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5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.
- Source :
-
Methods . Jun2018, Vol. 142, p39-46. 8p. - Publication Year :
- 2018
-
Abstract
- Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus ( in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C. [ABSTRACT FROM AUTHOR]
- Subjects :
- *MAMMAL genetics
*CHROMOSOME structure
*DNA primers
*CARBON copy
*GENE mapping
Subjects
Details
- Language :
- English
- ISSN :
- 10462023
- Volume :
- 142
- Database :
- Academic Search Index
- Journal :
- Methods
- Publication Type :
- Academic Journal
- Accession number :
- 129975540
- Full Text :
- https://doi.org/10.1016/j.ymeth.2018.05.005