genetics: epigenetics:

Transcription

1 Thomas Cline practicing developmental geneticist (Drosophila melanogaster) former Berkeley undergrad ( 64-68) My goals: genetics vs. molecular biology biochemistry molecular genetics Office hours: Monday 5-6pm (door 5:15p) Friday 4-5 pm 11 Koshland Hall What distinguishes the way geneticists work and think? and it is a different (more abstract) way of thinking as illustrated by: How do geneticists operationally define the gene? How do geneticists generate and use genetic variation? finish up with some sex ed. Topics for today: From your textbook s glossary: recombination (genetic maps) complementation (bacterio)phage as an experimental system genetics: the science of heredity famous geneticists Reading for today and Monday: Chapter 7 (and skim Chapter 8) epigenetics: study of states of gene functionality that are not encoded within the DNA sequence but that are still heritable from one generation to the next. Problems: Chp 7, From your textbook s glossary: From your textbook s glossary: genetics: the science of genes genetics: the science of heredity genes epigenetics: study of states of gene functionality that are not encoded within the DNA sequence but that are still heritable from one generation to the next. gene: basic unit of biological information; specific segment of DNA in a discrete region of a chromosome that serves (only in cis) as a unit of function by encoding a particular RNA or protein. encodes what what about aspects relevant to when? where? how much? 1

2 gene: basic unit of biological information; specific segment of DNA in a discrete region of a chromosome that serves (only in cis) as a unit of function by encoding a particular RNA or protein. gene: basic unit of biological information; information?: a difference that makes a difference w/ respect to biological function What do we do with the Drosophila Dscam gene? (Down syndrome cell adhesion molecule) encodes 38,000 different proteins (via alternative pre-mrna splicing) (Drosophila has only ~13,000 genes) Here is a difference that makes a difference: nonsense DNA sequence gene DNA sequence VS. (encodes nothing (encodes particular RNA or protein) such as DNA between genes?) information?: a difference that makes a difference gene DNA sequence (encodes particular RNA or protein) nonsense DNA sequence VS. (encodes nothing such as DNA between genes?) Here is a difference that makes a difference: gene DNA sequence (encodes particular RNA or protein) nonsense DNA sequence VS. (encodes nothing such as DNA between genes?) This is NOT the difference that really concerns geneticists. vs. genetic map Mendel defined alleles (but it is not a particularly useful definition): The difference that really concerns geneticists: given: Heritable character difference (e.g. seed color) alleles: alternative forms of a single gene IF: i.e. DIFFERENT forms of a single gene If you understand the concept of allelism, you will understand what genetics is all about and what geneticists mean by genes hybrid yellow (genotype) (phenotype) (color & breeding behavior) 2

3 IF: hybrid yellow (genotype) (phenotype) (color & breeding behavior) exactly hybrid yellow Then: This particular seed color difference is due to a difference in (the alleles of) a single gene Y & y are alleles; hybrid yellow is Y/y in the limit: NOTHING ELSE (with respect to seed color & breeding behavior) This is a negative test: something is defined by not seeing something, but how hard do we have to look before reaching a conclusion? THE CHARACTERS: and by extension the allele differences responsible for the difference between the recessive and dominant characters hybrid yellow Y vs. y are alleles as defined by MENDEL s segregation test (1) unchanged in the hybrid (2) segregate randomly during meiosis The gene defined as the unit of segregation during meiosis ( not with respect to function) hybrid yellow Another problem with a segregational test for allelism: What if there are really TWO genes responsible for the difference that are very closely linked? AB/AB ab/ab The gene defined as the unit of segregation during meiosis ( not with respect to function) AB/ab self almost all: AB/AB AB/ab ab/ab but occasionally rare recombinants ( non-parentals ) such as: Ab/ab 3

4 AB/AB ab/ab AB/ab self almost all: AB/AB AB/ab ab/ab How hard do we have to look before deciding we must be dealing with a single gene difference? but occasionally rare recombinants ( non-parentals ) such as: Ab/ab Problem with the segregational definition of allelism (= definition of the gene as the unit of segregation) arose in the case of multiple alleles difference between pb. white eosin vs. white + = one gene diff. = alleles difference between pb. white -1 vs. white + = one gene diff. = alleles difference between pb. white -1 vs. white eosin = one gene diff. = alleles (all based on Mendel s test for segregation) Hence, two different alternative mutant forms (w e = orange, & w -1 = white) of one wildtype gene: white + (= red) w + w -1 w e What s the problem with multiple alleles? w -1 /w eosin w -1 /Y Must not be true alleles (true alternative forms of the same gene) but rather pseudoalleles y - w -1 sn - / y + w e sn + y + w + sn - y - w + sn + very rarely: w + /Y (hardly unchanged in the hybrid ) Isn t this just a revertant? 1) only from heterozygous moms 2) always associated with recombination of flanking genetic markers and a specific nonparental arrangement of those markers! genetic map: yellow w -1 w e singed white-a white-b genes as beads on a string genetic map: yellow w -1 w e singed white-a white-b genetic map: yellow w -1 w e singed white-a white-b genes as beads on a string Didn t pass the smell test for two (pseudo)genes? Didn t pass the smell test for two (pseudo)genes? Because: w -1 /w eosin hybrid looked different from wildtype Because: w -1 /w eosin hybrid looked different from wildtype But according to Mendel, it is the segregation of information for a difference between pure-breeding parents, rather than the looks of the hybrid, that defines a single-gene differenc (what we now would call a monogenic traite ) 4

5 The first example of pseudoallelism was lozenge: Gene A Gene B Aa Bb ---> could get a lz + allele out by recombination The cis-trans (complementation) test, 1949: lozenge (M. Greene) Two different recessive mutants, both with the same phenotype (small eyes and fused facets). Are they mutations in the same gene? Make two different fly lines and compare their phenotypes. And many more cases followed in flies, and even more in micro-organisms where one had much greater mapping resolution power (almost everything degraded into pseudoalleles when you looked closely enough) Cis: Trans: Cis: Trans: This is a control experiment. The flies should be wild-type regardless of whether BS and g are in the same gene or not. If flies are normal, then mutations are in different genes. If the phenotype is still mutant, then BS and g must be in the same gene!!! This is a control experiment. The flies should be wild-type regardless of whether BS and g are in the same gene or not. If flies are normal, then mutations are in different genes. If the phenotype is still mutant, then BS and g must be in the same gene!!! A test for allelism (a definition of the gene) based on the PHENOTYPE OF THE HYBRID (function, not segregation & NOT MENDEL!) white 1 e white 1 e genetic map based on segregation frequencies meiotic recombination can separate the parts of a gene like white or lozenge Raises important questions genetic map based on segregation frequencies How does a genetic map of regions within a gene as defined by the complementation test compare with that for regions between genes as defined by the complementation test? do true segregational alleles exist, and if so, how do they compare with functional alleles? 5

6 In thinking about how to answer those two important questions, consider what the master said: American Naturalist, v56 p32 (1922) =bacteriophage bacteriophage + d Hérelle substance Fig p228 6