5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
| Autor: | Ji Hun Kim, Jonathan A. Beagan, Wanfeng Gong, Zhendong Cao, Katelyn R. Titus, Jennifer E. Phillips-Cremins |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
In situ Loop (graph theory) Computer science Cell Culture Techniques Computational biology Genome Polymerase Chain Reaction General Biochemistry Genetics and Molecular Biology Chromosomes Article Chromosome conformation capture 03 medical and health sciences Mice medicine Animals Molecular Biology Cells Cultured DNA Primers Physics Resolution (electron density) Chromosome Mapping Mouse Embryonic Stem Cells Folding (DSP implementation) Sequence Analysis DNA Chromatin Mice Inbred C57BL 030104 developmental biology medicine.anatomical_structure Nucleic Acid Conformation Restriction digest Primer (molecular biology) Nucleus |
| Zdroj: | Methods (San Diego, Calif.). 142 |
| ISSN: | 1095-9130 |
| Popis: | 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 generates high quality, high resolution maps of looping interactions genome-wide, but is intractable for high-throughput screening of loops across conditions due to the requirement of an enormous number of reads (>6 Billion) per library. Here, we describe 5C-ID, an updated 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 new double alternating design. 5C-ID reduces spatial noise and enables higher resolution 3D genome folding maps than canonical 5C, allowing for a marked improvement in sensitivity and specificity of loop detection. 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. |
| Databáze: | OpenAIRE |
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