User:Petersoapes/sandbox

Meiotic Recombination

During meiosis (that is, how an individual creates reproductive cells -- to create offspring for the next generation) (In every species) there is programmed machinery to ensure that copies of the maternal and paternal chromosomes <come together>// join in a CO/Holiday junction/ or heterodulex DNA molecule. (structure of 4 DNA strands). <A genetic outcome is that the 2 homologous chromosomes exchange portions of their material to result a chromosome distinct from either the original paternal chromosome, because it connects mutations that may have been unique to one parent onto the same DNA molecule/chromosome. It is the rate at which the homologous chromosomes in an individual recombine/exchange that is the recombination rate. recombination rates averages and variance are different within individuals (cell to cell variation), across sexes (oocyte to spermatocyte variation) and across species (interspecific variation).

events in recombination DSBs -> strand invasion -> heteroduplex DNA -> HdJ resolution -> CO chromosome

meiosis is the process (in diploids) of genomic duplication followed by 2 divisions (reductional and divisional) resulting in haploid cells. or mathmatically 2n -> 4n -> 2n -> 1n

meiotic recombination is a subset of genetic recombination and generally refers to the genetic recombiantion between homologous chromosomes during meiosis. Other forms of genetic recombination can occur in bacteria or in somatic cells. Meiotic recombination can happen incorrectly in 3 ways (and can result in deletions, duplications of inversions) intrachromosomal recombination,ectopic recombination, and homeologous recombination

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Cellular Function The main reason for meiotic recombination is theorized to ensure proper segregation. While there are species that have one sex with a achiasmate method of segregation, no sexually reproducing species produce all gametes without COs. Chiasmate or COs create the tension between bivalents needed to pass the spindle checkpoint in prophase I of meiosis. Failure to form a chiasmata or placement in the incorrect place can result in mistakes during segregation and annueploidy.

molecular events meiotic recombination begins in prophase I of meiosis. DSBs are formed by the topoisomerase (as a dimer) which directs cuts across the DNA in the chromosomes. The ends of the breaks are re-sectioned (or cut back) and the ssDNA is stabilized by supporting proteins, such as RAD51. For most orgainisms, after DSBs are made, the single strands of DNA proceed through homology searching, where by they find matching sequence on the homologous chromosome. After homologous chromosomes are lined up, a proteinacious structure, called the synaptonemeal complex starts to form. The DNA in forms of chromatin, transitions from a messy form to a more linear form to make the homologous pairing easier. The axial / lateral elements start to form first at (nucleation?) sites. <at the early sites of the SC, the chromatin starts to form loops, with the bottom of the loop associated with the SC proteins which hold it in place. The size of the DNA loops control the relative size of the SC. It is along the length of the SC that DNA strands from the 2 homologous chromosomes come together and are able to participate in Crossing Over.

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Theoretical Models most advances in the theory of the evolution of recombination rate has been through explaining the effects of physical linkage. That is, making predictions for LD in sequences.

Population genetic implications <kondroshov hatchet> and overcoming Muller's ratchet. breaking up unfit alleles/linkage and bringing together Only mutation creates new genetic variation (by creating new alleles), but recombination plays a very important role in creating new combinations of alleles (for selection to act on).

recombination and DNA repair//similarities to mitotic recombination

Methods to measure Recombination LD and Linkage Maps genetic maps first created... have been used since the beginning of the genetics field. requires sequence information of both parents and the offspring. <stretches of DNA sequence are inferred by markers or sequenced in the parent to find unique combinations of mutations/alleles. <recombination is detect in an offspring when parental unique alleles are found on the same chromosome. (this process isn't detected until meiosis in the F1 offspring -- so the F2 offspring needs to be measured to uncover this information)

when this method was first being developed by the <struarvant and Morgan lab> genetic markers -- mutations that resulted in a phenotypic change were used to infer information about the sequence.

Cytological counting of COs Immunohistology applied to meiotic cells allows for the visualization of cellular markers and features indicating recombination. First developed/used by Anderssen (yr?), this technique has several advantages; including that it does not require knowledge of the genomic sequence or it is agnostic to the sequence (ie it can be used on non-model organisms). Secondly it is much cheaper than sequencing costs.

Variation in Recombination Rates

Recombination varies at several scales

Fine Scale

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Sub-chromosomal Scale

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Genome wide scale

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Sexual Dimorphism, Heterochiasmy

Meiosis in both sexes serve the main purpose of producing haploid cells through the process of 2 cell divisions without DNA replication. It has been difficult to distinguish which aspects are the same across sexes and which follow sex specific patterns. Research has found that the cellular processes as similar in both sexes through prophase I. That is early in the cellular development pathway before gametogenesis specializes into the specific gametes. Heterochiasmy, or differences in recombination rates offers is an example of an early split in the meiotic pathways; DSBs are created in prophase I, COs and Holliday junctions are formed and resolved by diakinesis of prophase I. (this supports the comparison of molecular processes across the sexes -- The fundamental actions of molecules is likely to be conserved (motor proteins, spindle assembly ect.) but the expression, modifications, timing and control (ie. checkpoints) of these processes are likely to present the most dimorphic patterns.

points of dimorphism 1 Spindle checkpoint -- when proteins important for the spindle checkpoint are knocked out, a general pattern observed is that male fertility is more extremely impaired than female fertility. This pattern observed in multiple models (and other forms of evidence) seem to indicate that the spindle checkpoint is more extreme in males. A possible process which may produce the sexual dimorphism in recombination rates is the resolution of Holliday junctions. It is known that DSBs numbers are decoupled from final CO number -- whether DNA heteroduplexes (Holliday junctions) are resolved into CO (or NCO) is possible point of regulation in the recombination pathway. (ref Cole, Klenckner)

2. Pachytene Checkpoint there is also a checkpoint in the pachytene stage -- but data indicating strong dimorphic patterns are lacking.

mammals

Celegans

yeast

plants

zebrafish MLH1 staining in Zebrafish has revealed distal positioning of chiasmata in spermatocytes . The following study also found RPA foci (as an markers of early SC formation) tend to occur at the ends of chromosomes. a later study finds that there are similar sex-specific patterns of recombination in Zebra fish, that is both in the chiasmata positioning and degree of genome wide recombination (1:1.55 male to female ratio of recombination)

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meiosis vs gametogenesis