This web page was produced as an assignment for an undergraduate course at Davidson College

Microarray Analysis of my Favorite Yeast Genes


A Brief Introduction to Microarrays:

The use of microarrays is a brand new technique that allows a researcher to examine the response of an entire genome to changing conditions. A microarray is a slide onto which single-stranded copies of thousands of genes have been spotted. Experimentally treated cells are lysed and their RNA is allowed to hybridize with the DNA on the chip. By comparing the amount of bound RNA between experimental and control cells, changes in expression resulting from the experimental treatment can be seen.


Microarray analysis of the annotated gene TUB1/YML085C:

On the previous page I explained that TUB1 is the yeast gene that encodes for alpha tubulin, an important component of microtubules in the cell cytoskeleton and an integral player in chromosome movement during mitosis. To see this page click here. On this page I will analyze expression patterns of TUB1 under a variety of experimantal conditions using microarray data available at http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl .

TUB1 expression when exposed to alpha factor hormone:

Yeast (Saccharomyces cerevisiae) are capable of reproducing either asexually (budding) or sexually. Alpha factor is a hormone that stimulates yeast to reproduce sexually (3). Exposure to alpha factor arrests cells in the G1 phase of the cell cycle and prompts the expression of genes involved in sexual reproduction (3). TUB1 is generally repressed when exposed to alpha factor. The repression is greatest (about a 1-fold repression) at an alpha factor concentration of about 200 nM. This makes sense because when a call is exposed to alpha factor it stops budding and therefore stops mitosis. As tubulin is involved in chromosome sorting during mitosis it makes sense that TUB1 is repressed. Not surprisingly, TUB2 and TUB3, other components of tubulin (see other page) showed very similar expression patterns to TUB1. In addition, the gene STU2, a gene encoding a protein involved in microtubule nucleation also showed a similar expression pattern. When TUB1 expression over time after exposure to alpha factor was examined, quick repression with a gradual rise back to control levels was observed. Repression was greatest after about 48 minutes and had returned to control levels by 120 minutes. In this experiment, TUB1 was seen to have an expression pattern similar to SPC34, another gene encoding a protein involved in microtubule nucleation.

Expression of TUB1 under varying concentrations of alpha factor (1)
Expression of TUB1 over time after exposure to alpha factor (1)
Below: Genes that show similar expression patterns to TUB1 under varying concentrations of alpha factor (1)

 

Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YML085C

 

TUB1

 

 

mitotic chromosome segregation*

 

structural protein of cytoskeleton

 

spindle pole body*

YPL227C

 

ALG5

 

 

not yet annotated

 

dolichyl-phosphate beta-glucosyltransferase

 

not yet annotated

YGR108W

 

CLB1

 

 

regulation of CDK activity*

 

G2/M-specific cyclin

 

cellular_component unknown

YJR076C

 

CDC11

 

 

establishment of cell polarity (sensu Saccharomyces)*

 

structural protein of cytoskeleton

 

septin ring (sensu Saccharomyces)*

YFL037W

 

TUB2

 

 

mitotic chromosome segregation*

 

structural protein of cytoskeleton

 

spindle pole body*

YPL155C

 

KIP2

 

 

mitotic anaphase B*

 

microtubule motor

 

cytoplasmic microtubule*

YLR235C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML124C

 

TUB3

 

 

mitotic chromosome segregation*

 

structural protein of cytoskeleton

 

spindle pole body*

YCR034W

 

FEN1

 

 

fatty acid biosynthesis*

 

molecular_function unknown

 

endoplasmic reticulum membrane

YDR240C

 

SNU56

 

 

mRNA splicing

 

not yet annotated

 

not yet annotated

YOL111C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR113W

 

HOG1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPL116W

 

HOS3

 

 

biological_process unknown

 

molecular_function unknown*

 

not yet annotated

YOR372C

 

NDD1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YMR001C

 

CDC5

 

 

protein amino acid phosphorylation*

 

protein serine/threonine kinase

 

cytoplasm*

YDR182W

 

CDC1

 

 

mating (sensu Saccharomyces)*

 

molecular_function unknown

 

cell

YBL003C

 

