Ribonucleic acid (RNA) interactions

A method of analysing ribonucleic acid-ribonucleic acid (RNA-RNA) interactions comprising:

• a. cross-linking base-paired nucleotides within at least one RNA molecule and/or base-paired nucleotides between at least one pair of RNA molecules using a reversible cross-linking agent comprising a tag to produce at least one cross-linked RNA molecule and/or at least one pair of cross-linked RNA molecules comprising said tag;
• b. fragmenting the said cross-linked RNA molecule and/or pair of cross-linked RNA molecules using metal ion hydrolysis to produce a plurality of fragments of cross-linked RNA molecule and/or pair of cross-linked RNA molecules
• c. using said tag to extract said cross-linked RNA molecule and/or pair of cross-linked RNA molecules obtained from the preceding step;
• d. ligating together ends of said cross-linked RNA fragment(s) to produce cross-linked ligated RNA chimera(s) wherein the ligating does not comprise the use of a linker between the RNA fragment(s);
• e. reversing the cross-linking of the said RNA molecule and/or pair of RNA molecules to produce a ligated RNA chimera molecule(s) and/or RNA chimera pair(s);
• f. sequencing the ligated RNA chimera molecule(s) or pair(s) to generate a sequence library;
• and
• g. analysing the sequence library to determine RNA-RNA interactions wherein the method does not comprise analysing RNA-RNA interactions through their association with an RNA binding protein.