Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

TY - JOUR

T1 - Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

AU - Splinter, E.

AU - de Wit, E.

AU - van de Werken, H.J.

AU - Klous, P.

AU - de Laat, W.

N1 - Reporting year: 2012

PY - 2012

Y1 - 2012

N2 - Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.

AB - Chromosome Conformation Capture (3C) and 3C-based technologies are constantly evolving in order to probe nuclear organization with higher depth and resolution. One such method is 4C-technology that allows the investigation of the nuclear environment of a locus of choice. The use of Illumina next generation sequencing as a detection platform for the analysis of 4C data has further improved the sensitivity and resolution of this method. Here we provide a step-by-step protocol for 4C-seq, describing the procedure from the initial template preparation until the final data analysis, interchanged with background information and considerations.

U2 - 10.1016/j.ymeth.2012.04.009

DO - 10.1016/j.ymeth.2012.04.009

M3 - Article

SN - 1046-2023

VL - 58

SP - 221

EP - 230

JO - Methods

JF - Methods

IS - 3

ER -