Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain

Clustering of strong replicators associated with active promoter are sufficient to establish an early-replicating domain Repli-Seq: A Wt DT40 chicken cell line and one clonal homozygous cell line containing one module of cis-regulatory elements inserted into a mid-late replicating region of chromosome one (chr1:71,981,290-73,532,377 bp, galGal5) on the two alleles were analyzed (See Hassan-Zadeh et al. 2012, Fig.9). Immunoprecipitated nascent strands from the four S-phase fractions collected by flow cytometry or from an asynchronous cell population were sequenced to determine the replication timing profiles of the targeted region. Hi-C: A Wt DT40 chicken cell line and two clonal cell lines containing two modules of cis-regulatory elements inserted into a mid-late replicating region of chromosome 1 at two genomic positions separated by 30kb (chr1:72,565,520 bp and chr1: 72,536,060 bp, galGal5) on one chromosome (named chromosome 1) and one reporter module inserted in the middle (chr1: 72,548,589 bp, galGal5) on the other chromosome (named chromosome 2) were analyzed. After modification, the chromosome 1 is changing its replication timing toward early replication whereas the chromosome 2 keeps its natural temporal program. Hi-C experiments were used to identify compartment status genome wide. The existence of significant and specific preference of interaction of the allele 1 with different loci was tested.