Comparison of Hi-C results using in-solution versus in-nucleus ligation.

ABSTRACT:

Background

Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. During development of single-cell Hi-C, we devised an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing in-nucleus ligation with the standard in-solution ligation.

Results

We show in-nucleus ligation results in consistently lower levels of inter-chromosomal contacts. Through chromatin mixing experiments we show that a significantly large fraction of inter-c

SUBMITTER: Nagano T 

PROVIDER: S-EPMC4580221 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature