# US 8,541,345 B2 · Compositions and methods for the identification and use of epigenetic markers useful in the study of normal and abnormal mammalian gametogenesis

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- Number: US 8,541,345 B2
- Document ID: US8541345B2
- Status: Granted
- Kind: B2
- Application number: 12/948,552
- Filed: 2010-11-17
- Published: 2011-06-23
- Granted: 2013-09-24
- Earliest claimed: 2009-11-17
- Assignees: The Trustees of the University of Pennsylvania
- Applicants: Shelley L. Berger; Jerome Govin
- Inventors: Shelley L. Berger; Jerome Govin
- Web page: https://patentgrep.com/patent/US8541345B2

## CPC

- C12N 15/81: for yeasts
- C12Q 1/6897: involving reporter genes operably linked to promoters
- C40B 40/08: Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
- G01N 33/689: {related to pregnancy or the gonads}
- G01N 2333/395: from Saccharomyces
- G01N 2800/367: Infertility, e.g. sperm disorder, ovulatory dysfunction
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

The invention includes compositions comprising a S. cerevisiae yeast library, and methods of identifying an epigenetic marker for the diagnosis of infertility or a disorder associated with gametogenesis in an individual.

## Claims

### Claim 1

A composition comprising an S. cerevisiae strain SK1 yeast library, wherein each member of the yeast library has histone H3 and histone H4 deleted from its genome; and wherein the wild-type histone sequence of one of said two histones H3 and H4 is expressed from a plasmid; and wherein the remaining one of said two wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant histone sequence has one of its wild-type amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H3 and H4 is present at least one time in said library.

### Claim 2

A composition comprising an S. cerevisiae strain SK1 yeast library, wherein each member of said yeast library has histone H2A and histone H2B deleted from its genome; and wherein the wild-type histone sequence of one of said two histones H2A and H2B is expressed from a plasmid; and wherein the remaining one of said two wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant histone sequence has one of its wild-type amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H2A and H2B is present at least one time in said library.

### Claim 3

A composition comprising an S. cerevisiae strain SK1 yeast library, wherein each member of said yeast library has histone H2A, histone H2B, histone H3 and histone H4 deleted from its genome; and wherein the wild-type histone sequence of three of said four histones H2A, H2B, H3, and H4 is expressed from a plasmid; and wherein the remaining one of said four wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant historic sequence has one of its amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H2A, H2B, H3 and H4 is present at least one time in said library.

### Claim 4

A method of identifying an epigenetic marker for diagnosis of infertility or a disorder associated with gametogenesis, said method comprising the steps of:
(a) creating an S. cerevisiae strain SK1 yeast library of mutant histones,
(b) inducing sporulation,
(c) assessing efficiency of said sporulation in individual mutants,
(d) identifying particular amino acid positions of said mutants with diminished efficiency of said sporulation,
(e) evaluating epigenetic modifications at said amino acid positions, and,
(f) evaluating epigenetic modifications at the same amino acid position of a mammalian histone,
whereby, when the epigenetic modification state of said yeast histone is the same as said mammalian histone, said epigenetic marker for said diagnosis of said infertility or said disorder associated with gametogenesis is identified.

### Claim 5 (depends on 4)

The method of claim 4, wherein each member of the yeast library has historic H3 and histone H4 deleted from its genome; and wherein the wild-type histone sequence of one of said two histones H3 and H4 is expressed from a plasmid; and wherein the remaining one of said two wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant histone sequence has one of its wild-type amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H3 and H4 is present at least one time in said library.

### Claim 6 (depends on 4)

The method of claim 4, wherein each member of said yeast library has histone H2A and histone H2B deleted from its genome; and wherein the wild-type histone sequence of one of said two histones H2A and H2B is expressed from a plasmid; and wherein the remaining one of said two wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant histone sequence has one of its wild-type amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H2A and H2B is present at least one time in said library.

### Claim 7 (depends on 4)

The method of claim 4, wherein each member of said yeast library has histone H2A, histone H2B, histone H3 and histone H4 deleted from its genome; and wherein the wild-type histone sequence of three of said four histones H2A, H2B, H3, and H4 is expressed from a plasmid; and wherein the remaining one of said four wild-type histone sequences that is not expressed from a plasmid is substituted with a mutant histone sequence expressed from a plasmid; and wherein said mutant histone sequence has one of its amino acid residues substituted with alanine; and wherein each member of said yeast library has only a single mutation; and wherein each amino acid position mutation in H2A, H2B, H3 and H4 is present at least one time in said library.

### Claim 8 (depends on 4)

The method of claim 4, wherein said marker is restricted to meiosis.

### Claim 9 (depends on 4)

The method of claim 4, wherein the presence of said marker during said yeast sporulation correlates with the presence of said marker during said gametogenesis.

### Claim 10 (depends on 4)

The method of claim 4, wherein said marker is at least one selected from the group consisting of a methylation marker, an acetylation marker, and a phosphorylation marker.

### Claim 11 (depends on 4)

The method of claim 4, wherein said marker is phosphorylated H3T11.