polymers, SUMO added to repress RAD51 recruitment and anchor HC DSBs to nuclear periphery; outside: repression degraded, BRCA2 replaces RPA with RAD51 and repair completes

repeats concentrated in HC

if HC disrupted and unable to move, DSBs stay in HC, brings in RAD51 which leads to massive chromosome rearrangement and cells cant divide

no

they become visible in the nucleus

actin and myosin are active outside HC, but Brownian motion inside HC

method in which the phenotype of a double mutant is compared with that of single mutants.

They used epistatic analysis by investigating Depletion of Arp2/3 alone, Scar and Wash
together, Arp2/3, Scar and Wash together, and Scar or Wash alone. and found evidence suggeting that Scar and Wash
independently activate Arp2/3 for relocalization.

generate the genetic diversity critical to evolution and natural selection

2 fold cost, mating rituals

the initial contact and recognition between homologous chromosomes

the assembly of the synaptonemal complex between paired chromosomes, which zippers them up into side-by-side alignment

creates mechanical linkages between the nucleus and the cytoplasmic cytoskeleton; these connections lead to processive chromosome movements along the NE

in mitosis, all cohesion is released just before anaphase, in meiosis, arms lose cohesion in anaphase 1 but centromere cohesion stays until anaphase 2, so sisters stay together

phosphorylation primes Rec8 (part of the SMC complex) to be cleaved by separase. in meiosis 1, separase cleaves arm Rec8s, but shugoshin protects the pericentric Rec8 until meiosis 2

In mitosis, sister kinetochores attach to the opposite poles. In meiosis I, sister kinetochores attach to the same pole and homologous kinetochores attach to the opposite poles

meoisis 1 sister kinetochores attach to same pole, in meoisis 2 sister kinetochores attach to opposite poles

antagonizes kinase activity near the centromere by recruiting a phosphatase, protecting Rec8 from separase

trisomies; in 13, 18, 21, and X

the viable ones encode the least amount of genes, so having an extra has slightly less consequences

mother, meiotic chromosome segragation happens deacdes after meiotic prophase

"arrest" between prophase and segregation is not stable over long periods of time; time leads to erosion of cohesion, kinetochores, spindles, etc. environmental exposures also disrupt chromosome segregation

increases variation by generating new combinations of genes; unequal exchange among repeated DNA generates duplications and deletions, which can go on to become new genes/new functions

induced by topoisomerase-like enzyme, spo11

no, they are still repaired and result in local replacement of genetic information, not exchanging like in crossovers

provides counter-force to maintain tension between homologous kinetochores; also need cohesion between the sister chromatids

assurance = at least 1 crossover per pair of chromosomes; interference = crossovers far apart, often 1 per pair of homologs

no, suppressed by centromeres and telomeres

histone methyltransferase; epigenetically regulates the distribution of crossovers by upregulating the activity and recruitment of DSB induction machinery like spo11

binds to specific sequence determined by zinc fingers, then its SET domain modifies chromatin (H3K4me3 and H3K36me3) and recruits a reader that only binds tails containing both modifications

altered distribution of crossovers and non-crossovers; inefficient DSB repair

Both crossover and noncrossover recombination result in changes to sequences near DSBs, which is inconsistent with sequence-based determination of DSB hotspots

evolutionary arms race; PRDM9 is one of the most rapidly evolving genes, especially in the zinc fingers

sharing same ancestral PDRM9, one species may select for one variant, while the other may select for a different variant' these PRDM9 variants lead to hybrid incompatibility and will be infertile due to DSB abnormalities and meiotic segregation failures

COs located near centromeres or telomeres

deletions and duplications in gametes, which can be good or bad for evolution

no, can be determined by temperature, location, stress, etc.

sex chromosomes, haplodiploid, paternal chromosome elimination

homologs differentiated (like X and Y) in structure/sequence and function, can carry many genes that are necessary and/or sufficient to specify sex

males are haploid, females are diploid; Males come from unfertilized eggs, so a female that has not mated still produces male offspring

males are haploid, females are diploid; males inherit but fail to pass on their father's genome

heterogametic is the one with mismatched sex chromosomes;

male heterogametity

gene on the Y chromosome that determines (male) sex in eutherian mammals

obligate crossover in PAR1 to ensure chiasmata formation and normal meiosis 1 segregation

viable but defective development and/or fertility

higher, because crossing over is mandatory, and DSBs are needed for crossing over

unequal exchange in PAR region

Y chromosomes have large palindromes, so they are repaired through intra-chromosomal gene conversion (do not need a sister), which generates large deletions, leading to infertility

compensation for the difference in X chromosome gene dosage between males and females, since the X chromosome has so many more genes than the Y

Y determines sex, but one X is inactivated and one is active since they act through different mechanisms

mammals randomly inactivate 1 X chromosome in females, flies have double transcription rate of male X, and worms decrease transcription of X in hermaphrodites

mostly in females, present in males only if infertile (rare); mosaics only for X-linked genes

inactive X chromosome; curled up to not be expressed

X-inactivation is random in each cell, so if there is heterozygosity at the orange locus, different patches will express different colors based on the active X chromosome

most critical non-coding RNA locus on the X-inactivation center; contains tandem repeats crucial for gene silencing and recruiting epigenetic modifiers, creating the Barr body

anti-sense RNA that inactivates Xist

inhibits recuitment of active marks, recruits silencing modifications, and maintains silencing

without Xite, Tsix would be downregulated, thus more Xist-induced silencing than WT

In placental mammal early development, first nonrandom inactivation of paternal X, then reactivation, then random X-inactivation

dosage compensation in mammals evolved in two steps: a twofold hyperactivation of the X chromosome in both sexes to compensate for gene losses on the Y chromosome, and silencing of one X in females to restore optimal dosage

loss of SPEN is associated with deficient XCI at multiple loci

used an auxin-inducible degron (AID), which conditionally induces the degradation of any protein by the proteasome by adding auxin