Method of constructing cdna tag for identifying expressed gene and method of analyzing gene expression

• US 20040142337A1
• Filed: 03/10/2004
• Published: 07/22/2004
• Est. Priority Date: 03/15/2001
• Status: Abandoned Application

• Current Assignee: Kureha Corporation, Naoki Yamamoto
• Original Assignee: Kureha Corporation, Mikio Yamamoto, Naoki Yamamoto
• Inventors: Yamamoto, Mikio, Sakai, Jun, Yamamoto, Naoki, Hirose, Kunitaka
• Application Number:
  US10/468,753
• Publication Number:
  US 20040142337A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor

Abstract

There are provided a method for the preparation of cDNA tags for identifying expressed genes and a method for analysis of gene expression. The cDNA tags for identifying expressed genes are prepared by the method comprising a kind of type II restriction enzyme, two kinds of type IIS restriction enzymes and linkers X and Y having a recognition site for one of two kinds of type IIS restriction enzymes. The cDNA tags can be used alone or in combination like chain (concatemer) formed by combining process to analyze gene expression.

Claims

1. A method for the preparation of cDNA tags for identifying expressed genes comprising:

providing complementary deoxyribonucleic acids (cDNAs);

cleaving the cDNAs with a type II restriction enzyme to prepare cDNA fragments;

ligating the cDNA fragments to linker Xes which have a recognition site of a first type IIS restriction enzyme and which form a recognition site of a second type IIS restriction enzyme at the site linking with the cleavage end-sites of the cDNA fragments formed by the type II restriction enzyme to prepare linker X-cDNA fragment complexes;

cleaving the linker X-cDNA fragment complexes with the second type II restriction enzyme to prepare linker X-cDNA tag complexes;

ligating linker Ys which have a recognition site of the first type IIS restriction enzyme to the cleavage end-sites of the linker X-cDNA tag complexes formed by the second type IIS restriction enzyme to prepare linker X-cDNA-tag-linker Y complexes;

amplifying the linker X-cDNA fragment-linker Y complexes; and

cleaving the amplified products thus obtained with the first type IIS restriction enzymes simultaneously or in turn to prepare the cDNA tags for identifying expressed genes.

2. The method according to claim 1 further comprising the step of refining the linker X-cDNA fragment complexes.

3. The method according to claim 1 further comprising the step of processing the end-sites of the cDNA fragments in the linker X-cDNA fragment complexes to make the end-sites capable of binding to the linker Ys having a recognition site of the first type IIS restriction enzyme.

4. The method according to claim 2 further comprising the step of processing the end-sites of the cDNA fragments in the linker X-cDNA fragment complexes to make the end-sites capable of binding to the linker Ys having a recognition site of the first type IIS restriction enzyme.

5. The method according to any one of claims 1, 2, 3 or 4 further comprising the step of separating the obtained cDNA tags for identifying expressed genes.

6. The method according to claim 1 wherein the cDNAs are prepared from the mRNAs derived from cells to be examined.

7. The method according to claim 1 wherein the cDNAs are prepared from the mRNAs derived from cells to be examined using oligo-dT primers immobilized on a solid phase as an oligo-dT primer.

8. The method according to claim 7 wherein the oligo-dT primers comprise oligo-dT primers immobilized on latex beads or magnet beads.

9. The method according to claim 1 wherein the type II restriction enzyme has the recognition site of four base pairs.

10. The method according to claim 1 wherein the type 11 restriction enzyme is selected from the group consisting of AfaI, AluI, CviRI, DpnI, HpyCH4V, HpyF44III, RsaI, BfaI, Csp6I, HpyCH4IV, MaeI, MaeII, TaqAlphaI, TaqI, TthHB8I, XspI, Bsp143I, DpnII, MboI, NdeII, Sau3AI, NlaIII, AccII, Bsh1236I, BstUI, BsuRI, FnuDII, HaeIII, MvnI, AciI, BsiSI, HapII, Hin6I, HinPI, HpaII, MspI, SciNI, CfoI, HhaI, MseI, TruII, Tru9I, TasI, Tsp509I and TspEI.

11. The method according to claim 1 wherein the first type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I, GsuI, BsmFI, BcefI, FokI, BbvI, Bsp423I, Bst71I, RleAI, EciI, BseMII, BseRI, HgaI, LweI, SfaNI, AprI, BspMI, HphI, MboII, Mn1I, BbsI, BciVI, BbvII, BpiI, BpII, BpuAI and FauI.

12. The method according to claim 1 wherein the first type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I, GsuI, BsmFI, BcefI, FokI, BbvI, Bsp423I, Bst71I, RleAI, EciI, BseMII, BseRI and HgaI.

13. The method according to claim 1 wherein the first type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I and GsuI.

14. The method according to claim 1 wherein the second type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I, GsuI, BsmFI, BcefI, FokI, BbvI, Bsp423I, Bst71I, RleAI, EciI, BseMII, BseRI, HgaI, LweI, SfaNI, AprI, BspMI, HphI, MboII, MnII, BbsI, BciVI, BbvII, BpiI, Bp1I, BpuAI and FauI.

15. The method according to claim 1 wherein the second type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I, GsuI, BsmFI, BcefI, FokI, BbvI, Bsp423I, Bst7I, RleAI, EciI, BseMII, BseRI and HgaI.

16. The method according to claim 1 wherein the second type IIS restriction enzyme is selected from the group consisting of MmeI, BpmI, BsgI, BspGI, Eco57I and GsuI.

