Methods of identifying interactions between genomic loci
AssigneesUniversity of Massachusetts, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, President and Fellows of Harvard College
InventorsJob Dekker, Erez Lieberman, Nynke Van Berkum, Andreas Gnirke, Eric Lander, Chad Nusbaum, Louise Williams, Alexandre Melnikov, Georgia Giannoukos
Life of this patent
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Abstract
The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.
Claims77
A method, comprising:
- a) providing;
- i) a nuclear matrix comprising a first region and a second region;
- and
- ii) a junction marker;
- b) incorporating the labeled linker into the nuclear matrix;
- and
- c) identifying an interaction frequency within the nuclear matrix.
A method, comprising;
- a) providing;
- i) a cell comprising at least one chromosome, wherein said at least one chromosome comprises a first region and a second region;
- and
- ii) a junction marker;
- b) extracting said at least one chromosome from said cell;
- c) incorporating said junction marker into said extracted chromosome;
- and
- d) identifying an interaction frequency involving the chromosome.
A method, comprising:
- a) providing;
- i) a cell comprising a crosslinked genome;
- ii) a join, wherein said join comprises two ligated nucleic acid sequences derived from said crosslinked genome;
- and
- iii) a plurality of paired end sequencing adaptors;
- b) ligating said paired end adaptors to said join;
- c) sequencing said join;
- and
- d) comparing said join sequence to said genome.
A method, comprising;
- a) providing;
- i) a mammalian cell comprising a crosslinked genome;
- ii) a join, wherein the join comprises two ligated nucleic acid sequences derived from the crosslinked genome;
- and
- iii) a plurality of paired end sequencing adaptors;
- b) ligating the paired end adaptors to the join;
- c) sequencing the join;
- and
- d) comparing the join sequence to the genome.
A kit, comprising:
- i) a fixation agent capable crosslinking nucleic acid and/or protein;
- ii) an enzyme capable of fragmenting nucleic acids,
- iii) a junction marker capable of providing selective purification;
- and
- iv) a paired end sequencing adaptor compatible with a high throughput sequencing device.
A method, comprising:
- a) providing a cross-linked genome and a linker;
- b) fragmenting said cross-linked genome to produce a fragmented, cross-linked genome;
- c) treating said fragmented, cross-linked genome in the presence of said linker under conditions such that there is ligation among at least a portion of the fragments, said ligation creating ligation junctions, said ligation junctions being marked with said linker.
Dependencies are inferred from the claim text.