Team:UCSF/Materials and Methods

1. General Cloning/Molecular biology
Constructs were cloned using the AarI method, developed by Sergio Pesajovich and the 2007 UCSF iGEM team. To learn more about AarI cloning:

Everything you ever wanted to know about AarI

In brief: yeast genomic DNA was used as a template to PCR amplify "parts". Parts were TOPO cloned, validated by sequencing, and then combinatorially cloned into the following AarI adapted acceptor vectors:

To make the silencers:

1. pRS315, Adh1P/Adh1t

2. pRS315, Cyc1P/Adh1t

3. pRS315, Fig1P/Adh1t

4. pRS305, Ga11P/Adh1t

To make the reporters: (same plasmids as above, with a 5' or 3' 8X LexA operator array)

1. pRS315, Adh1P/Adh1t

2. pRS315, Cyc1P/Adh1t

3. pRS315, Fig1P/Adh1t

4. pRS305, Ga11P/Adh1t

In some cases, finished constructs were subcloned as cassettes (using Kpn1 or PspOMI and SacI sites) into various pRS3__ series vectors to swap the markers.

The regional silencing construct was constructed by PCR amplification of a Cyc1P-mCherry-Adh1t cassette with Kpn1 ends, which was cloned into the Kpn1 site upstream of the 5' LexA operators in the GFP reporter plasmid.

Yeast Strains
SF992/W303 or CB008: W303 MATa, Ste5::KanR, bar1::NatR, far1D, his 3, trp1, leu2, ura3 (for pheromone experiments) were transformed with finished plasmids using standard protocols. A typical strain contains a silencer (LexA-Sir2) and a reporter (GFP or mCherry with LexA Operators). For the Strengthening Silencing experiment, the weakly silenced Fig1P reporter strains were additionally transformed with pRS315 vectors containing Sir3 or Ssn8 (a component of mediator complex) under the control of the high constitutive Adh1 promoter. The dual-tagged strain used for the cooperativity experiment was built in SF992, and was gal2::NatR, allowing graded activation of galactose inducible promoters ([[Media:Hawkins and Smolke.pdf]]).

2. Silencing Assay
In cases where galactose induction was required, yeast were re-streaked on complete or dropout synthetic Raffinose plates, plus or minus 2% galactose. Overnight cultures in the same media were diluted in the morning (typically 1:50 or 1:100), and 3 hours later, at OD600 0.05-0.1 range, flow cytometry measurements were taken using a BD LSR-II flow cytometer (BD Biosciences). For each sample, 10,000 cells were counted, and GFP fluorescence was measured by exciting at 488 nm with a 100 mW Coherent Sapphire laser. For experiments with pheromone-inducible promoters, cultures were grown to early log phase (OD600=0.1-0.3) in complete synthetic dropout media and then treated with 1 μM α-factor (Zymo Research) to activate the pathway. Cultures were analyzed after 3 hours of growth.

Representative flow cytometery plots are shown for all experiments, but each experiment was conducted in triplicate (using different clones) with consistent results.