Capture and characterized co-localized chromatin (4C) technology

• US 8,153,373 B2
• Filed: 01/04/2008
• Issued: 04/10/2012
• Est. Priority Date: 07/04/2005
• Status: Active Grant

• Current Assignee: Erasmus University Medical Center Rotterdam
• Original Assignee: Erasmus University Medical Center Rotterdam
• Inventors: Grosveld, Frank, De Laat, Wouter
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): THOMAS, DAVID C
• Application Number:
  US12/006,747
• Publication Number:
  US 20100075861A1
• Time in Patent Office: 1,558 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2523/101 Crosslinking agents, e.g. psoralen
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides

Abstract

The present invention relates in one aspect to a method for analyzing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (e.g., one or more genomic loci) comprising the steps of: (a) providing a sample of cross-linked DNA; (b) digesting the cross-linked DNA with a primary restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross linking; (e) digesting the nucleotide sequences with a secondary restriction enzyme; (f) ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest; (g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequence of interest; (h) hybridising the amplified sequence(s) to an array; and (i) determining the frequency of interaction between the DNA sequences.

Claims

1. A method for analyzing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest comprising the steps of:

(a) providing a sample of cross-linked DNA;

(b) digesting the cross-linked DNA with a primary restriction enzyme;

(c) ligating the cross-linked nucleotide sequences;

(d) reversing the cross linking;

(e) digesting the nucleotide sequences with a secondary restriction enzyme;

(f) ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest;

(g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridizes to the DNA sequences that flank the nucleotide sequences of interest;

(h) hybridizing the amplified sequence(s) to an array; and

(i) determining the frequency of interaction between the DNA sequences.

2. The method according to claim 1, wherein the ligation reaction in step (f) results in the formation of DNA circles.

3. The method according to claim 1, wherein the target nucleotide sequence is selected from the group consisting of a genomic rearrangement, promoter, an enhancer, a silencer, an insulator, a matrix attachment region, a locus control region, a transcription unit, an origin of replication, a recombination hotspot, a translocation breakpoint, a centromere, a telomere, a gene-dense region, a gene-poor region, a repetitive element and a viral integration site.

4. The method according to any of the preceding claims, wherein the target nucleotide sequence is a nucleotide sequence that is associated with or causes a disease, or is located up to or greater than 15 Mb on a linear DNA template from a locus that is associated with or causes a disease.

5. The method according to claim 1, wherein the target nucleotide sequence is selected from the group consisting of AML1, MLL, MYC, BCL, BCR, ABL1, IGH, LYL1, TAL1, TAL2, LMO2, TCRα

δ

, TCRβ and

HOX or other loci associated with disease.

6. The method according to claim 1, wherein the primary restriction enzyme is a restriction enzyme that recognizes a 6-8 bp recognition site.

7. The method according to claim 6, wherein the primary restriction enzyme is selected from the group consisting of BglII, HindIII, EcoRI, BamHI, SpeI, PstI, and NdeI.

8. The method according claim 1, wherein the secondary restriction enzyme is a restriction enzyme that recognizes a 4 or 5 bp nucleotide sequence recognition site.

9. The method according to claim 1, wherein the secondary restriction enzyme recognition site is located at greater than 350 bp from the primary restriction site in the target nucleotide sequence.

10. The method according to claim 1, wherein the nucleotide sequence is labeled.

13. A method for identifying one or more DNA-DNA interactions that are indicative of a particular disease state comprising the step of performing steps (a)-(i) of claim 1 wherein in step (a) a sample of cross-linked DNA is provided from a diseased and a non-diseased cell, and wherein a difference between the frequency of interaction between the DNA sequences from the diseased and non-diseased cells indicates that the DNA-DNA interaction is indicative of a particular disease state.

14. A method of diagnosis or prognosis of a disease or syndrome caused by or associated with a change in a DNA-DNA interaction comprising the step of performing steps (a)-(i) of claim 1, wherein step (a) comprises providing a sample of cross-linked DNA from a subject;

and wherein step (i) comprises comparing the frequency of interaction between the DNA sequences with that of an unaffected control;

wherein a difference between the value obtained from the control and the value obtained from the subject is indicative that the subject is suffering from the disease or syndrome or is indicative that the subject will suffer from the disease or syndrome.

15. The method according to claim 14, wherein a transition from low to high interaction frequencies is indicative of the location of a balanced and/or unbalanced breakpoint.

