Zolan Lab

Jonathan NowackiSchool of Informatics Master of Science in Bioinformatics

Sun Kim Ph.D. Mimi Zolan Ph.D.

Discovery and Visualization of Germline Genes in a Mushroom with Synchronous Cellular Division

Zolan Lab

Outline

• Background & Goals• The Mushroom• Microsatellites• Exon Prediction• Microarray• Gbrowse• Summary• Acknowledgments

Outline

Zolan Lab

Cellular Division

Importance– Aging– Cancer– Disease– Stem cell research– Reproduction

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Zolan Lab

Goals

1. Partial Genome– Use Microsatellite data to find a

region of importance– Predict Exons using FGENE=

2. Whole Genome– Use Microarray data to find a genes

that are up-regulated in germ line cells.

3. Visualization– Gbrowse

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Zolan Lab

What’s been done• Rad3/Rad9 Mre11• MIT Whitehead Institute• Southeast Missouri

Problems• Coprinus isn’t mapped• Converging data• NBS1

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Background on progress

Zolan Lab

• It’s not a mammal

• Short life cycle

• Synchronous division

• Easy to maintain

Why Coprinus?

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Partial Genome

1. Wet lab– Locate an area of interest– Focus on NBS1

• DNA repair• Expressed during meiosis

2. Exon Prediction– FGENE

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Zolan Lab

Microsatellite Search

• Purpose– Locate genes with known

phenotype but unknown sequence.

– Locate area of interest.

• Tools– GCG, Findpatterns– 119 microsatellites were used

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Zolan Lab

What is a microsatellite?

AAAAA

CACACA

CTTCTTCTTOutlineBackgroundMicrosatellites

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Utility of Microsatellites

8C11

MicrosatellitesMicrosatellites

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Recombination

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Finding Microsatellites

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GCG – Find patterns

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Electrophoresis

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Electrophoresis

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Finer resolution

• Micro satellites are small– Agarose wasn’t good enoug– High grade “Fufi” agarose wasn’t

good enough– Moved to polyacrylamide

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Finest resolution

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Mapping

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Microsatellite Results

• Microsatellites were found

• Polymorphism was low, for a variety of reasons, but a few usable markers were found

• Wasn’t the most effective method

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Exon Prediction

• Used to find and predict genes– FGENE– Hidden Markov models

• Compared to known genes– Exons blasted vs. NCBI NR

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FGENE highlights

• Phanerochaete chrysosporium– 220 exons predicted

• Cryptococcus neoformans– 216 exons predicted

• Ustilago– 234 exons predicted

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Exons

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Blast

• 6 frame translation

ATGCTCGGGACTGATCGA

ATGCTCGGGACTGATCGA

ATGCTCGGGACTGATCGA

TCGATCAGTCCCGAGCAT

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Phase 2: Whole Genome

• Microarray– Map genes active in meiosis

• Visualization– Gbrowse

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Microarray

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Microarray

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Microarray

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Microarray

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Germ line

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Microarray

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Results

• Drosophila– 254 / 781 – 633 / 2340

• Worm – 553 / 2496

• Testis Fly– pending

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Microarray

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Visualizing the Genome

• Data– Microarray– Microsatellite– Exon

• Needs– Easy analysis of genetic data– Doesn’t require computer

science background– Web based for portability.

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MicroarrayGbrowse

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Gbrowse

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MicroarrayGbrowse

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Default Values

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MicroarrayGbrowse

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Solution: A Dynamic database

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MicroarrayGbrowse

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More Specificity

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MicroarrayGbrowse

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Highly Specific

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MicroarrayGbrowse

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Summary

• Coprinus is ideal for studying cellular division

• Microsatellite data for mapping

• Microarray data for gene function

• Gbrowse visualization

• Dynamic Database

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MicroarrayGbrowseSummary

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Conclusion

• Gbrowse

• Microarray comparisons

• Exon Prediction

• Microsatellites

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MicroarrayGbrowseSummary

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Acknowledgments

• Dr. Sun Kim

• Dr. Mimi Zolan

• Dr. Haixu Tang

• Dr. John Colbourne

• Henry Paik

• Danny Rice

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MicroarrayGbrowseSummaryAcknowledgments