17. The method according to claim 1 wherein the type II restriction enzyme is selected from the group consisting of AfaI, RsaI, CviRI, HpyCH4V, HpyF441II, AciI, HhaI, HinP1I, Hin6I, SciNI, DpnI and CfoI and the second type IIS restriction enzyme is selected from the group consisting of MmeI, BsmFI, RleAI, HgaI, LweI, SfaNI, MnII, BbsI, BbvII, BpiI, BpII, BpuAI and FauI.

18. The method according to claim 1 wherein the type II restriction enzyme is HpyCH4V, and the second type IIS restriction enzyme is RleAI.

19. The method according to claim 1 wherein the type II restriction enzyme is AfaI, and the second type IIS restriction enzyme is BsmFI.

20. The method according to claim 1 wherein the type II restriction enzyme is RsaI, and the second type IIS restriction enzyme is BsmFI.

21. The method according to claim 1 wherein the type II restriction enzyme is HinPII, and the second type IIS restriction enzyme is HgaI.

22. The method according to claim 1 wherein the type II restriction enzyme is AfaI, and the second type IIS restriction enzyme is MmeI.

23. The method according to claim 1 wherein the type II restriction enzyme is RsaI, and the second type IIS restriction enzyme is MmeI.

24. The method according to claim 1 wherein the length of the cDNA tags for identifying expressed genes ranges from 6 base pairs (bp) to 25 bp.

25. The method according to claim 1 wherein the length of the cDNA tags for identifying expressed genes ranges from 10 bp to 25 bp.

26. The method according to claim 1 wherein the length of the cDNA tags for identifying expressed genes ranges from 10 bp to 16 bp.

32. Library of cDNA tags for identifying expressed genes prepared by the method according to any one of claims 1, 2, 3 or 4.

35. A method for the analysis of gene expression comprising the steps of concatenating cDNA tags prepared by the method according to any one of claims 1, 2, 3 or 4 each other to form concatemers and sequencing the concatemers.

36. The method according to claim 35 wherein the concatemer consists of 3 to 200 of the cDNA tags for identifying expressed genes.

37. The method according to claim 35 wherein the concatemer consists of 3 to 80 of the cDNA tags for identifying expressed genes.

38. The method according to claim 35 wherein the concatemer consists of 16 to 40 of the cDNA tags for identifying expressed genes.

39. The method for the qualitative analysis of gene expression according to claim 36 wherein the concatemers are sequenced and then each of the cDNA tags are sequenced on the basis of the sequences of the concatemers.

40. The method for the quantitative analysis of gene expression according to claim 36 wherein the concatemers are sequenced and then each of the cDNA tags are sequenced and measured in frequency of occurrences on the basis of the sequences of the concatemers.

41. A concatemer consisting of the cDNA tags prepared by the method according to any one of claims 1, 2, 3 or 4 wherein no spacer sequence exists among the cDNA tags.

42. The concatemer according to claim 41, which consists of 3 to 200 of the cDNA tags.

43. The concatemer according to claim 41, which consists of 3 to 80 of the cDNA tags.

44. The concatemer according to claim 41, which consists of 16 to 40 of the cDNA tags.

45. A concatemer consisting of the cDNA tags prepared by the method according to any one of claims 1, 2, 3 or 4 wherein spacer sequences exist among the cDNA tags.

46. The concatemer according to claim 45, which consists of 3 to 200 of the cDNA tags.

47. The concatemer according to claim 45, which consists of 3 to 80 of the cDNA tags.

48. The concatemer according to claim 45, which consists of 16 to 40 of the cDNA tags.

27. Linker X comprising a recognition site of the first type IIS restriction enzymes and being capable of forming a recognition site of the second type IIS restriction enzyme at the position linking to the cDNA fragment cleaved by the type II restriction enzyme.

28. The linker X according to claim 27 comprising base sequences of SEQs 12 and 13.

29. Linker X-cDNA fragment complex comprising cDNA fragment formed by cleaving with a type II restriction enzyme and linker X having a recognition site of the first type IIS restriction enzymes and being capable of forming a recognition site of the second type IIS restriction enzyme at the position linking to the cDNA fragment cleaved by the type II restriction enzyme.

30. Linker X-cDNA tag-linker Y complex wherein linker Y having a recognition site of the first type IIS restriction enzyme is ligated at the cleavage end of linker X-cDNA fragment complex of claim 29.

31. The linker X-cDNA tag-linker Y complex according to claim 29 comprising base sequence of SEQ 18 and its complementary sequence.

33. A method for the analysis of gene expression wherein the library of cDNA tags according to claim 31 is contacted with a detector on which nucleic acids to be detected are immobilized.

34. The method for the analysis of gene expression according to claim 33 wherein the detector comprises DNA chip having spots on which nucleic acids to be detected are immobilized.

49. A kit for the preparation of cDNA tags for identifying expressed genes wherein the kit comprises a type II restriction enzyme, a first type IIS restriction enzyme, a second type IIS restriction enzyme, linker Xes which have a recognition site of the first type IIS restriction enzyme and which form a recognition site of the second type IIS restriction enzyme at the site linking with the cleavage end of the cDNA fragments formed by the type II restriction enzyme, and linker Ys which have a recognition site of the first type IIS restriction enzyme.

50. The kit according to claim 49 wherein the kit comprises primer Xes which hybridize the linker Xes and primer Ys which hybridize linker Ys.