Bioinformatical dissection of fission yeast DNA replication origins.

Open Biology
Koji MasudaTakashi Sutani

Abstract

Replication origins in eukaryotes form a base for assembly of the pre-replication complex (pre-RC), thereby serving as an initiation site of DNA replication. Characteristics of replication origin vary among species. In fission yeast Schizosaccharomyces pombe, DNA of high AT content is a distinct feature of replication origins; however, it remains to be understood what the general molecular architecture of fission yeast origin is. Here, we performed ChIP-seq mapping of Orc4 and Mcm2, two representative components of the pre-RC, and described the characteristics of their binding sites. The analysis revealed that fission yeast efficient origins are associated with two similar but independent features: a ≥15 bp-long motif with stretches of As and an AT-rich region of a few hundred bp. The A-rich motif was correlated with chromosomal binding of Orc, a DNA-binding component in the pre-RC, whereas the AT-rich region was associated with efficient binding of the DNA replicative helicase Mcm. These two features, in combination with the third feature, a transcription-poor region of approximately 1 kb, enabled to distinguish efficient replication origins from the rest of chromosome arms with high accuracy. This study, hence, provides a mod...Continue Reading

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Methods Mentioned

BETA
dissection
flow cytometry
immunoprecipitation
ChIP
ChIP-seq
RNA-seq
PCR

Software Mentioned

R computing environment
MEME
kernlab
DME2
ROCR
DROMPA2
PRROC
R
Bowtie2
LOESS

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