RT Journal Article
SR Electronic
T1 Repli-seq: genome-wide analysis of replication timing by next-generation sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 104653
DO 10.1101/104653
A1 Claire Marchal
A1 Takayo Sasaki
A1 Daniel Vera
A1 Korey Wilson
A1 Jiao Sima
A1 Juan Carlos Rivera-Mulia
A1 Claudia Trevilla García
A1 Coralin Nogues
A1 Ebtesam Nafie
A1 David M. Gilbert
YR 2017
UL http://biorxiv.org/content/early/2017/03/01/104653.abstract
AB Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyze genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing RT allelic asynchrony, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.