wk10-DNA recombination I

How can homologous recombination lead to gene conversion?

-Heteroduplex DNA that is created by recombination can have mismatched sequences where the recombining alleles are not identical -repair systems may remove mismatches by changing one of the strands so that sequence is complementary to the other→two copies of the same allele→gene conversion -two possible ways this can occur(mechanisms):or both 1-DNA mismatch repair 2-DNA gap repair synthesis

Gene conversion

-Zickler used the term to describe a phenomenon in which one allele is converted to the allele on the homologous chromosome through recombination -studies by several researchers confirmed this phenomenon in yeast and Neurospora -occurred at too a high rate to be explained by new mutations -research showed that gene conversion often occurs in a chromosomal region where a crossover has taken place

Gene conversion by Mismatch DNA repair

-mismatch repair of heteroduplex may result in gene conversion 1-two parental chromosomes had diff. alleles due to a single-base-pair difference in their DNA sequences 2-during recombination, branch migration occurs across this region→creates 2 heteroduplexes with base mismatches 3-DNA mismatches are recognized by DNA repair systems(non Watson and Crick) and repaired to a double helix that obeys the AT/GC rule •2 mismatches can be repaired in 4 possible ways: >two→no gene conversion >two→gene conversion

Evidence for the Holliday model

-model can account for the general properties of recombinant chromosomes formed during eukaryotic meiosis -original model based on results in fungi→products of meiosis are contained in a single ascus -molecular research in other organisms supported the central principles of the model -convincing evidence comes from EM studies in which recombination structures can be visualized -structure has been called a chi form→shape similar to the Greek letter Χ(chi)

Refinement of the Holliday Model

-more detailed studies of homologous recombination led to a refinement of the Holliday model -more recent models modified the initiation phase of recombination >homologous recombination is not likely to involve nicks at identical sites in one strand of each homologous chromatid >more likely for one DNA helix to incur a break in both strands of one chromatid or a single nick >either of these is enough to initiate recombination

Crossing over between sister chromatids: Sister chromatid Exchange(SCE)

-occurs in meiosis I and occasionally in mitosis = a cross over that occurs between sister chromatids >sister chromatids are genetically identical→doesn't produce recombinant alleles

Crossing over between homologous chromosomes: Homologous recombination

-occurs in meiosis I and occasionally in mitosis =crossing over that occurs between non-sister chromatids 1-pair of homologous chromosomes align 2-breakage at analogous locations 3-exchange of corresponding segments 4-non parental recombinant phenotype produced >often have diff. alleles >can make recombinant germ cells/chromosomes -often goes wrong →why most fertilisation never occurs

recombination nodules

-only visible link between two sides of synaptonemal complex -spherical/cylindrical structures observed in fungi + insects -lie across the complex -occur with same frequency and distribution as chiasmata→may be sites of recombination

Structure of the synaptonemal complex

-tripartite structure -axial element: a proteinaceous structure around which the chromosomes condense at the start of synapsis -lateral element: a structure in the synaptonemal complex that forms when a pair of sister chromatids condenses on to an axial element >2 lateral elements -central element: a structure that lies in the middle of the complex, along which the lateral elements of homologous chromosomes align >separates lateral elements from each other >fine but dense

genetic diversity from homologous recombination

-crossover → genetic diversity -gene conversion is impt in evolution and recombination

Molecular view of synaptonemal complex

-distinctive structural features due to 2 groups of protein: 1-cohesins: form a single linear axis for each pair of sister chromatids from which loops of chromatin extend -equivalent to lateral element >stick things together 2-lateral elements are connected by transverse filaments that are equivalent to the central element. >transverse filaments are formed from Zip proteins >zip proteins zip up homologous chromosomes for crossing over >crossing over happens where there is no Zip proteins -each pair of sister chromatids has an axis made of cohesins -loops of chromatin project from the axis -synaptonemal complex is formed from linking together axes by Zip proteins

Homologous recombination

-exchange of genetic material between non-sister chromatids on homologous chromosomes →from one homologous chromosome to another -can be seen under microscope due to being condensed (metaphase) -occurs at chiasmata=where crossing over happens -increases genetic variability of products

resolution

-final process of recombination -involve the breakage and rejoining of two strands to create two separate chromosomes

Gene conversion by DNA Gap Repair Synthesis

-gap repair synthesis can lead to gene conversion according to the double-strand break model 1-top chromosome carrying the recessive b allele suffers a double-strand break in this gene→gap is created by the digestion of the DNA in the double helix→b allele is eliminated 2-two template strands used in gap repair synthesis are from one homologous chromatid→helix carries the dominant B allele -complimentary strand encoding the B allele invades the region of the recipient and provides the template to synthesis the ds region 3-after gap repair synthesis and resolution takes place the top and bottom chromosome both carry the B allele >Gene conversion changed the recessive b allele → dominant B allele -genes with alleles are often recombination hotspots→genetic diversity -how DNA repair often works

The Double-Strand break repair model(DSBR) of recombination

-initiated by making a double-strand break in one (recipient) DNA duplex -relevant for meiotic and mitotic homologous recombination -In 5' end resection: >exonuclease action generates 3'-single-stranded ends that invade the other (donor) duplex -DSBR is a way of replacing damaged pieces of DNA→hot spots for recombination >explains why chromosomes recombine at recombination hot spots >DNA damage is linked to recombination >needs a template 4 repair

What is genetic recombination?

