2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

Autor: Mathieu Blanchette, Josée Dostie, Denis Paquette, Reid Warsaba, Xue Qing David Wang, Dana Segal, Christopher J. F. Cameron
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
Chromatin Immunoprecipitation
lcsh:QH426-470
lcsh:Biotechnology
Gene Expression
Computational biology
Biology
Proteomics
Real-Time Polymerase Chain Reaction
01 natural sciences
DNA sequencing
Deep sequencing
Ligation-mediated amplification
Epigenesis
Genetic
03 medical and health sciences
lcsh:TP248.13-248.65
Genetics
Humans
Epigenetics
Cells
Cultured
030304 developmental biology
0303 health sciences
Methodology Article
Genes
Homeobox
High-Throughput Nucleotide Sequencing
Cell Differentiation
Genomics
Sequence Analysis
DNA
Chip
HOX
Chromatin
lcsh:Genetics
ComputingMethodologies_PATTERNRECOGNITION
5C
subTAD
Differentiation
Long non-coding RNA
Next-generation sequencing
RNA
Long Noncoding
DNA microarray
Chromatin immunoprecipitation
Transcription
010606 plant biology & botany
Biotechnology
Zdroj: BMC Genomics
BMC Genomics, Vol 20, Iss 1, Pp 1-16 (2019)
ISSN: 1471-2164
Popis: Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. Results Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. Conclusions 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5532-5) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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