Week 5 Reflections

It was all about recombination! We learned about the inheritance patterns of linked genes nearby one another on a chromosome, most importantly how to quantitatively express the incidence of co-inheritance of linked markers in terms of recombination frequencies (or, genetic distance as measured in cM). In addition, we gained an understanding of how patterns of genetic distance between marker genes with clear associated phenotypes led to the creation of genetic maps: maps revealing the relative ordering of genes along chromosome physical space. These genetic maps have been enormously helpful to both scientists learning about genetic and other biological processes in their study systems, and also to plant and animal breeders interested in producing high-value crops and livestock in the world of agriculture. The three-point testcross – appearing in lecture, homeworks, and recitation – illustrates the basic logic that underlies the construction of genetic maps.

We also learned about recombination rates (not covered in the book).  This is an expressed as the genetic distance (in cM) divided by the physical distance (in Mb).  Looking at recombination this way, it becomes very apparent that different regions of DNA can vary extensively in term of how ‘recombinogenic’ they are.  A human chromosome example was provided, showing lots of recombination hotspots, and coldspots, across the length of the chromosome space.

We started to talk about the molecular mechanism of homologous recombination on Thursday and I discussed things a bit differently than the treatment in the book.  Understanding the molecular DNA-level actions and movements of DNA during recombination has been a central area of genetics research for decades. This was an area of great controversy for a very long time, until the development of the double-stranded DNA break and repair (DSBR) model was established, which has been well-accepted and experimentally supported every since. The first model was the Holliday Model which posited that the whole process began with a pair of single-stranded DNA nicks at homologous positions at the two participating DNA molecules. After nicking, reciprocal strand invasion occurred (forming Holliday or chi structure) followed by branch migration followed by endonucleolytic resolution. Though many of the details were right, the Holliday model was ultimately discounted because there was no known enzymatic activity that could cause ssDNA nicks at the same exact (homologous) sites in two DNA molecules – still nothing known to this day that can do that. The Meselson-Radding (M-R) Model modified things by suggesting that a single-stranded nick could start the process – the free end of the nicked strand (“donor strand”, gray in diagram) could then carry out strand invasion of the “acceptor” DNA molecule (pink in diagram) which would then cause a displacement loop (or, D-loop) strand from the acceptor that could undergo base-pairing with homologous sites in the invading molecule. This model was widely regarded as essentially correct, but there was still one puzzle related to recombination – gene conversion – that could not be explained by the M-R model. Gene conversion, originally only observed in certain species of fungi, is a process whereby there is allelic “conversion” during meiosis that is in opposition to predictions of basic Mendelian genetics (e.g. one ‘a’ allele is “converted” into a ‘A’ allele in the example shown). Since this phenomenon was only observed in gametes, it was presumed to be closely associated with a meiosis-specific process such as recombination. This led researchers to develop the double-strand break & repair (DSBR) model. The DSBR model has been strongly supported over the last few decades in all lab experiments and is also able to effectively account for gene conversion. At the end of the DSBR mechanism there are tracts of DNA at the end of the process where there is base pairing between nucleotides from the “donor” strand and the “acceptor” strand. There is the possibility of nucleotide mispairing between these two strands (because they originally came from different dsDNA molecules) – these mispairings are recognized by the mismatch DNA repair enzymatic machinery that ultimately removes one of the mismatching nucleotides and replaces it with a correct complementary base. Thus, there is the possibility in this DSBR path for one allele to be converted into the other allele! Since this was all worked out, we’ve come to discover that gene conversion outcomes occur much more frequently than recombinant chromosome outcomes of the molecular recombination process in virtually all eukaryotic life forms, from fungus to human.

Week 6 Sneak Peek: Next week we will quickly recap recombination, and then transition to talk about the mutation process (Ch. 12) on Tuesday. On Thursday we will talk about the molecular genetics of cancer (Ch. 13), and how yeast (a single-celled organism…) provided key insights into the genetic underpinnings of cancer in humans.

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