HTA2

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YOR025W

 

HST3

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YLR045C

 

STU2

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YDR130C

 

FIN1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPR185W

 

APG13

 

 

autophagy*

 

molecular_function unknown

 

cellular_component unknown

 

 

 

 

 

 

 

 

 

 

 

 

 

 

  Below: Genes that show similar expression patterns to TUB1 over time after exposure to alpha factor (1)

 

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YML085C

 

TUB1

 

 

mitotic chromosome segregation*

 

structural protein of cytoskeleton

 

spindle pole body*

YLR182W

 

SWI6

 

 

cell cycle

 

transcription factor

 

not yet annotated

YOR255W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR244W

 

PEX5

 

 

protein-peroxisome targeting*

 

peroxisome targeting sequence binding*

 

cytosol*

YKR037C

 

SPC34

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YLR056W

 

ERG3

 

 

ergosterol biosynthesis

 

C-5 sterol desaturase

 

endoplasmic reticulum

YIL132C

 

CSM2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR113W

 

DAM1

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YBL083C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR231C

 

AOR1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YPL127C

 

HHO1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YEL017W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR090W

 

PXL1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR055C

 

BUB2

 

 

mitotic spindle checkpoint

 

molecular_function unknown

 

spindle pole body

YLR358C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR015C

 

MNN2

 

 

protein amino acid glycosylation

 

not yet annotated

 

not yet annotated

YBL082C

 

RHK1

 

 

protein amino acid glycosylation

 

not yet annotated

 

not yet annotated

YIL140W

 

AXL2

 

 

axial budding*

 

molecular_function unknown

 

integral plasma membrane protein*

YGR152C

 

RSR1

 

 

polar budding*

 

signal transducer*

 

plasma membrane*

YHR083W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YER088C

 

DOT6

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

 

 

TUB1 expression in response to changing environmental conditions:

In an experiment that measured the expression of yeast genes under a wide range of environmental changes including heat and cold chock and exposure to menadione and DDT, TUB1 was found to cluster with some of the same genes that it clustered with in the alpha factor experiments. Not surprisingly, these included TUB2 and TUB3. Also included was CIS3, a gene that encodes for a protein involved in cell wall structure. It is not surprising that many of the structural protein genes cluster together in many of these experiments.

TUB1 expression through the cell cycle:

Levels of TUB1 expression were found to vary throughout the cell cycle. This makes sense as differing amounts of microtubules and consequently differing levels of alpha tubulin are necessary at differing points in the cell cycle. Again, TUB1 was found to cluster with TUB2 and CIS3 in this experiment.

Expression of TUB1 through the cell cycle (1)

In Conclusion:

The microarray data presented here support the fact that TUB1 encodes alpha tubulin, part of tubulin that makes up microtubules. TUB1 consistently clusters with TUB2 and TUB3, the genes that encode the other subunits of tubilin. In addition, it clusters with other genes involved in microtubule formation such as CIS3 and SPC34.


Microarray Analysis of the Unannotated Yeast Gene LEE1/YPL054W:

LEE1 is an unannotated yeast gene whose function has yet to be scientifically investigated. In the previous page BLAST searches discovered tow zinc finger regions that lead me to hypothesize that LEE1 may encode a transcription factor. To see these data, click here. Now I will analyze microarray data using microarray data available at http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl to see if I can make any further hypotheses on the function of LEE1.

LEE1 expression when exposed to alpha factor hormone:

LEE1 showed almost no change when exposed to varying concentrations of alpha hormone. The lack of change in this experiment is explained when the response to alpha factor over time is examined. LEE1 shows almost no change in expression for the first 48 minutes after being exposed to alpha factor. Then there is a sharp, almost 1.5 fold induction that gradually falls afterwards. These data suggest that LEE1 is somehow involved in yeast mating. Probably, since it takes so long to be induced, LEE1 could be involved in the replication or exchange of DNA after two cells have mated. Unfortunately, though, almost all of the genes that show expression patterns similar to LEE1 are unannotated so it is hard to predict exactly what role LEE1 might play in this process.

