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HC70AL Spring 2009Gene Discovery Laboratory
RNA and Tools For Studying Differential Gene
Expression During Seed Development
4/20/09tratorp
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Controlling Gene ActivityFrom Gene to Functional Protein & Phenotype
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Production of the Phenotype: DNA RNA
Functional Protein
Phenotype
Gene
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Eukaryotic Gene Activity: Genes to Functional Proteins
Post-Transcription
& Post-Translation
Specific Phenotype
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Regulating Eukaryotic Gene Activity: Major Control Points
Knock-Out Mutations Can Affect Each Control Point As Well As Coding
Sequences
Post-Translation
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RNA Structure & Transcription
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Gene XBeginning End
T A T A A T A G C T C G A A C A T T T T
TRANSCRIBED STRAND
SENSE STRAND
5’ END 3’ END
A T A T T A T C G A G C T T G T A A A A
Genetic Code (Function)START
“SWITCH” OR
PROMOTER
TERMINATION “SWITCH”
Downstream
Next GeneUpstream
Next Gene
5’ END 3’ ENDA G C U C G A A C P OH
mRNA X
START TRANSCRIPTION
END TRANSCRIPTION
CONTROLS
When & Where a gene
becomes active?
UNIQUE CELLS !
COMPLEMENTARY TO TRANSCRIBED STRAND =TEMPLATE FOR RNA
Gene Anatomy-A Review
Note: mRNA Sequence = Sense Strand Sequence
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Sense Strand
Anti-Sense Strand
Same Sequence & Polarity as Sense Strand
Transcription: An Overview
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Transcription: A “Ground Level” View
Requires: DNA Template, RNA Polymerase, and Ribonucleotides (Note: No Primer)
3’ 5’
5 3’ RNA Synthesis
3’ RNA End
5’ RNA End
Sense Strand
Anti-Sense Strand
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Visualizing Transcription in an Electron Microscope
5’ End of Gene (Beginning)
3’ End of Gene (End)
5’ RNA Ends
Intergenic RegionNo Transcription
5’
3’
RNA
Gene
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RNA Has Ribose Sugar in Nucleotide
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RNA Has a Uracil Instead of Thymine
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Eukaryotic RNAs Are Single-Stranded Polynucleotides
NucleotidesJoined By
Phosphodiester Bonds Like All Nucleic Acids
Order 5’ 3’ Leads to Function:
Co-Linear With Gene Sequence
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RNA Has Intra-Strand Double Helices or Secondary Structure
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Figure 6-5 Molecular Biology of the Cell (© Garland Science 2008)
RNA Intra-Strand Secondary Structure Formed By Intra-Chain Complementary Base
Pairing
One RNAStrand
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A Comparison of RNA and DNA Structures
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There Are Many Different Types of RNA
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Differential Gene Activity Programs Development
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Animal Cloning Demonstrates That the Genome of a Differentiated Cell Contains All of the Genes Required To Program the
Entire Life Cycle
Corollary: Differentiation Must Be Programmed By Differential Gene
Expression
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Plant Cell Cloning Demonstrates That the Genome of a Differentiated Plant Cell Contains All of the Genes Required To
Program the Entire Life Cycle
Corollary: Plant Differentiation Must Be Programmed By Differential Gene
Expression
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Tools For Investigating Differential Gene Activity
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Two-Dimensional Protein Gel Electrophoresis
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2-D Protein Gel Electrophoresis Demonstrates Differential Gene Activity in Animal Organs
Charge
Molecular
Weight
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RNA Blots Detect Specific RNAs in an RNA Population
Need Specific Probe to Detect RNA
RNA
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RNA Blot Demonstrates Differential Gene Activity
Control
SRYTarget RNA
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In Situ Hybridization Demonstrates
Differential Gene Activity
Hybridization of Specific Probe to Tissue
In Situ (i.e., In Place)
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Using Reverse Transcriptase to Synthesize cDNA Copiesof mRNAs (Note: cDNA=copy DNA)
Requirements1. RNA Template2. dXTPs3. Reverse
Transcriptase4. RNase H or S-1 Nuclease5. Oligo dT
Primer
Note: Reverse Transcriptase is a DNN Polymerase
RNA Primers For 2nd Strand
PolyA Tail
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A Comparison of PCR and RT-PCR
PCR RT-PCR
Need To Synthesize
cDNABefore PCR
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Generating Double-Stranded cDNA Copies of Specific mRNAs Using Reverse
Transcription PCR
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Using RT-PCR to Investigate Seed Gene Activity
Root Seed Flower
Ovule Markers
1.6 kb
mRNAs
Which “Tissue” Has the Most bobg mRNA?
