Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Journal of Visualized Experiments : JoVE
Stefan SchoenfelderPeter Fraser

Abstract

The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the spatio-temporal expression of their target genes through physical contact, often bridging considerable (in some cases hundreds of kilobases) genomic distances and bypassing nearby genes. The human genome harbors an estimated one million enhancers, the vast majority of which have unknown gene targets. Assigning distal regulatory regions to their target genes is thus crucial to understand gene expression control. We developed Promoter Capture Hi-C (PCHi-C) to enable the genome-wide detection of distal promoter-interacting regions (PIRs), for all promoters in a single experiment. In PCHi-C, highly complex Hi-C libraries are specifically enriched for promoter sequences through in-solution hybrid selection with thousands of biotinylated RNA baits complementary to the ends of all promoter-containing restriction fragments. The aim is to then pull-down promoter sequences and their frequent interaction partners such as enhancers and other potential regulatory elements. After high-throughput paired-end sequencing, a statistical test is applied to each promoter-ligated restriction fragm...Continue Reading

Citations

Jan 22, 2019·Genes, Chromosomes & Cancer·Andrew J FritzRonald Berezney
May 29, 2020·Molecular Biology and Evolution·Giulia Zancolli, Nicholas R Casewell
Jan 16, 2019·BMC Genomics·Peter HansenPeter N Robinson
Jul 3, 2020·Computational and Structural Biotechnology Journal·Barbara HöllbacherN Henriette Uhlenhaut
May 18, 2021·Frontiers in Immunology·Shuai Liu, Keji Zhao
Aug 8, 2021·International Journal of Molecular Sciences·Kinga SzymanMichał Dąbrowski
Aug 21, 2021·Cellular and Molecular Life Sciences : CMLS·Helen Ray-Jones, Mikhail Spivakov

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Methods Mentioned

BETA
Hi-C
Promoter Capture Hi-C
Capture Hi-C
PCR
electrophoresis
Pull-down
for
''
pull
restriction

Software Mentioned

Primer3
HiCUP
Capture Hi - C
Hi
PCHi
HiCUP PCHi - C
Capture
HiCap

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