Bi190-2013 Lecture 8 Genetic Pathways and Genetic Screens
WT A 2X:2A her-1 tra-1 1X:2A her-1 tra-1 Female body Male body Female body Male body her-1(lf) B 2X:2A her-1(lf) tra-1 1X:2A her-1(lf) tra-1 Female body Male body Female body Male body tra-1(lf) C 2X:2A her-1 tra-1(lf) 1X:2A her-1 tra-1(lf) Female body Male body Female body Male body tra-1(lf; her-1(lf) D 2X:2A her-1(lf) tra-1(lf) 1X:2A her-1(lf) tra-1(lf) Female body Male body Female body Male body
confused epistasis with non-null alleles AR cell c + AR cell survives d + neuroar forms e + neuroar makes E and is functional 100% Functional neuroar AR cell c 2 AR cell survives d + neuroar forms Functional 80% neuroar e + neuroar makes E and is functional 20% no AR 50% Functional neuroar AR cell c + AR cell survives d 2 neuroar forms e + neuroar makes E and is functional 50% no neuroar AR cell c 2 AR cell survives d 2 neuroar forms e + neuroar makes E and is functional 40% Functional neuroar 20% no AR 40% no neuroar
confused epistasis with non-null alleles h + OM cell h 1 OM cell j 3 OM cell h 1 j 3 OM cell gene H gene J black pigment black h + OM cell h 1 OM cell j 3 OM cell h 1 j 3 OM cell gene J gene H black pigment
If a hypomorph is epistatic to a null, an inference can be made genotype f + g + phenotype white pigment f null g + black pigment f + f null g hypo g hypo white pigment white pigment gene F gene G black pigment white pigment
combining epistasis with site of action
Additivity and less than additivity with incompletely penetrant loss-of-function alleles. A. The r1 and s1 alleles display additive phenotypes. B. T he t1 and u1 alleles display less than additive phenotype. A r + s + r 1 s + r + s 1 r 1 s 1 All alive 30% alive 30% alive 10% alive B t + u + t 1 u + t + u 1 t 1 u 1 All alive 30% alive 30% alive 30% alive
2 vulval lineage polarity wild-type phenotype Reversed phenotype wild-type wild-type polarity Reversed Polarity cdh-3::cfp; ceh-2::yfp Takao Inoue et al (Cell 2004)
A ligand-1 receptor-1 100% viable penetrance 0% ligand-1 receptor-1 30% viable 70% ligand-1 receptor-1 30% viable 70% ligand-1 receptor-1 30% viable 70% B ligand-2 receptor-2 100% viable 0% ligand-2 receptor-2 70% viable 30% ligand-2 receptor-2 70% viable 30% ligand-2 receptor-2 70% viable 30% C
A ligand-1 receptor-1 100% viable penetrance 0% ligand-1 receptor-1 30% viable 70% ligand-1 receptor-1 30% viable 70% ligand-1 receptor-1 30% viable 70% B ligand-2 ligand-2 ligand-2 receptor-2 receptor-2 receptor-2 100% viable 70% viable 70% viable 0% 30% 30% ligand-2 receptor-2 70% viable 30% C ligand-1 ligand-2 receptor-1 receptor-2 0% viable 100% ligand-1 ligand-2 receptor-1 receptor-2 0% viable 100% ligand-1 ligand-2 receptor-1 receptor-2 0% viable 100% ligand-1 ligand-2 receptor-1 receptor-2 0% viable 100% D ligand-1 ligand-2 receptor-1 receptor-2 100% viable 0%
C. elegans programmed cell death A wild type B photo of dying cell(s) http://www.wormbook.org/chapters/www_programcelldeath/pcdfig1.jpg C no cell death D all cell death
ced-3(lf) NO cell death ced-4(lf) NO cell death ced-1(lf), 2, etc No engulfment ced-9(gf) NO cell death ced-9(gf+lf) EXTRA cell death nuc-1 No DNA degradation ced-3(lf) ced-9(lf) NO cell death ced-3 (lf) nuc-1(lf) NO cell death
A ced-4(gf) or ced-3(gf) B ced-3(gf); ced-4(lf) C ced-3(lf); ced-4(gf) D pathway ced-9 ced-4 ced-3 cell death
Genetic Screens
Positive Modulation E A B C
Negative Modulation D A B C
A B gf C D Extra Product E A B gf C D Extra Product E A B gf C D lf Less Product E A B gf C D Product E lf
C. elegans EGF-receptor signaling: a branched signaling pathway
C. elegans Vulval Development Screen viable lethal/ste unknown dominant lin-1 16 lin-3 2 lin-25 2 lin-12 7 lin-2 13 lin-8 1 n300 1 lin-24 2 lin-7 13 lin-9 1 lin-33 2 lin-10 3 lin-13 2 let-60(gf) 1 lin-18 2 lin-26 1 lin-14 2 lin-31 11 let-23 1 unc-83 10 unc-84 16 let-60 0 lin-15 5 lin-45 0 lin-4 1 sem-5 0 lin-11 4 mpk-1 0 lin-17 5 lin-44 0
m=0.1 m=0.3 m=1 m=3
Empirical Saturation
Why no mutations? 1. Redundancy Do an enhancer screen to see if you can bias the threshhold. 2. Pleiotropy Use tissue specific promoters or mosaic screens 3. maternal rescue of phenotype/epigenetics go the extra generation 4. bad target (size, place in chromosome, refractory to mutagen, missing from collection) molecular biology
LET-23 EGF-R [IP2] PLCγ [IP3] [PIP2] ITR-1 IP3 Receptor SEM-5 Grb2 LET-341 SOS LET-60 RAS Ovulation Vulval development
Extragenic suppressors of partially defective LET-23 activated: LET-60 Ras loss of: UNC-101 = clathrin adaptor medium chain SLI-1 = cbl proto-oncogene homolog GAP-1 = GAP homolog Gregg Jongeward, Junho Lee & Charles Yoon
Enhancers of sli-1 mutations loss of: UNC-101 = clathrin adaptor medium chain ARK-1 = Ack-related Kinase GAP-1 = GAP homolog Junho Lee, Chris Lacenere & Neil Hopper
LET-23 EGF-R [IP2] PLCγ [IP3] [PIP2] ITR-1 IP3 Receptor SEM-5 Grb2 LET-341 SOS LET-60 RAS Ovulation Vulval development
let-23(lf) LET-23 EGF-R [IP2] PLCγ [IP3] [PIP2] SEM-5 Grb2 LET-341 SOS ITR-1 IP3 Receptor LET-60 RAS Ovulation Vulval development
let-23(lf) let-60(gf) LET-23 EGF-R [IP2] PLCγ [IP3] [PIP2] SEM-5 Grb2 LET-341 SOS ITR-1 IP3 Receptor LET-60 RAS** Ovulation Vulval development
let-23(lf) itr-1(gf) LET-23 EGF-R [IP2] PLCγ [IP3] [PIP2] SEM-5 Grb2 LET-341 SOS ITR-1 IP3 Receptor** LET-60 RAS Ovulation Vulval development
let-23(lf) let-60(gf) itr-1(gf) [IP2] LET-23 EGF-R PLCγ [IP3] [PIP2] SEM-5 Grb2 LET-341 SOS ITR-1 IP3 Receptor** LET-60 RAS** Ovulation Vulval development
mutagenize! +! Balancer A! X! Balancer A! Balancer B! m! Balancer B! X! Balancer A! Balancer B! F1! B non-a! m! F2! Balancer B! X! Non-B non-a! m! F3! m! m! Balancer B! m/bal! X!!