OriDB Curated Paper

A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Ivan Liachko, Anand Bhaskar, Chanmi Lee, Shau Chee Claire Chung, Bik-Kwoon Tye, Uri Keich

PLoS Genet. (2010), 6(5):e1000946PubMed | PubMed Central | PLoS Genet.

Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.

OriDB annotation of this paper:

ARS assay

ARS810, ARS823, ARS823.5, ARS1210, ARS1211.5, ARS1212.5, ARS1235, ARS1304, ARS1307.5, ARS1319, ARS1322, ARS1609, ARS511.5, ARS805.5, ARS1509.3

2D gel

None curated.

ChIP of replication origin proteins

None curated.

Replication timing

None curated.

Replication in hydroxyurea

None curated.

Predicted origins

None curated.

Confirmed sequence element

None curated.

Predicted sequence element

None curated.