Methods of detecting long range chromosomal interactions

Abstract

The present invention relates to a method of monitoring epigenetic changes comprising monitoring changes in conditional long range chromosomal interactions at at least one chromosomal locus where the spectrum of long range interaction is associated with a specific physiological condition, the method comprising the steps of: —(i) in vitro crosslinking of said long range chromosomal interactions present at the at least one chromosomal locus; (ii) isolating the cross linked DNA from said chromosomal locus; (iii) subjecting said cross linked DNA to restriction digestion with an enzyme that cuts at least once within the at least one chromosomal locus; (iv) ligating said cross linked cleaved DNA ends to form DNA loops; (v) identifying the presence of said DNA loops; wherein the presence of DNA loops indicates the presence of a specific long range chromosomal interaction.

1 . A method of monitoring epigenetic changes comprising monitoring changes in conditional long range chromosomal interactions at least one chromosomal locus where the spectrum of long range interaction is associated with a specific physiological condition, said method comprising the steps of:
 (i) in vitro crosslinking of said long range chromosomal interactions present at the at least one chromosomal locus;   (ii) isolating the cross linked DNA from said chromosomal locus;   (iii) subjecting said cross linked DNA to restriction digestion with an enzyme that cuts at least once within the at least one chromosomal locus;   (iv) ligating said cross linked cleaved DNA ends to form DNA loops;   (v) identifying the presence of said DNA loops;   wherein the presence of DNA loops indicates the presence of a specific long range chromosomal interaction.   
     
     
         2 . The method according to  claim 1 , wherein the presence of the DNA loops are identified using PCR techniques. 
     
     
         3 . The method according to  claim 1 , wherein the presence of a DNA loop indicates an altered transcription state indicative of a specific physiological condition. 
     
     
         4 . The method according to any one of  claim 1 , wherein said physiological condition is selected from amongst cancer, cardiovascular disorders, inflammatory conditions, including autoimmune disorders and inflammatory responses to infectious diseases, and inherited genetic disorders modulated by epigenetic mechanisms. 
     
     
         5 . A method of monitoring epigenetic changes comprising monitoring changes in conditional long range chromosomal interactions at least one chromosomal locus where the spectrum of long range interaction is associated with a specific physiological condition, said method comprising the step of identifying a change in the antisense RNA profile expressed from the at least one chromosomal locus. 
     
     
         6 . The method according to  claim 5 , wherein the change in the antisense RNA profile is a change in the size start position, and/or number of antisense RNA transcripts. 
     
     
         7 . A method of diagnosing a disorder associated with at least one epigenetic change in a subject, said method comprising identifying in a sample previously isolated from the subject a change in one or more long range chromosomal interactions at least one chromosomal locus associated with said disorder; wherein said method comprises the method of any one of  claim 1 . 
     
     
         8 . The method according to  claim 7 , wherein the epigenetic change results in altered transcription from the chromosomal locus. 
     
     
         9 . The method according to  claim 7 , wherein the change in the altered transcription is up regulation, repression, or production of an alternative transcript. 
     
     
         10 . The method according to any one of  claim 7 , wherein the epigenetic change causes a change in the expression of at least one gene. 
     
     
         11 . A method of regulating transcription of at least one gene in a patient suffering from a disorder associated with altered gene expression, said method comprising administering to said patient an antisense RNA in an amount effective to alter transcription of said at least one gene. 
     
     
         12 . The method according to  claim 11 , wherein said disorder results from over expression of said gene. 
     
     
         13 . The method according to  claim 11 , wherein said disorder results from repression of said gene. 
     
     
         14 . The method according to  claim 11 , wherein said disorder results from production of an altered gene product. 
     
     
         15 . The method according to any one of  claim 11 , wherein said antisense RNA targets at least one CTCF binding site. 
     
     
         16 . The method according to any one of  claim 11 , wherein administration of said antisense RNA results in modulation of HDAC enzymes. 
     
     
         17 . Antisense RNA for use in the treatment of a disorder associated with altered gene expression, wherein said antisense RNA regulates transcription of said gene. 
     
     
         18 . The antisense RNA according to  claim 17 , wherein said RNA represses transcription of said gene. 
     
     
         19 . The antisense RNA according to  claim 17 , wherein said RNA induces transcription of said gene. 
     
     
         20 . A method of identifying the transcription status of a chromosomal locus comprising the steps of; identifying the antisense RNA transcript profile expressed from said chromosomal locus; and comparing said profile with the antisense RNA transcript profile of said chromosomal locus in a known state. 
     
     
         21 . The method of  claim 20 , wherein said method is performed in vitro. 
     
     
         3000 . TAGMATION.