4C technology: protocols and data analysis

TY - JOUR

T1 - 4C technology: protocols and data analysis

AU - van de Werken, H.J.

AU - de Vree, P.J.

AU - Splinter, E.

AU - Holwerda, S.J.

AU - Klous, P.

AU - de Wit, E.

AU - de Laat, W.

N1 - Reporting year: 2012

PY - 2012

Y1 - 2012

N2 - Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis.

AB - Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis.

U2 - 10.1016/B978-0-12-391938-0.00004-5

DO - 10.1016/B978-0-12-391938-0.00004-5

M3 - Article

SN - 0076-6879

VL - 513

SP - 89

EP - 112

JO - Methods in Enzymology

JF - Methods in Enzymology

ER -