BIO-5009A 2024 Model Organisms Part 2 PDF

BIO-5009A Genetics BIO-5011A Clinical Genetics 2024 Model Organisms – part 2 Dr Philip Leftwich – [email protected]  Deep dive on Drosophila Model Life history organisms - 2 Genome features Learning Resources Outcomes  Drosop...

BIO-5009A Genetics BIO-5011A Clinical Genetics 2024 Model Organisms – part 2 Dr Philip Leftwich – [email protected]  Deep dive on Drosophila Model Life history organisms - 2 Genome features Learning Resources Outcomes  Drosophila melanogaster Order Diptera Family Drosophilidae Genus Sopophora Human commensal Found on every continent (except Antarctica) A powerful model organism Easy to care for, many offspring, short generation time Well studied genome  Life cycle Gene expression shifts that initiate Drosophila metamorphosis mediated by the hormone ecdysone Metamorphosis – larval tissues break down, adult tissues develop from 19 imaginal discs (tissue-specific progenitor cells) https://doi.org/10.1146/annurev-ento-  Husbandry Wild Drosophila feed on yeast, bacteria and rotting plant matter In the lab – standardised diets consist of cornmeal/yeast/agar Adult flies lay their eggs on the food surface, larvae hatch and burrow into the food. Wandering third instars crawl out and pupate on the sides of vials  Genome Features The entire D. melanogaster genome size is estimated at ∼180 Mb Four pairs of chromosomes, one sex chromosome, two standard autosomes, one ‘dot’ chromosome  Sex Determination The presence of a Y chromosome does not directly participate in sex determination in fruit flies. Sex determination in D. melanogaster is regulated by an X chromosome counting mechanism that “senses” the dosage of X chromosomes XO flies are males due to the decreased X dosage. https://doi.org/10.4161/  Genome Features The first physical maps of chromosomes were created by Calvin Bridges in 1935 Drosophila have polytene chromosomes in the salivary glands Adding a chemical dye to polytene chromosomes gives rise to unique banding patterns for each chromosomal region; these banded regions were numbered Genome Features  Genome Annotation 13,920 protein-coding genes predicted based on the latest genome assembly modENCODE data – 72% of the genome is “functional” More than half of D.melanogaster genes show alternative splicing 45% of genes produce more than one protein https://dx.doi.org/  Forward Genetics - mutagenesis Applications – Work by the Heberlein lab found genes associated with alcohol tolerance and alcoholism barfly & tipsy Showed that neural responses have a basic similarity with humans Singh and Heberlein 2000  Reverse Genetics Analyse the phenotype of a specifically edited gene - Direct gene editing - Transgenics - UAS/Gal4 & P-elements  Transposable elements ~ 150 families of transposons in the D.melanogaster genome TEs are often deleterious, as they can insert into genes or cause chromosomal rearrangements The P element https://doi.org/10.1016/0092- Transgenics Gal4/UAS  Gal4/UAS – Muscle tissue drivers One UAS-GFP reporter line x 3 different Promoter gene – Gal4 lines http://dx.doi.org/10.7717/peerj.4167 Gene knockout  Crosses and balancers Gal4 lines – c.9000 UAS lines – 6000 Balancer lines – 400  Drosophila for the win! https://doi.org/10.1016/ j.coi.2013.01.008 https://doi.org/10.1534/ genetics.115.185157  Deep dive on Drosophila Model Life history organisms - 2 Genome features Learning Resources Outcomes Further Reading – Genetics: from genes to genomes Core reading - Chapters 1& 2: Heredity - Chapter 5: Linkage, Recombination, Gene mapping - Chapter 19: Manipulating the Genomes of Eukaryotes Extra reading - Chapter 22: Genetic Analysis of Development