Primers Specific
For bobg mRNA
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Using Real-Time Quantitative RT-PCR To Measure Specific mRNA Accumulation Levels
Seed mRNA Flower mRNA
Curves Visualize the Replication Process Over Time
That is, the Amount of DNA Synthesized at Each PCR Cycle
Primers Specific
For bobg mRNA
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Genes Can Have Different “Expression” Levels That Are Reflected in Differing Amounts of mRNAs Accumulating in
the Cytoplasm
What Cellular ProcessesCan Lead to Different
mRNA Amounts?
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Using Microarrays to Investigate the “Expression’ of Thousands of Genes at a Time:
Part One
Each Spot RepresentsA Different Gene
cDNAs Are SynthesizedFrom Each mRNA With a Different Fluorescent
Nucleotide
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Using Microarrays to Investigate the “Expression’ of Thousands of Genes at a Time:
Part Two
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Using Microarrays to Investigate the “Expression’ of Thousands of Seed Genes
Red=Seed
Green=Leaf
Which Genes Are
1. Seed Specific?
2. Leaf Specific?
3. Active in Both “Tissues?”
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Using Hierarchical Clustering to Reveal Co-Regulated Gene (mRNA) Sets
Genes
24h
1 2 Etc.
Clustering Algorithms Find Similar Patterns
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Hierarchical Clustering of Up-Regulated mRNAs in Different Cancer Tissues
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Using Microarrays To InvestigateGene Activity in Arabidopsis Seeds
1. Whole Seeds2. Specific Seed Compartments
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Genome-Wide Profiling of mRNAs During Arabidopsis Seed Development & Plant Life
Cycle
Differentiation Prepare For Dormancy & Germination
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Identification of Seed-Specific mRNAs in the Arabidopsis Life Cycle Using Whole Seeds
( ) Indicates number of transcription factor mRNAs
Pre- & Post-Fertilization
Top 2,000 Shared mRNAs
mRNAs
7,203 (453 TF) mRNAs vary quantitatively throughout the life cycle (p<0.01)
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QuickTime™ and aMPEG-4 Video decompressor
are needed to see this picture.
Using Laser Capture Microdissection (LCM) and
GeneChips To Profile mRNAs in Specific Seed Cells, Tissues, and Compartments
Embryo ProperSuspensor
Seed Coat
Arabidopsis Seed After Fertilization estdb.biology.ucla/seed/presentation
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Gene Activity in Globular-Stage Arabidopsis
Seed Compartments
GSC PE MPE EP SUS CHE CHSC
mRNA BR1 11,402 11,445 7,844 10,532 11,273 7,709 12,440
mRNA BR2 12,316 9,972 10,658 10,674 12,965 7,002 11,818
mRNA BR3 -
9,793 -
Total mRNAs 10,513 9,136 7,216 9,130 10,692 7,776 10,794
Unique mRNA 108 54 14 56 95 133 152
Unique TFs 16 3 0 17 8 10 26
Shared 4,028
General Seed Coat
Peripheral Endosperm
Chalazal Seed Coat
Embryo
Micropylar Endosperm
Chalazal Endosperm
EP
S
CHE
PE
MPE
SUS
EP
GSc
CHSc
Top 2000 Shared mRNAs
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Arabidopsis Genes You Are Investigating This QuarterAre Active in Specific Seed Compartments
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Microarray Experiments Can Be Used To IdentifyMetabolic Pathways in Specific Seed Compartments
Jasmonic Acid Biosynthetic Pathway in the Arabidopsis Seed Coat