Analysis of Gene Expression and Gene Networks Biclustering 2.
Plant biotechnology Lab 1. Strategies of gene analysis Promotor analysis Function of gene/protein...
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Transcript of Plant biotechnology Lab 1. Strategies of gene analysis Promotor analysis Function of gene/protein...
Plant biotechnology Lab 1Plant biotechnology Lab 1
Strategies of gene analysisStrategies of gene analysis
Promotoranalysis
Function of gene/protein
Expressionpattern of
genes
1.GUS
staining
2.RT-PCR
GTL1 geneGTL1 gene
• Research project in Prof. Hasegawa’s lab
• GTL1 is member of GT-2 family
• Act as a transcription factor that binds to GT-elements (GGTTAA, GGTAAT, or GGTAAA)
• Data suggests dark/light regulation of GTL1
GUS reporter systemGUS reporter system Reporter gene: GUS (beta-glucuronidase) Substrate: X-gluc (5-bromo-4-
chloro- 3-indolyl glucuronide)
• Plants have very low X-GLUC cleavage activity
• GUS is fused to native promotor of gene of interest (GOI)
• Enables analysis of temporal and spatial expression pattern of GOI
1. GUS cleaves the substrate X-gluc
2. One product → indigo3. Dark blue color
PCRPCR• Polymerase Chain Reaction (PCR)
• in vitro DNA polymerization with DNA dependent DNA polymerase
• First described 1971 by Kepple et al. but fresh enzyme added each cycle
• Kary Mullis, 1984, introduced the idea of using thermostable DNA -polymerase from Thermus aquaticus (Taq)
Kary Mullis
Reverse transcriptaseReverse transcriptase• Reverse Transcriptase (RT) is a RNA-
dependent DNA polymerase
• RNA (retro)viruses and transposons in eukaryotes use RT
• Catalyzes RNA-directed extension of 3'-end of DNA strand by 1 deoxynucleotide at a time
• Cannot initiate a chain de novo → requires a RNA or DNA primer
• DNA can also serve as template Human immunodeficiency virus (HIV) uses RT without proof reading function
Source: PDB entry 1HMV
RT-PCRRT-PCR
PCR
cDNA Synthesis
L.V. Kendall et al, 2000
5’ 3’
5’
Can be RT (HIV-RT 3’-5’ endonuclease activity, J.J. DeStefano et al, 1991)
3’ 5’
5’
5’ 3’
5’
Introduction
Background
Safety
Start GUS staining assay
Setup PCR reaction
1. 2.3.
Gel electrophoresis
of PCR