Expression of LEE1 under varying concentrations of alpha factor (1)
Expression of LEE1 over time after exposure to alpha factor (1)
Below: Genes that show similar expression patterns to LEE1 over time after exposure to alpha factor (1)

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YPL054W

 

LEE1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL159C

 

RCN1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YKL161C

 

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YDL222C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR009C

 

FOX2

 

 

fatty acid beta-oxidation

 

3-hydroxyacyl-CoA dehydrogenase*

 

peroxisomal matrix

YLR267W

 

BOP2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR127W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDL238C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL055C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YNR007C

 

AUT1

 

 

autophagy*

 

molecular_function unknown

 

cellular_component unknown

YNL200C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL123C

 

RNY1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YIR039C

 

YPS6

 

 

not yet annotated

 

aspartic-type endopeptidase

 

not yet annotated

YJL153C

 

INO1

 

 

not yet annotated

 

inositol-3-phosphate synthase

 

not yet annotated

YPL219W

 

PCL8

 

 

regulation of glycogen biosynthesis

 

cyclin-dependent protein kinase regulator

 

not yet annotated

YJR019C

 

TES1

 

 

fatty acid metabolism

 

not yet annotated

 

not yet annotated

YLR149C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL030W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL133C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR098C

 

UBP11

 

 

not yet annotated

 

ubiquitin-specific protease

 

cellular_component unknown

YKL107W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

 

 

LEE1 expression through the cell cycle:

LEE1 shows varying expression throughout the cell cycle. It does show a marked peak though during S phase. S phase is when replication occurs (2), indicating that LEE1 may be involved in DNA replication. Unfortunately, again, almost no genes with known function cluster with LEE1 in this experiment.

Expression of LEE1 through the cell cycle (1)

LEE1 expression during sporulation:

This experiment found that LEE1 is initially induced and then repressed during sporulation. This would be consistent with the hypothesis that LEE1 is involved in replication of DNA. In this case, DNA would be replicated first and then spore formation would ensue. Although this may seem similar to alpha factor response, the initial lag before induction of LEE1 in response to alpha factor could be explained be the time it takes for a yeast to shmoo to another yeast cell before DNA replication begins.

Expression of LEE1 during sporulation (1)
Below: Genes that show similar expression patterns to LEE1 during sporulation (1)

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YPL054W

 

LEE1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR129W

 

SCD6

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YOR353C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR162C

 

YRR1

 

 

transport

 

not yet annotated

 

not yet annotated

YIL014W

 

MNT3

 

 

O-linked glycosylation

 

alpha-1,3-mannosyltransferase

 

cellular_component unknown

YLR108C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR063C

 

PAN5

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YIL061C

 

SNP1

 

 

mRNA splicing

 

not yet annotated

 

not yet annotated

YMR090W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR386W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR353W

 

BUD8

 

 

pseudohyphal growth*

 

molecular_function unknown

 

cell

YGL124C

 

MON1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YPL186C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR005W

 

SSL1

 

 

transcription initiation, from Pol II promoter*

 

general RNA polymerase II transcription factor

 

transcription factor TFIIH

YOR230W

 

WTM1

 

 

meiosis

 

transcription factor

 

not yet annotated

YLR321C

 

SFH1

 

 

chromatin modeling

 

molecular_function unknown

 

nucleosome remodeling complex

YJL078C

 

PRY3

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR111C

 

YSA1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFL067W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR001W

 

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YKR036C

 

CAF4

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

 

In Conclusion:

The gene clustering data for LEE1 from these experiments was not very informative. In most cases the vast majority of clustered genes were of unknown function and those that were known did not show any clear trends. From expression patterns, though, it seems at least possible that LEE1 may be involved in DNA replication. Coupled with the data from the previous page that suggest that LEE1 is a transcription factor, my best guess would be that LEE1 is a transcription factor that regulates genes involved in DNA replication.


Sources:

1) SGD, Expression connection. 2001.http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

2) "The Cell Cycle" http://pc65.frontier.osrhe.edu/hs/science/bcell2.htm

3) Zymo Research. 2001. Alpha-factor mating pheromone. http://pc65.frontier.osrhe.edu/hs/science/bcell2.htm


please email me at jdwillson@davison.edu with comments or questions

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