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Methods. 2019 Jun 26. pii: S1046-2023(18)30478-X. doi: 10.1016/j.ymeth.2019.06.022. [Epub ahead of print]

C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries.

Author information

1
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Mental Health Research Center, Moscow, Russia.
2
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.
3
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
4
Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia; Pirogov Russian National Research Medical University, Research Institute of Translational Medicine, Department of Regenerative Medicine, Moscow, Russia.
5
MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
6
Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia. Electronic address: aleksey.a.gavrilov@gmail.com.

Abstract

Studies performed using Hi-C and other high-throughput whole-genome C-methods have demonstrated that 3D organization of eukaryotic genomes is functionally relevant. Unfortunately, ultra-deep sequencing of Hi-C libraries necessary to detect loop structures in large vertebrate genomes remains rather expensive. However, many studies are in fact aimed at determining the fine-scale 3D structure of comparatively small genomic regions up to several Mb in length. Such studies typically focus on the spatial structure of domains of coregulated genes, molecular mechanisms of loop formation, and interrogation of functional significance of GWAS-revealed polymorphisms. Therefore, a handful of molecular techniques based on Hi-C have been developed to address such issues. These techniques commonly rely on in-solution hybridization of Hi-C/3C-seq libraries with pools of biotinylated baits covering the region of interest, followed by deep sequencing of the enriched library. Here, we describe a new protocol of this kind, C-TALE (Chromatin TArget Ligation Enrichment). Preparation of hybridization probes from bacterial artificial chromosomes and an additional round of enrichment make C-TALE a cost-effective alternative to existing many-versus-all C-methods.

KEYWORDS:

C-methods; Genome folding; Hi-C; In-solution hybridization

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