5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

Methods : a Companion to Methods in Enzymology
Ji Hun KimJennifer E Phillips-Cremins

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.

Citations

Jul 4, 2019·Scientific Reports·Harvey HuangJennifer E Phillips-Cremins
Sep 29, 2020·Wiley Interdisciplinary Reviews. Developmental Biology·Viraat Y Goel, Anders S Hansen
Dec 19, 2019·Nature Reviews. Genetics·Rieke Kempfer, Ana Pombo
Aug 30, 2020·Genome Biology·Lindsey R FernandezJennifer E Phillips-Cremins
Jun 27, 2019·Nature Methods·Ji Hun KimJennifer E Phillips-Cremins
May 27, 2020·Nature Neuroscience·Jonathan A BeaganJennifer E Phillips-Cremins
Mar 25, 2019·Cell Systems·Thomas G Gilgenast, Jennifer E Phillips-Cremins

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