Methods for predicting transcription levels

• US 20030120433A1
• Filed: 10/17/2002
• Published: 06/26/2003
• Est. Priority Date: 10/17/2001
• Status: Abandoned Application

• Current Assignee: ADVANCED RESEARCH & TECHNOLOGY INSTITUTE
• Original Assignee: ADVANCED RESEARCH & TECHNOLOGY INSTITUTE
• Inventors: Yokota, Hiroki, Sun, Hui Bin
• Application Number:
  US10/274,095
• Publication Number:
  US 20030120433A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6897 involving reporter genes operably linked to promoters
• CPC Class Codes: C12Q 2525/143 incorporating a promoter sequence
• CPC Class Codes: C12Q 2537/161 A competitive reaction step
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

Methods are provided for empirically determining transcription levels of target genes based on the number of cis-acting elements provided in untranslated regulatory regions.

Claims

1. A method for predicting an expression level of a target gene or gene family comprising:

a) selecting a target gene or gene family;

b) experimentally determining the number and type of cis-acting elements and mRNA expression levels of other genes within said target gene family to obtain a first data set; and

c) applying a PROBE algorithm to said data set, thereby generating the estimated expression level of said target gene as a function of the weighed frequencies of said cis-acting elements present in the 5′

untranslated regulatory region of said target gene.

2. The method of claim 1, wherein said cis-acting elements are selected from the group consisting of at least one of AP1, AP2, NFY, PEA3, Sp1, TFIID, NF-kappa B, STAT, GATA1, Oct-1 and TIE.

3. The method of claim 1, wherein said gene family is selected from the group consisting of matrix metalloproteinases, cytokines, hormones, IL-1 responsive genes, cyclins, growth factor receptors, growth factors, oncogenes, and transcription factors.

4. The method of claim 1, wherein said 5′

regulatory region comprises at least 500 base pairs.

5. The method of claim 1, wherein said 5′

regulatory region comprises at least 800 bases.

6. The method of claim 1, wherein said target genes are present on a microrray.

7. A method for predicting an expression level of a target gene or gene family in a particular cellular state, comprising:

a) selecting a target gene or gene family;

b) experimentally determining the number and type of cis-acting elements and mRNA expression levels of other genes within said target gene family in said cellular state relative to genes not in said cellular state to obtain a first data set; and

c) applying a non-linear model algorithm to said data set, thereby generating the estimated expression level of said target gene as a function of the cellular state and the weighed frequencies of said cis-acting elements present in the 5′

untranslated regulatory region of said target gene.

8. The method of claim 7, wherein said cis-acting elements are selected from the group consisting of at least one of AP1, AP2, NFY, PEA3, Sp1, TFIID, NF-kappa B, STAT, GATA1, Oct-1 and TIE.

9. The method of claim 7, wherein said gene family is selected from the group consisting of matrix metalloproteinases, cytokines, hormones, IL-1 responsive genes, cyclins, growth factor receptors, growth factors, oncogenes, and transcription factors.

10. The method of claim 7, wherein said 5′

regulatory region comprises at least 500 base pairs.

11. The method of claim 7, wherein said 5′

regulatory region comprises at least 800 bases.

12. The method of claim 7, wherein said target genes are matrix metallproteinases and said cellular state is induced by growing synovial cells under mechanical shear conditions.

13. The method of claim 7, wherein said target genes are present on a microarray.

14. A method for determining contribution of cis-acting elements to levels of mRNA expression of target genes, comprising:

a) providing a host cell population;

b) contacting said host cell with oligonucleotides encoding cis-acting element DNA, said cis-acting elements also being present in said target genes;

c) isolating mRNA from said host cells;

d) reverse transcribing said mRNA into cDNA;

e) performing polymerase chain reaction to amplify said cDNA and assessing alterations of expression levels of said target genes in the presence and absence of said oligonucleotide encoding cis-acting element DNA, altered mRNA expression levels indicating the presence of the oligonucleotide cis-acting element in the untranslated regulatory region of said target gene.

15. The method as claimed in claim 14, wherein said oligonucleotides are selected from the group consisting of CAGGC, CGCCC, CCGCC, CACCG, GCGCC, ATGGG, GGGAA and CCGCG.

16. The method of claim 14, wherein said target genes encode matrix metalloproteinases, said cis acting element is NF-kappa B and said oligonucleotide is TGCAGGGGATYCCCGACT.