16. The method according to 14, wherein an inversed pattern of DNA-DNA interaction frequencies for the subject sample as compared to the control is indicative of an balanced and/or unbalanced inversion.

17. The method according to claim 14, wherein a reduction in the DNA-DNA interaction frequency for the subject sample as compared to the control, in combination with an increase in DNA-DNA interaction frequency for more distant regions, is indicative of a balanced and/or unbalanced deletion.

18. The method according to claim 14, wherein an increase or a decrease in DNA-DNA interaction frequency for the subject sample as compared to the control is indicative of a balanced and/or unbalanced duplication or insertion.

19. A method according to claim 14, wherein spectral karyotyping and/or FISH is used prior to performing said method.

20. The method according to claim 14, wherein the disease is a genetic disease.

21. The method according to claim 14, wherein the disease is cancer.

22. A method of diagnosis or prognosis of a disease or syndrome caused by or associated with a change in a DNA-DNA interaction comprising the step of:

performing steps (a)-(i) of claim 1, wherein step (a) comprises providing a sample of cross-linked DNA from a subject; and

wherein said method comprises the additional step of;

(j) identifying one or more loci that have undergone a genomic rearrangement that is associated with a disease.

23. The method according to claim 22, wherein the two or more amplified sequences are differentially labeled.

24. The method according to claim 22, wherein the two or more amplified sequences are identically labeled when the sequences reside on different chromosomes.

25. The method according to claim 22, wherein the two or more amplified sequences are identically labeled when the sequences reside on the same chromosome at a distance that is far enough for minimal overlap between DNA-DNA interaction signals.

26. An assay method for identifying one or more agents that modulate a DNA-DNA interaction comprising the steps of:

(a) contacting a sample with one or more agents; and

(b) performing steps (a) to (i) of claim 1, wherein step (a) comprises providing cross-linked DNA from the sample;

wherein a difference between (i) the frequency of interaction between the DNA sequences in the presence of the agent and (ii) the frequency of interaction between the DNA sequences in the absence of the agent is indicative of an agent that modulates the DNA-DNA interaction.

27. A method for detecting the location of a balanced and/or unbalanced breakpoint (a translocation) comprising the step of:

(a) performing steps (a) to (i) of any of claim 1; and

(b) comparing the frequency of interaction between the DNA sequences with that of a control;

wherein a transition from low to high DNA-DNA interaction frequency in the sample as compared to the control is indicative of the location of a breakpoint.

28. A method for detecting the location of a balanced and/or unbalanced inversion comprising the steps of:

(a) performing steps (a) to (i) of claim 1; and

(b) comparing the frequency of interaction between the DNA sequences with that of a control;

wherein an inversed pattern of DNA-DNA interaction frequencies for the sample as compared to the control is indicative of an inversion.

29. A method for detecting the location of a deletion comprising the steps of:

(a) performing steps (a) to (i) of claim 1; and

(b) comparing the frequency of interaction between the DNA sequences with that of a control;

wherein a reduction in the DNA-DNA interaction frequency for the sample as compared to the control is indicative of deletion.

30. A method for detecting the location of a duplication comprising the steps of:

(a) performing steps (a) to (i) of claim 1; and

(b) comparing the frequency of interaction between the DNA sequences with that of a control;

wherein an increase or a decrease in DNA-DNA interaction frequency for the subject sample as compared to the control is indicative of a duplication or insertion.

11. A method for analyzing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences comprising the steps of:

(a) providing a sample of cross-linked DNA;

(b) digesting the cross-linked DNA with a primary restriction enzyme;

(c) ligating the cross-linked nucleotide sequences;

(d) reversing the cross linking;

(e) digesting the nucleotide sequences with a secondary restriction enzyme;

(f) circularizing the nucleotide sequences;

(g) amplifying the one or more nucleotide sequences that are ligated to the target nucleotide sequence;

(h) optionally hybridizing the amplified sequences to an array; and

(i) determining the frequency of interaction between the DNA sequences.

12. A method for preparing a circularized nucleotide sequence comprising the steps of:

(a) providing a sample of cross-linked DNA;

(b) digesting the cross-linked DNA with a primary restriction enzyme;

(c) ligating the cross-linked nucleotide sequences;

(d) reversing the cross linking;

(e) digesting the nucleotide sequences with a secondary restriction enzyme; and

(f) circularizing the nucleotide sequences.