-involves chromosomes breaking and rejoining→new combinations -exchange of genetic material but at molecular level -its complex and depends on type of DNA

1-Homologous recombination

-between DNA segments that are homologous→no identical but v. similar -segments break and rejoin to form new combinations -requires crossing over in order for segments to swap

2 ways the 2 Holliday Junctions can be resolved

-branch migration→Holliday Junction resolution→recombinant/non recombinant chromosomes+short heteroduplex -end result can be non recombinant or recombinant containing a short duplex heteroduplex depends on whether junctions are resolved vertically or horizontally •horizontally→non recombinant chromosomes •vertically→recombinant chromosomes

Crossing over in prophase

-chromosomes must synapse(pair) for chiasmata to for 1-synaptonemal complex forms to join up the homologous chromosomes→runs up length of chromosome 2-bivalent forms that holds structure at exchange site >if not held up→chromosome breakage 3-alignment across chiasmata >site is freed so crossing over can occur >synaptonemal complex dissociates where crossing over is mean to occur

Synaptonemal complex

-connects recombining meiotic chromosomes -chromatin=DNA -joining -held together in central element -early meiosis (prophase): homologous chromosomes are paired in the synaptonemal complex =morphological structure of synapsed chromosomes -proteinaceous complex(axial element): separates the mass of chromatin of each homolog from the other -brings chromosomes into juxtaposition -120nm wide

The Holliday Model for Homologous recombination

-proposed by Robin Holliday in 1964 -discovered under EM -first model of homologous recombination

When does homologous recombination occur in meiosis I?

-recombination occurs during the first meiotic extended prophase

Resolving the Holliday Junction

-resolved into 2 separate duplex molecules by nicking 2 of the connecting strands -recombinant formation depends on which strands are broken

2-site specific recombination

-when non homologous DNA segments are recombined at specific sites in the chromosomes -involves consensus DNA sequences

3-Transposition

-when small segments of DNA(transposons) move from one site in the genome to another (within the host's chromosomal DNA)

3 main types of recombination

1-Homologous recombination 2-Site specific recombination 3-Transposition

2 new proposed models

1-Matthew Meselson and Charles Radding(1975): -single nick in one DNA strand initiates recombination 2-Jack Szostak, Terry Orr-Weaver, Rodney Rothstein and Franklin Stahl(Double strand break model): -suggests that a double-strand break initiates the recombination process >recent evidence suggests that double-strand breaks commonly promote homologous recombination during meiosis and DNA repair

What happens in DSBR?

1-a small region near the break is degraded→single-stranded DNA segment that can invade the intact double helix and base pair with it 2-strand displaced by the invading segment forms a branched structure called a displacement loop(D-loop) >after D-loop is formed→2 regions have a gap in DNA >provides a template for new piece of DNA 3-DNA gap repair synthesis: =DNA synthesis that occurs in the short gaps where DNA strand is missing >produces 2 Holliday Junctions -strand exchange→stretch of heteroduplex DNA→consists of one strand from each parent

What happens in the Holliday Model for Homologous recombination?

1-homologous chromosomes align 2-nick occurs at identical locations in one strand of each of the 2 homologous chromatids >nick is essential for strand exchange >2 alleles: A+B and a+b >variations of an allele found in chromatids 3-DNA strand invades the homologous region in the other duplex and base-pair with the complementary strands 4-covalent joining of the invading strand to the homologous strand forming a region of crossed DNA=Holliday Junction=cross structure formed due to interaction between 2 homologous chromatids 5-Holliday Junction can move in a lateral direction(from L→R) by branch migration >movement by strand displacement: a strand in one helix is swapped for a DNA strand in another helix→extending interaction 6-sequences of homologous chromosomes are similar but not identical→2 heteroduplex regions(diff. sequences on both strands)→contain mismatched pairs >mismatches form b4 repair resolved by Holliday Junction resolution

2 ways that the Holliday Junction is resolved(2 different planes)

1-without isomerization: breakage occurs in the same 2 DNA strands that were originally nicked at the beginning of this process→joining of strands→nonrecombinant chromosomes+heteroduplex region 2-with isomerization: breakage occurs in the strands that were not originally nicked→rejoining process→recombinant chromosomes+ heteroduplex region >same structure but rotated 180°=cruciform structure

heteroduplex

=a region in the dsDNA that contains base mismatches

Crossing over

=exchange of material from one chromosome to another -Use: >in meoisis(mostly I)→produces genetic diversity and forms chromosome segregation >in mitosis→repairs DNA damage and stalled replication forks -2 types between replicated chromosomes in diploid species depending on where it takes place 1-results in recombinant chromosomes 2-results in non recombinant chromosomes -no crossing over between A and B genes→only non-recombinant gametes

Branch migration

=the ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous -new DNA synthesis replaces material that has been degraded -branch migration can occur in either direction when an unpaired single strand displaces a paired strand